1 Chemistry at HARvard Macromolecular Mechanics (CHARMM) - Developmental Version 37b2 February 15, 2013 Copyright(c) 1984-2001 President and Fellows of Harvard College All Rights Reserved Current operating system: Linux-2.6.32-504.30.3.el6.x86_64(x86_64)@lon Created on 11/12/15 at 12:29:17 by user: u0723235 Maximum number of ATOMS: 240480, and RESidues: 80160 PID of the current process is: 15683 RDTITL> * -----------------------------* CHARMM SETUP SCRIPT RDTITL> * -----------------------------* RDTITL> CHARMM> CHARMM> CHARMM> set sim ac Parameter: SIM <- "AC" CHARMM> set ff all36_na Parameter: FF <- "ALL36_NA" CHARMM> set ffname c36 Parameter: FFNAME <- "C36" CHARMM> set input "init_charmm.pdb" Parameter: INPUT <- ""init_charmm.pdb"" CHARMM> set inputions "ions.pdb" Parameter: INPUTIONS <- ""ions.pdb"" CHARMM> set outvac "c36-vac.pdb" Parameter: OUTVAC <- ""c36-vac.pdb"" CHARMM> set outcio "c36-cio.pdb" Parameter: OUTCIO <- ""c36-cio.pdb"" CHARMM> CHARMM> set comment "Initial ApC model" Parameter: COMMENT <- ""Initial ApC model"" CHARMM> CHARMM> ! CHARMM> ! number of waters and guess on initial box size CHARMM> ! CHARMM> set waters = 1081 Parameter: WATERS <- "1081" CHARMM> set box = 35.00 Parameter: BOX <- "35.00" CHARMM> CHARMM> CHARMM> set finish = 0 Parameter: FINISH <- "0" CHARMM> CHARMM> ! CHARMM> ! we need to build a box bigger than we need and cut it down to CHARMM> ! appropriate size. This is the "pad". CHARMM> ! CHARMM> CHARMM> set pad = 13.0 Parameter: PAD <- "13.0" CHARMM> set solutecut 2.5 Parameter: SOLUTECUT <- "2.5" CHARMM> CHARMM> bomblev -3 MISCOM> Setting BOMLev < -2 is NOT a good idea. CHARMM> CHARMM> ! CHARMM> ! read in force field and topology information CHARMM> ! CHARMM> open unit 1 read card name top_@ff.rtf Parameter: FF -> "ALL36_NA" VOPEN> Attempting to open::top_all36_na.rtf:: OPNLGU> Unit 1 opened for READONLY access to /uufs/chpc.utah.edu/common/home/u0723235/tmp/charmm-example/ac/run2/top_all36_na.rtf CHARMM> read rtf card unit 1 MAINIO> Residue topology file being read from unit 1. TITLE> * \\\\ CHARMM36 ALL-HYDROGEN NUCLEIC ACID TOPOLOGY FILE //// TITLE> * ALEXANDER D. MACKERELL JR. AND COWORKERS TITLE> * APRIL 2011 TITLE> * ALL COMMENTS TO THE CHARMM WEB SITE: WWW.CHARMM.ORG TITLE> * PARAMETER SET DISCUSSION FORUM TITLE> * CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> open unit 1 read card name par_@ff.prm Parameter: FF -> "ALL36_NA" VOPEN> Attempting to open::par_all36_na.prm:: OPNLGU> Unit 1 opened for READONLY access to /uufs/chpc.utah.edu/common/home/u0723235/tmp/charmm-example/ac/run2/par_all36_na.prm CHARMM> read param card unit 1 flex PARAMETER FILE BEING READ FROM UNIT 1 TITLE> * \\\\ CHARMM36 ALL-HYDROGEN NUCLEIC ACID PARAMETER FILE //// TITLE> * ALEXANDER D. MACKERELL JR. AND COWORKERS TITLE> * APRIL 2011 TITLE> * ALL COMMENTS TO THE CHARMM WEB SITE: WWW.CHARMM.ORG PARAMETER TITLE> * SET DISCUSSION FORUM TITLE> * **** Warning **** The following extraneous characters were found while command processing in PARRDR CL PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> ! CHARMM> ! create rna ("rna") CHARMM> ! CHARMM> CHARMM> read sequence card MAINIO> Sequence information being read from unit 5. RDTITL> 2 RDTITL> No title read. SEQRDR> 2 SEQRDR> ADE CYT RESIDUE SEQUENCE -- 2 RESIDUES ADE CYT CHARMM> generate rna first 5ter last 3ter setup warn THE PATCH '5TER' WILL BE USED FOR THE FIRST RESIDUE THE PATCH '3TER' WILL BE USED FOR THE LAST RESIDUE ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . ATOMS "P " "OP1 " WERE REQUESTED. ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . ATOMS "P " "OP2 " WERE REQUESTED. ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . ATOMS "P " "O5' " WERE REQUESTED. ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 ADE . ATOMS "OP1 " "P " WERE REQUESTED. ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 ADE . ATOMS "OP2 " "P " WERE REQUESTED. ** WARNING ** BOND NOT FOUND FOR RESIDUE 2 CYT . ATOMS "O3' " "+P " WERE REQUESTED. GENPSF> Segment 1 has been generated. Its identifier is RNA. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 1 Number of residues = 2 Number of atoms = 63 Number of groups = 7 Number of bonds = 67 Number of angles = 117 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 15 Number of HB donors = 8 Number of NB exclusions = 0 Total charge = -1.00000 CHARMM> CHARMM> ! CHARMM> ! CHARMM by default builds RNA; to get DNA you patch or modify the CHARMM> ! RNA using the commands below... Commented out at present. CHARMM> ! CHARMM> !patch dog5 rna 1 CHARMM> !patch doa rna 2 CHARMM> !patch doc rna 3 CHARMM> !patch doc3 rna 4 CHARMM> CHARMM> open read card unit 1 name @input Parameter: INPUT -> ""init_charmm.pdb"" VOPEN> Attempting to open::init_charmm.pdb:: OPNLGU> Unit 1 opened for READONLY access to /uufs/chpc.utah.edu/common/home/u0723235/tmp/charmm-example/ac/run2/init_charmm.pdb CHARMM> read coordinates pdb unit 1 select segid rna end read CHARMM-pdb format SELRPN> 63 atoms have been selected out of 63 SPATIAL COORDINATES BEING READ FROM UNIT 1 TITLE> * ** WARNING ** For atom in coordinate file, the residue type does not match that (RESN) in the PSF: 1 PSF= ADE INPUT= DE ** WARNING ** For atom in coordinate file, the residue type does not match that (RESN) in the PSF: 1 PSF= ADE INPUT= DE ** WARNING ** For atom in coordinate file, the residue type does not match that (RESN) in the PSF: 1 PSF= ADE INPUT= DE ** WARNING ** For atom in coordinate file, the residue type does not match that (RESN) in the PSF: 1 PSF= ADE INPUT= DE ** WARNING ** For atom in coordinate file, the residue type does not match that (RESN) in the PSF: 1 PSF= ADE INPUT= DE ** WARNING ** 63 atoms in coordinates file had a sequence mismatch. *** LEVEL 0 WARNING *** BOMLEV IS -3 CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> ic param CHARMM> ic build CHARMM> CHARMM> hbuild ***** LEVEL 4 WARNING FROM ***** ***** Zero selection specified ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 CHARMM> autogenerate angles dihedrals AUTOGEN: All angles are removed and regenerated. AUTOGEN: All dihedrals are removed and regenerated. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 1 Number of residues = 2 Number of atoms = 63 Number of groups = 7 Number of bonds = 67 Number of angles = 117 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 15 Number of HB donors = 8 Number of NB exclusions = 0 Total charge = -1.00000 CHARMM> CHARMM> coor orient mass select all end SELRPN> 63 atoms have been selected out of 63 ORIENT THE COORDINATES TO ALIGN WITH AXIS MOMENTS 2009.56910347 -171.57347032 834.43814647 2587.01653765 154.70580773 3038.92266675 Transpose of the rotation matrix 0.874953 0.057430 0.480790 0.048456 0.977572 -0.204951 -0.481777 0.202619 0.852547 CENTER OF ATOMS BEFORE TRANSLATION -0.37529 0.27147 -0.02730 AXIS OF ROTATION IS -0.389894 -0.920820 0.008585 ANGLE IS 31.51 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> coor stat sele all end SELRPN> 63 atoms have been selected out of 63 STATISTICS FOR 63 SELECTED ATOMS: XMIN = -4.979795 XMAX = 5.890171 XAVE = 0.129684 YMIN = -4.271213 YMAX = 3.948279 YAVE = -0.025749 ZMIN = -4.250214 ZMAX = 3.438575 ZAVE = 0.085077 WMIN = 0.000000 WMAX = 0.000000 WAVE = 0.000000 CHARMM> CHARMM> ! CHARMM> ! Write out the in-vacuo files needed CHARMM> ! CHARMM> open unit 1 write card name @sim_@ffname_vac.psf Parameter: SIM -> "AC" Parameter: FFNAME -> "C36" VOPEN> Attempting to open::ac_c36_vac.psf:: OPNLGU> Unit 1 opened for WRITE access to /uufs/chpc.utah.edu/common/home/u0723235/tmp/charmm-example/ac/run2/ac_c36_vac.psf CHARMM> write psf unit 1 card RDTITL> * AC "Initial ApC model" RDTITL> * CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> open unit 1 write card name @sim_@ffname_vac.pdb Parameter: SIM -> "AC" Parameter: FFNAME -> "C36" VOPEN> Attempting to open::ac_c36_vac.pdb:: OPNLGU> Unit 1 opened for WRITE access to /uufs/chpc.utah.edu/common/home/u0723235/tmp/charmm-example/ac/run2/ac_c36_vac.pdb CHARMM> coor write unit 1 pdb select all end RDTITL> * AC "Initial ApC model" RDTITL> * Write CHARMM-pdb format SELRPN> 63 atoms have been selected out of 63 CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> open unit 1 write card name @sim_@ffname_vac.cor Parameter: SIM -> "AC" Parameter: FFNAME -> "C36" VOPEN> Attempting to open::ac_c36_vac.cor:: OPNLGU> Unit 1 opened for WRITE access to /uufs/chpc.utah.edu/common/home/u0723235/tmp/charmm-example/ac/run2/ac_c36_vac.cor CHARMM> coor write unit 1 card select all end RDTITL> * AC "Initial ApC model" RDTITL> * SELRPN> 63 atoms have been selected out of 63 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> close unit 1 CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. CHARMM> CHARMM> CHARMM> CHARMM> ! CHARMM> ! create Na+ counterions ("ions") CHARMM> ! CHARMM> CHARMM> CHARMM> read sequence card MAINIO> Sequence information being read from unit 5. RDTITL> 11 RDTITL> No title read. ***** LEVEL 1 WARNING FROM ***** ***** Title expected. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 SEQRDR> 11 SEQRDR> NA NA CLA NA CLA NA CLA NA CLA NA CLA RESIDUE SEQUENCE -- 11 RESIDUES NA NA CLA NA CLA NA CLA NA CLA NA CLA CHARMM> generate ions setup first none last none NO PATCHING WILL BE DONE ON THE FIRST RESIDUE NO PATCHING WILL BE DONE ON THE LAST RESIDUE GENPSF> Segment 2 has been generated. Its identifier is IONS. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 2 Number of residues = 13 Number of atoms = 74 Number of groups = 18 Number of bonds = 67 Number of angles = 117 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 15 Number of HB donors = 8 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> open read card unit 1 name @inputions Parameter: INPUTIONS -> ""ions.pdb"" VOPEN> Attempting to open::ions.pdb:: OPNLGU> Unit 1 opened for READONLY access to /uufs/chpc.utah.edu/common/home/u0723235/tmp/charmm-example/ac/run2/ions.pdb CHARMM> read coordinates pdb unit 1 select segid ions end read CHARMM-pdb format SELRPN> 11 atoms have been selected out of 74 SPATIAL COORDINATES BEING READ FROM UNIT 1 INFO: A subset of total atoms will be read. TITLE> * CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> CHARMM> CHARMM> coordinate orient mass select all end SELRPN> 74 atoms have been selected out of 74 ORIENT THE COORDINATES TO ALIGN WITH AXIS MOMENTS 11230.01871065 -11847.03688306 78.95987261 28415.47130935 -1610.31454589 11685.01137544 Transpose of the rotation matrix 0.064209 -0.889640 0.452125 0.992776 0.010931 -0.119482 0.101354 0.456531 0.883916 CENTER OF ATOMS BEFORE TRANSLATION -0.57577 3.64888 -1.07234 AXIS OF ROTATION IS -0.288067 -0.175422 -0.941406 ANGLE IS 91.17 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> coordinate statistics select all end SELRPN> 74 atoms have been selected out of 74 STATISTICS FOR 74 SELECTED ATOMS: XMIN = -12.569386 XMAX = 8.362970 XAVE = 2.272928 YMIN = -7.179462 YMAX = 6.249631 YAVE = 0.369658 ZMIN = -3.717809 ZMAX = 8.818009 ZAVE = -0.290852 WMIN = 0.000000 WMAX = 0.000000 WAVE = 0.000000 CHARMM> CHARMM> CHARMM> ! CHARMM> ! MINIMIZE ION POSITIONS CHARMM> ! CHARMM> ! ...change the ion "type" from IP (31) to IB (32) CHARMM> ! CHARMM> !scalar type set 32 select segid ions end CHARMM> ! CHARMM> !cons fix select segid rna .and. .not. type H* end CHARMM> ! CHARMM> !mini abnr nstep 1000 CHARMM> ! CHARMM> ! ...change the ion "type" back! CHARMM> ! CHARMM> !scalar type set 31 select segid ions end CHARMM> ! CHARMM> !open unit 1 write card name @outcio CHARMM> !write coor pdb unit 1 select all end CHARMM> !* B-DNA @sim CHARMM> !* ion positions gas-phase minimized CHARMM> !* CHARMM> !close unit 1 CHARMM> ! CHARMM> !cons fix select none end CHARMM> CHARMM> CHARMM> open unit 1 write card name @sim_@ffname_cio.psf Parameter: SIM -> "AC" Parameter: FFNAME -> "C36" VOPEN> Attempting to open::ac_c36_cio.psf:: OPNLGU> Unit 1 opened for WRITE access to /uufs/chpc.utah.edu/common/home/u0723235/tmp/charmm-example/ac/run2/ac_c36_cio.psf CHARMM> write psf unit 1 card RDTITL> * AC "Initial ApC model" RDTITL> * 1 NA+ + 5 NACL IONS RDTITL> * CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> open unit 1 write card name @sim_@ffname_cio.pdb Parameter: SIM -> "AC" Parameter: FFNAME -> "C36" VOPEN> Attempting to open::ac_c36_cio.pdb:: OPNLGU> Unit 1 opened for WRITE access to /uufs/chpc.utah.edu/common/home/u0723235/tmp/charmm-example/ac/run2/ac_c36_cio.pdb CHARMM> coor write unit 1 pdb select all end RDTITL> * AC "Initial ApC model" RDTITL> * 1 NA+ + 5 NACL IONS RDTITL> * Write CHARMM-pdb format SELRPN> 74 atoms have been selected out of 74 CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> open unit 1 write card name @sim_@ffname_cio.cor Parameter: SIM -> "AC" Parameter: FFNAME -> "C36" VOPEN> Attempting to open::ac_c36_cio.cor:: OPNLGU> Unit 1 opened for WRITE access to /uufs/chpc.utah.edu/common/home/u0723235/tmp/charmm-example/ac/run2/ac_c36_cio.cor CHARMM> coor write unit 1 card select all end RDTITL> * AC "Initial ApC model" RDTITL> * 3 NA+ IONS RDTITL> * SELRPN> 74 atoms have been selected out of 74 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> close unit 1 CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. CHARMM> CHARMM> CHARMM> define SOLUTE select .not. segid wat end SELRPN> 74 atoms have been selected out of 74 CHARMM> CHARMM> CHARMM> set boxlen 31.1661028 Parameter: BOXLEN <- "31.1661028" CHARMM> read sequence wat 1000 CHARMM> generate wat noangle nodihedral NO PATCHING WILL BE DONE ON THE FIRST RESIDUE NO PATCHING WILL BE DONE ON THE LAST RESIDUE GENPSF> Segment 3 has been generated. Its identifier is WAT. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1013 Number of atoms = 3074 Number of groups = 1018 Number of bonds = 3067 Number of angles = 1117 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1015 Number of HB donors = 2008 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> open read formatted unit 1 name wat1000.cor.tip3p VOPEN> Attempting to open::wat1000.cor.tip3p:: OPNLGU> Unit 1 opened for READONLY access to /uufs/chpc.utah.edu/common/home/u0723235/tmp/charmm-example/ac/run2/wat1000.cor.tip3p CHARMM> read coordinates card unit 1 append select segid wat end SELRPN> 3000 atoms have been selected out of 3074 SPATIAL COORDINATES BEING READ FROM UNIT 1 A RESIDUE OFFSET OF 13 WILL BE USED. INFO: A subset of total atoms will be read. TITLE> * CHARMM SETUP SCRIPT: SOLVATION/WATER TEST TITLE> * CONVERT A PDB TO COORDINATE SET TITLE> * DATE: 3/18/97 22:38:44 CREATED BY USER: CHEATHAM TITLE> * CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> ! CHARMM> ! Make the box pretty big for now... CHARMM> ! CHARMM> generate watx duplicate wat GENPSF> Segment 4 has been generated. Its identifier is WATX. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 4 Number of residues = 2013 Number of atoms = 6074 Number of groups = 2018 Number of bonds = 6067 Number of angles = 2117 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 2015 Number of HB donors = 4008 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> coor duplicate select segid wat end select segid watx end SELRPN> 3000 atoms have been selected out of 6074 SELRPN> 3000 atoms have been selected out of 6074 CHARMM> coor translate xdir @boxlen select segid watx end Parameter: BOXLEN -> "31.1661028" SELRPN> 3000 atoms have been selected out of 6074 TRANSLATION VECTOR 31.166103 0.000000 0.000000 SELECTED COORDINATES TRANSLATED IN THE MAIN SET. CHARMM> join wat watx renumber SEGMENTS "WAT " AND "WATX" HAVE BEEN JOINED. THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 2013 Number of atoms = 6074 Number of groups = 2018 Number of bonds = 6067 Number of angles = 2117 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 2015 Number of HB donors = 4008 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> generate waty duplicate wat GENPSF> Segment 4 has been generated. Its identifier is WATY. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 4 Number of residues = 4013 Number of atoms = 12074 Number of groups = 4018 Number of bonds = 12067 Number of angles = 4117 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 4015 Number of HB donors = 8008 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> coor duplicate select segid wat end select segid waty end SELRPN> 6000 atoms have been selected out of 12074 SELRPN> 6000 atoms have been selected out of 12074 CHARMM> coor translate ydir @boxlen select segid waty end Parameter: BOXLEN -> "31.1661028" SELRPN> 6000 atoms have been selected out of 12074 TRANSLATION VECTOR 0.000000 31.166103 0.000000 SELECTED COORDINATES TRANSLATED IN THE MAIN SET. CHARMM> join wat waty renumber SEGMENTS "WAT " AND "WATY" HAVE BEEN JOINED. THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 4013 Number of atoms = 12074 Number of groups = 4018 Number of bonds = 12067 Number of angles = 4117 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 4015 Number of HB donors = 8008 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> generate watz duplicate wat GENPSF> Segment 4 has been generated. Its identifier is WATZ. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 4 Number of residues = 8013 Number of atoms = 24074 Number of groups = 8018 Number of bonds = 24067 Number of angles = 8117 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 8015 Number of HB donors = 16008 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> coor duplicate select segid wat end select segid watz end SELRPN> 12000 atoms have been selected out of 24074 SELRPN> 12000 atoms have been selected out of 24074 CHARMM> coor translate zdir @boxlen select segid watz end Parameter: BOXLEN -> "31.1661028" SELRPN> 12000 atoms have been selected out of 24074 TRANSLATION VECTOR 0.000000 0.000000 31.166103 SELECTED COORDINATES TRANSLATED IN THE MAIN SET. CHARMM> join wat watz renumber SEGMENTS "WAT " AND "WATZ" HAVE BEEN JOINED. THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 8013 Number of atoms = 24074 Number of groups = 8018 Number of bonds = 24067 Number of angles = 8117 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 8015 Number of HB donors = 16008 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> define junk select .not. init show end The following atoms are currently set: SEGId RESId RESName .. TYPEs .. SELRPN> 0 atoms have been selected out of 24074 CHARMM> CHARMM> coordinate orient mass norotate select segid wat end SELRPN> 24000 atoms have been selected out of 24074 ORIENT THE COORDINATES TO ALIGN WITH AXIS CENTER OF ATOMS BEFORE TRANSLATION 15.72003 15.54927 15.46230 SELECTED COORDINATES TRANSLATED IN THE MAIN SET. CHARMM> coordinate statistics select all end SELRPN> 24074 atoms have been selected out of 24074 STATISTICS FOR 24074 SELECTED ATOMS: XMIN = -32.097027 XMAX = 31.829076 XAVE = -0.047005 YMIN = -31.944267 YMAX = 31.846836 YAVE = -0.048835 ZMIN = -31.704296 ZMAX = 31.894806 ZAVE = -0.055120 WMIN = 0.000000 WMAX = 0.000000 WAVE = 0.000000 CHARMM> CHARMM> calc xbox ?XMAX - ?XMIN RDCMND substituted energy or value "?XMAX" to "31.8291" RDCMND substituted energy or value "?XMIN" to "-32.097" Evaluating: 31.8291--32.097 Parameter: XBOX <- "63.9261" CHARMM> calc ybox ?YMAX - ?YMIN RDCMND substituted energy or value "?YMAX" to "31.8468" RDCMND substituted energy or value "?YMIN" to "-31.9443" Evaluating: 31.8468--31.9443 Parameter: YBOX <- "63.7911" CHARMM> calc zbox ?ZMAX - ?ZMIN RDCMND substituted energy or value "?ZMAX" to "31.8948" RDCMND substituted energy or value "?ZMIN" to "-31.7043" Evaluating: 31.8948--31.7043 Parameter: ZBOX <- "63.5991" CHARMM> CHARMM> set boxmax Parameter: BOXMAX <- "" CHARMM> let boxmax = max @xbox @ybox Parameter: XBOX -> "63.9261" Parameter: YBOX -> "63.7911" WARNING from DECODF -- Zero length string being converted to 0. Parameter: BOXMAX <- "63.9261" CHARMM> let boxmax = max @boxmax @zbox Parameter: BOXMAX -> "63.9261" Parameter: ZBOX -> "63.5991" Parameter: BOXMAX <- "63.9261" CHARMM> CHARMM> calc cutimg = 1.0 Evaluating: 1.0 Parameter: CUTIMG <- "1" CHARMM> CHARMM> set boxincr 0.002 Parameter: BOXINCR <- "0.002" CHARMM> calc halfbox @box / 2.0 + 2.0 Parameter: BOX -> "35.00" Evaluating: 35.00/2.0+2.0 Parameter: HALFBOX <- "19.5" CHARMM> CHARMM> !if box .gt. @maxbox stop CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property x .lt. -@halfbox )) end Parameter: HALFBOX -> "19.5" SELRPN> 4476 atoms have been selected out of 24074 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1492 residues deleted. DELTIC: 4476 bonds deleted DELTIC: 1492 angles deleted DELTIC: 2984 donors deleted DELTIC: 1492 acceptors deleted PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 6521 Number of atoms = 19598 Number of groups = 6526 Number of bonds = 19591 Number of angles = 6625 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 6523 Number of HB donors = 13024 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> delete atom select .byres. (atom WAT * O .and. (property x .gt. @halfbox )) end Parameter: HALFBOX -> "19.5" SELRPN> 4584 atoms have been selected out of 19598 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1528 residues deleted. DELTIC: 4584 bonds deleted DELTIC: 1528 angles deleted DELTIC: 3056 donors deleted DELTIC: 1528 acceptors deleted PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 4993 Number of atoms = 15014 Number of groups = 4998 Number of bonds = 15007 Number of angles = 5097 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 4995 Number of HB donors = 9968 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> delete atom select .byres. (atom WAT * O .and. (property y .lt. -@halfbox )) end Parameter: HALFBOX -> "19.5" SELRPN> 2766 atoms have been selected out of 15014 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 922 residues deleted. DELTIC: 2766 bonds deleted DELTIC: 922 angles deleted DELTIC: 1844 donors deleted DELTIC: 922 acceptors deleted PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 4071 Number of atoms = 12248 Number of groups = 4076 Number of bonds = 12241 Number of angles = 4175 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 4073 Number of HB donors = 8124 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> delete atom select .byres. (atom WAT * O .and. (property y .gt. @halfbox )) end Parameter: HALFBOX -> "19.5" SELRPN> 2742 atoms have been selected out of 12248 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 914 residues deleted. DELTIC: 2742 bonds deleted DELTIC: 914 angles deleted DELTIC: 1828 donors deleted DELTIC: 914 acceptors deleted PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 3157 Number of atoms = 9506 Number of groups = 3162 Number of bonds = 9499 Number of angles = 3261 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 3159 Number of HB donors = 6296 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> delete atom select .byres. (atom WAT * O .and. (property z .lt. -@halfbox )) end Parameter: HALFBOX -> "19.5" SELRPN> 1764 atoms have been selected out of 9506 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 588 residues deleted. DELTIC: 1764 bonds deleted DELTIC: 588 angles deleted DELTIC: 1176 donors deleted DELTIC: 588 acceptors deleted PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 2569 Number of atoms = 7742 Number of groups = 2574 Number of bonds = 7735 Number of angles = 2673 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 2571 Number of HB donors = 5120 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> delete atom select .byres. (atom WAT * O .and. (property z .gt. @halfbox )) end Parameter: HALFBOX -> "19.5" SELRPN> 1764 atoms have been selected out of 7742 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 588 residues deleted. DELTIC: 1764 bonds deleted DELTIC: 588 angles deleted DELTIC: 1176 donors deleted DELTIC: 588 acceptors deleted PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1981 Number of atoms = 5978 Number of groups = 1986 Number of bonds = 5971 Number of angles = 2085 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1983 Number of HB donors = 3944 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1981 Number of atoms = 5978 Number of groups = 1986 Number of bonds = 5971 Number of angles = 2085 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1983 Number of HB donors = 3944 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> label loop2 CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "35.00" Parameter: BOX -> "35.00" Parameter: BOX -> "35.00" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 35.00000 B = 35.00000 C = 35.00000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 9.6212 2 1 -1 0 -1 2.3418 3 1 -1 1 -1 2.6955 4 1 0 -1 -1 4.2161 5 1 0 0 -1 1.8833 6 1 0 1 -1 1.7040 7 1 -1 -1 0 3.1923 8 1 -1 0 0 1.3832 9 1 -1 1 0 2.2895 10 1 0 -1 0 2.1551 11 1 0 1 0 2.1551 12 1 -1 -1 1 3.4517 13 1 -1 0 1 4.5877 14 1 -1 1 1 4.6892 15 1 0 -1 1 1.7040 16 1 0 0 1 1.8833 17 1 0 1 1 4.2161 18 1 1 1 1 9.6212 19 1 1 0 1 2.3418 20 1 1 -1 1 2.6955 21 1 1 1 0 3.1923 22 1 1 0 0 1.3832 23 1 1 -1 0 2.2895 24 1 1 1 -1 3.4517 25 1 1 0 -1 4.5877 26 1 1 -1 -1 4.6892 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 5904 atoms have been selected out of 5978 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 19 OPERATED ON BY TRANSFORMATION C022 RESIDUE 22 OPERATED ON BY TRANSFORMATION C011 RESIDUE 23 OPERATED ON BY TRANSFORMATION C022 RESIDUE 27 OPERATED ON BY TRANSFORMATION C011 RESIDUE 32 OPERATED ON BY TRANSFORMATION C022 RESIDUE 36 OPERATED ON BY TRANSFORMATION C011 RESIDUE 37 OPERATED ON BY TRANSFORMATION C017 RESIDUE 42 OPERATED ON BY TRANSFORMATION C011 RESIDUE 44 OPERATED ON BY TRANSFORMATION C016 RESIDUE 47 OPERATED ON BY TRANSFORMATION C016 RESIDUE 50 OPERATED ON BY TRANSFORMATION C011 RESIDUE 51 OPERATED ON BY TRANSFORMATION C018 RESIDUE 54 OPERATED ON BY TRANSFORMATION C011 RESIDUE 56 OPERATED ON BY TRANSFORMATION C017 RESIDUE 57 OPERATED ON BY TRANSFORMATION C022 RESIDUE 64 OPERATED ON BY TRANSFORMATION C011 RESIDUE 65 OPERATED ON BY TRANSFORMATION C016 RESIDUE 72 OPERATED ON BY TRANSFORMATION C011 RESIDUE 89 OPERATED ON BY TRANSFORMATION C022 RESIDUE 93 OPERATED ON BY TRANSFORMATION C011 RESIDUE 96 OPERATED ON BY TRANSFORMATION C016 RESIDUE 99 OPERATED ON BY TRANSFORMATION C016 RESIDUE 101 OPERATED ON BY TRANSFORMATION C011 RESIDUE 104 OPERATED ON BY TRANSFORMATION C011 RESIDUE 106 OPERATED ON BY TRANSFORMATION C022 RESIDUE 109 OPERATED ON BY TRANSFORMATION C011 RESIDUE 116 OPERATED ON BY TRANSFORMATION C016 RESIDUE 120 OPERATED ON BY TRANSFORMATION C011 RESIDUE 123 OPERATED ON BY TRANSFORMATION C016 RESIDUE 125 OPERATED ON BY TRANSFORMATION C011 RESIDUE 132 OPERATED ON BY TRANSFORMATION C011 RESIDUE 135 OPERATED ON BY TRANSFORMATION C016 RESIDUE 140 OPERATED ON BY TRANSFORMATION C016 RESIDUE 144 OPERATED ON BY TRANSFORMATION C016 RESIDUE 145 OPERATED ON BY TRANSFORMATION C011 RESIDUE 148 OPERATED ON BY TRANSFORMATION C011 RESIDUE 149 OPERATED ON BY TRANSFORMATION C016 RESIDUE 151 OPERATED ON BY TRANSFORMATION C016 RESIDUE 154 OPERATED ON BY TRANSFORMATION C011 RESIDUE 156 OPERATED ON BY TRANSFORMATION C019 RESIDUE 158 OPERATED ON BY TRANSFORMATION C022 RESIDUE 161 OPERATED ON BY TRANSFORMATION C022 RESIDUE 163 OPERATED ON BY TRANSFORMATION C022 RESIDUE 166 OPERATED ON BY TRANSFORMATION C022 RESIDUE 172 OPERATED ON BY TRANSFORMATION C016 RESIDUE 175 OPERATED ON BY TRANSFORMATION C021 RESIDUE 178 OPERATED ON BY TRANSFORMATION C022 RESIDUE 185 OPERATED ON BY TRANSFORMATION C022 RESIDUE 187 OPERATED ON BY TRANSFORMATION C011 RESIDUE 190 OPERATED ON BY TRANSFORMATION C011 RESIDUE 194 OPERATED ON BY TRANSFORMATION C022 RESIDUE 200 OPERATED ON BY TRANSFORMATION C016 RESIDUE 203 OPERATED ON BY TRANSFORMATION C016 RESIDUE 205 OPERATED ON BY TRANSFORMATION C022 RESIDUE 206 OPERATED ON BY TRANSFORMATION C016 RESIDUE 207 OPERATED ON BY TRANSFORMATION C022 RESIDUE 208 OPERATED ON BY TRANSFORMATION C011 RESIDUE 215 OPERATED ON BY TRANSFORMATION C016 RESIDUE 218 OPERATED ON BY TRANSFORMATION C022 RESIDUE 219 OPERATED ON BY TRANSFORMATION C016 RESIDUE 220 OPERATED ON BY TRANSFORMATION C011 RESIDUE 228 OPERATED ON BY TRANSFORMATION C022 RESIDUE 237 OPERATED ON BY TRANSFORMATION C022 RESIDUE 239 OPERATED ON BY TRANSFORMATION C016 RESIDUE 241 OPERATED ON BY TRANSFORMATION C021 RESIDUE 244 OPERATED ON BY TRANSFORMATION C022 RESIDUE 249 OPERATED ON BY TRANSFORMATION C016 RESIDUE 250 OPERATED ON BY TRANSFORMATION C016 RESIDUE 254 OPERATED ON BY TRANSFORMATION C017 RESIDUE 259 OPERATED ON BY TRANSFORMATION C011 RESIDUE 261 OPERATED ON BY TRANSFORMATION C008 RESIDUE 264 OPERATED ON BY TRANSFORMATION C017 RESIDUE 265 OPERATED ON BY TRANSFORMATION C011 RESIDUE 268 OPERATED ON BY TRANSFORMATION C009 RESIDUE 272 OPERATED ON BY TRANSFORMATION C011 RESIDUE 278 OPERATED ON BY TRANSFORMATION C008 RESIDUE 279 OPERATED ON BY TRANSFORMATION C017 RESIDUE 280 OPERATED ON BY TRANSFORMATION C011 RESIDUE 283 OPERATED ON BY TRANSFORMATION C016 RESIDUE 284 OPERATED ON BY TRANSFORMATION C016 RESIDUE 288 OPERATED ON BY TRANSFORMATION C011 RESIDUE 289 OPERATED ON BY TRANSFORMATION C009 RESIDUE 291 OPERATED ON BY TRANSFORMATION C017 RESIDUE 293 OPERATED ON BY TRANSFORMATION C008 RESIDUE 300 OPERATED ON BY TRANSFORMATION C016 RESIDUE 306 OPERATED ON BY TRANSFORMATION C008 RESIDUE 307 OPERATED ON BY TRANSFORMATION C008 RESIDUE 308 OPERATED ON BY TRANSFORMATION C016 RESIDUE 311 OPERATED ON BY TRANSFORMATION C008 RESIDUE 316 OPERATED ON BY TRANSFORMATION C011 RESIDUE 317 OPERATED ON BY TRANSFORMATION C008 RESIDUE 324 OPERATED ON BY TRANSFORMATION C008 RESIDUE 327 OPERATED ON BY TRANSFORMATION C008 RESIDUE 329 OPERATED ON BY TRANSFORMATION C017 RESIDUE 333 OPERATED ON BY TRANSFORMATION C008 RESIDUE 335 OPERATED ON BY TRANSFORMATION C008 RESIDUE 337 OPERATED ON BY TRANSFORMATION C016 RESIDUE 338 OPERATED ON BY TRANSFORMATION C016 RESIDUE 342 OPERATED ON BY TRANSFORMATION C008 RESIDUE 343 OPERATED ON BY TRANSFORMATION C016 RESIDUE 344 OPERATED ON BY TRANSFORMATION C009 RESIDUE 353 OPERATED ON BY TRANSFORMATION C008 RESIDUE 354 OPERATED ON BY TRANSFORMATION C017 RESIDUE 362 OPERATED ON BY TRANSFORMATION C011 RESIDUE 363 OPERATED ON BY TRANSFORMATION C013 RESIDUE 372 OPERATED ON BY TRANSFORMATION C016 RESIDUE 376 OPERATED ON BY TRANSFORMATION C011 RESIDUE 380 OPERATED ON BY TRANSFORMATION C016 RESIDUE 384 OPERATED ON BY TRANSFORMATION C011 RESIDUE 387 OPERATED ON BY TRANSFORMATION C008 RESIDUE 388 OPERATED ON BY TRANSFORMATION C016 RESIDUE 395 OPERATED ON BY TRANSFORMATION C011 RESIDUE 396 OPERATED ON BY TRANSFORMATION C016 RESIDUE 397 OPERATED ON BY TRANSFORMATION C011 RESIDUE 398 OPERATED ON BY TRANSFORMATION C011 RESIDUE 401 OPERATED ON BY TRANSFORMATION C011 RESIDUE 407 OPERATED ON BY TRANSFORMATION C016 RESIDUE 410 OPERATED ON BY TRANSFORMATION C011 RESIDUE 422 OPERATED ON BY TRANSFORMATION C008 RESIDUE 425 OPERATED ON BY TRANSFORMATION C008 RESIDUE 428 OPERATED ON BY TRANSFORMATION C008 RESIDUE 429 OPERATED ON BY TRANSFORMATION C011 RESIDUE 430 OPERATED ON BY TRANSFORMATION C011 RESIDUE 438 OPERATED ON BY TRANSFORMATION C011 RESIDUE 440 OPERATED ON BY TRANSFORMATION C011 RESIDUE 442 OPERATED ON BY TRANSFORMATION C008 RESIDUE 444 OPERATED ON BY TRANSFORMATION C008 RESIDUE 445 OPERATED ON BY TRANSFORMATION C008 RESIDUE 446 OPERATED ON BY TRANSFORMATION C016 RESIDUE 448 OPERATED ON BY TRANSFORMATION C016 RESIDUE 450 OPERATED ON BY TRANSFORMATION C011 RESIDUE 453 OPERATED ON BY TRANSFORMATION C016 RESIDUE 456 OPERATED ON BY TRANSFORMATION C016 RESIDUE 458 OPERATED ON BY TRANSFORMATION C016 RESIDUE 464 OPERATED ON BY TRANSFORMATION C016 RESIDUE 473 OPERATED ON BY TRANSFORMATION C008 RESIDUE 475 OPERATED ON BY TRANSFORMATION C008 RESIDUE 487 OPERATED ON BY TRANSFORMATION C011 RESIDUE 489 OPERATED ON BY TRANSFORMATION C008 RESIDUE 498 OPERATED ON BY TRANSFORMATION C011 RESIDUE 499 OPERATED ON BY TRANSFORMATION C016 RESIDUE 502 OPERATED ON BY TRANSFORMATION C014 RESIDUE 505 OPERATED ON BY TRANSFORMATION C010 RESIDUE 507 OPERATED ON BY TRANSFORMATION C016 RESIDUE 511 OPERATED ON BY TRANSFORMATION C016 RESIDUE 512 OPERATED ON BY TRANSFORMATION C022 RESIDUE 514 OPERATED ON BY TRANSFORMATION C010 RESIDUE 516 OPERATED ON BY TRANSFORMATION C023 RESIDUE 519 OPERATED ON BY TRANSFORMATION C022 RESIDUE 520 OPERATED ON BY TRANSFORMATION C010 RESIDUE 524 OPERATED ON BY TRANSFORMATION C010 RESIDUE 530 OPERATED ON BY TRANSFORMATION C016 RESIDUE 533 OPERATED ON BY TRANSFORMATION C016 RESIDUE 535 OPERATED ON BY TRANSFORMATION C010 RESIDUE 537 OPERATED ON BY TRANSFORMATION C016 RESIDUE 538 OPERATED ON BY TRANSFORMATION C010 RESIDUE 539 OPERATED ON BY TRANSFORMATION C016 RESIDUE 542 OPERATED ON BY TRANSFORMATION C019 RESIDUE 545 OPERATED ON BY TRANSFORMATION C010 RESIDUE 546 OPERATED ON BY TRANSFORMATION C010 RESIDUE 548 OPERATED ON BY TRANSFORMATION C016 RESIDUE 553 OPERATED ON BY TRANSFORMATION C010 RESIDUE 560 OPERATED ON BY TRANSFORMATION C010 RESIDUE 561 OPERATED ON BY TRANSFORMATION C010 RESIDUE 563 OPERATED ON BY TRANSFORMATION C022 RESIDUE 564 OPERATED ON BY TRANSFORMATION C010 RESIDUE 570 OPERATED ON BY TRANSFORMATION C022 RESIDUE 586 OPERATED ON BY TRANSFORMATION C016 RESIDUE 591 OPERATED ON BY TRANSFORMATION C016 RESIDUE 608 OPERATED ON BY TRANSFORMATION C016 RESIDUE 609 OPERATED ON BY TRANSFORMATION C010 RESIDUE 610 OPERATED ON BY TRANSFORMATION C016 RESIDUE 615 OPERATED ON BY TRANSFORMATION C022 RESIDUE 628 OPERATED ON BY TRANSFORMATION C016 RESIDUE 630 OPERATED ON BY TRANSFORMATION C010 RESIDUE 637 OPERATED ON BY TRANSFORMATION C015 RESIDUE 639 OPERATED ON BY TRANSFORMATION C010 RESIDUE 642 OPERATED ON BY TRANSFORMATION C016 RESIDUE 648 OPERATED ON BY TRANSFORMATION C016 RESIDUE 649 OPERATED ON BY TRANSFORMATION C022 RESIDUE 650 OPERATED ON BY TRANSFORMATION C022 RESIDUE 651 OPERATED ON BY TRANSFORMATION C022 RESIDUE 652 OPERATED ON BY TRANSFORMATION C010 RESIDUE 662 OPERATED ON BY TRANSFORMATION C022 RESIDUE 664 OPERATED ON BY TRANSFORMATION C022 RESIDUE 666 OPERATED ON BY TRANSFORMATION C023 RESIDUE 668 OPERATED ON BY TRANSFORMATION C010 RESIDUE 670 OPERATED ON BY TRANSFORMATION C010 RESIDUE 672 OPERATED ON BY TRANSFORMATION C010 RESIDUE 681 OPERATED ON BY TRANSFORMATION C016 RESIDUE 682 OPERATED ON BY TRANSFORMATION C016 RESIDUE 683 OPERATED ON BY TRANSFORMATION C022 RESIDUE 688 OPERATED ON BY TRANSFORMATION C010 RESIDUE 689 OPERATED ON BY TRANSFORMATION C010 RESIDUE 690 OPERATED ON BY TRANSFORMATION C016 RESIDUE 708 OPERATED ON BY TRANSFORMATION C022 RESIDUE 711 OPERATED ON BY TRANSFORMATION C010 RESIDUE 717 OPERATED ON BY TRANSFORMATION C022 RESIDUE 721 OPERATED ON BY TRANSFORMATION C010 RESIDUE 724 OPERATED ON BY TRANSFORMATION C016 RESIDUE 725 OPERATED ON BY TRANSFORMATION C016 RESIDUE 726 OPERATED ON BY TRANSFORMATION C016 RESIDUE 732 OPERATED ON BY TRANSFORMATION C022 RESIDUE 735 OPERATED ON BY TRANSFORMATION C022 RESIDUE 736 OPERATED ON BY TRANSFORMATION C022 RESIDUE 738 OPERATED ON BY TRANSFORMATION C023 RESIDUE 739 OPERATED ON BY TRANSFORMATION C019 RESIDUE 740 OPERATED ON BY TRANSFORMATION C016 RESIDUE 741 OPERATED ON BY TRANSFORMATION C019 RESIDUE 746 OPERATED ON BY TRANSFORMATION C022 RESIDUE 749 OPERATED ON BY TRANSFORMATION C015 RESIDUE 751 OPERATED ON BY TRANSFORMATION C016 RESIDUE 758 OPERATED ON BY TRANSFORMATION C010 RESIDUE 759 OPERATED ON BY TRANSFORMATION C016 RESIDUE 760 OPERATED ON BY TRANSFORMATION C008 RESIDUE 764 OPERATED ON BY TRANSFORMATION C016 RESIDUE 765 OPERATED ON BY TRANSFORMATION C016 RESIDUE 768 OPERATED ON BY TRANSFORMATION C008 RESIDUE 769 OPERATED ON BY TRANSFORMATION C010 RESIDUE 774 OPERATED ON BY TRANSFORMATION C010 RESIDUE 777 OPERATED ON BY TRANSFORMATION C007 RESIDUE 781 OPERATED ON BY TRANSFORMATION C016 RESIDUE 783 OPERATED ON BY TRANSFORMATION C016 RESIDUE 784 OPERATED ON BY TRANSFORMATION C016 RESIDUE 785 OPERATED ON BY TRANSFORMATION C010 RESIDUE 787 OPERATED ON BY TRANSFORMATION C008 RESIDUE 789 OPERATED ON BY TRANSFORMATION C016 RESIDUE 794 OPERATED ON BY TRANSFORMATION C008 RESIDUE 795 OPERATED ON BY TRANSFORMATION C007 RESIDUE 796 OPERATED ON BY TRANSFORMATION C016 RESIDUE 798 OPERATED ON BY TRANSFORMATION C008 RESIDUE 799 OPERATED ON BY TRANSFORMATION C016 RESIDUE 801 OPERATED ON BY TRANSFORMATION C010 RESIDUE 804 OPERATED ON BY TRANSFORMATION C010 RESIDUE 816 OPERATED ON BY TRANSFORMATION C016 RESIDUE 817 OPERATED ON BY TRANSFORMATION C010 RESIDUE 818 OPERATED ON BY TRANSFORMATION C016 RESIDUE 822 OPERATED ON BY TRANSFORMATION C008 RESIDUE 823 OPERATED ON BY TRANSFORMATION C016 RESIDUE 824 OPERATED ON BY TRANSFORMATION C016 RESIDUE 825 OPERATED ON BY TRANSFORMATION C008 RESIDUE 827 OPERATED ON BY TRANSFORMATION C008 RESIDUE 829 OPERATED ON BY TRANSFORMATION C008 RESIDUE 831 OPERATED ON BY TRANSFORMATION C008 RESIDUE 835 OPERATED ON BY TRANSFORMATION C016 RESIDUE 836 OPERATED ON BY TRANSFORMATION C010 RESIDUE 837 OPERATED ON BY TRANSFORMATION C016 RESIDUE 838 OPERATED ON BY TRANSFORMATION C010 RESIDUE 856 OPERATED ON BY TRANSFORMATION C015 RESIDUE 857 OPERATED ON BY TRANSFORMATION C010 RESIDUE 863 OPERATED ON BY TRANSFORMATION C008 RESIDUE 865 OPERATED ON BY TRANSFORMATION C016 RESIDUE 867 OPERATED ON BY TRANSFORMATION C015 RESIDUE 885 OPERATED ON BY TRANSFORMATION C016 RESIDUE 889 OPERATED ON BY TRANSFORMATION C010 RESIDUE 893 OPERATED ON BY TRANSFORMATION C010 RESIDUE 894 OPERATED ON BY TRANSFORMATION C010 RESIDUE 898 OPERATED ON BY TRANSFORMATION C008 RESIDUE 904 OPERATED ON BY TRANSFORMATION C010 RESIDUE 911 OPERATED ON BY TRANSFORMATION C010 RESIDUE 914 OPERATED ON BY TRANSFORMATION C010 RESIDUE 915 OPERATED ON BY TRANSFORMATION C008 RESIDUE 917 OPERATED ON BY TRANSFORMATION C010 RESIDUE 918 OPERATED ON BY TRANSFORMATION C008 RESIDUE 926 OPERATED ON BY TRANSFORMATION C008 RESIDUE 930 OPERATED ON BY TRANSFORMATION C013 RESIDUE 932 OPERATED ON BY TRANSFORMATION C008 RESIDUE 941 OPERATED ON BY TRANSFORMATION C008 RESIDUE 945 OPERATED ON BY TRANSFORMATION C008 RESIDUE 950 OPERATED ON BY TRANSFORMATION C015 RESIDUE 957 OPERATED ON BY TRANSFORMATION C016 RESIDUE 960 OPERATED ON BY TRANSFORMATION C010 RESIDUE 961 OPERATED ON BY TRANSFORMATION C016 RESIDUE 962 OPERATED ON BY TRANSFORMATION C010 RESIDUE 964 OPERATED ON BY TRANSFORMATION C010 RESIDUE 966 OPERATED ON BY TRANSFORMATION C008 RESIDUE 980 OPERATED ON BY TRANSFORMATION C010 RESIDUE 981 OPERATED ON BY TRANSFORMATION C016 RESIDUE 982 OPERATED ON BY TRANSFORMATION C010 RESIDUE 983 OPERATED ON BY TRANSFORMATION C016 RESIDUE 984 OPERATED ON BY TRANSFORMATION C016 RESIDUE 994 OPERATED ON BY TRANSFORMATION C013 RESIDUE 997 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1003 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1004 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1005 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1006 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1009 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1016 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1018 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1019 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1020 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1022 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1023 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1030 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1033 OPERATED ON BY TRANSFORMATION C021 RESIDUE 1036 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1037 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1038 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1041 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1048 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1052 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1055 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1062 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1064 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1071 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1073 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1076 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1077 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1079 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1082 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1084 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1085 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1086 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1087 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1091 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1094 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1102 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1103 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1104 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1109 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1113 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1119 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1120 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1122 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1124 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1125 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1138 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1144 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1148 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1157 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1161 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1167 OPERATED ON BY TRANSFORMATION C025 RESIDUE 1172 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1173 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1175 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1176 OPERATED ON BY TRANSFORMATION C025 RESIDUE 1177 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1178 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1183 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1189 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1192 OPERATED ON BY TRANSFORMATION C025 RESIDUE 1195 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1196 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1198 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1199 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1205 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1210 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1217 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1218 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1220 OPERATED ON BY TRANSFORMATION C021 RESIDUE 1224 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1231 OPERATED ON BY TRANSFORMATION C021 RESIDUE 1234 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1236 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1241 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1244 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1245 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1252 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1257 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1261 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1264 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1265 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1267 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1270 OPERATED ON BY TRANSFORMATION C002 RESIDUE 1271 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1276 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1283 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1284 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1298 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1299 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1303 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1314 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1318 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1321 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1325 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1327 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1329 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1333 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1334 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1335 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1339 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1340 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1342 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1345 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1346 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1349 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1351 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1352 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1353 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1355 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1356 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1358 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1359 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1367 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1373 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1378 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1385 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1391 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1392 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1399 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1410 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1418 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1420 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1423 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1425 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1430 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1433 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1435 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1438 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1446 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1448 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1450 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1453 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1455 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1456 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1458 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1462 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1464 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1466 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1467 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1469 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1471 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1472 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1477 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1480 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1481 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1486 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1488 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1490 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1499 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1503 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1506 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1508 OPERATED ON BY TRANSFORMATION C004 RESIDUE 1514 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1517 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1525 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1527 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1531 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1533 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1541 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1542 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1546 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1548 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1551 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1553 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1557 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1563 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1574 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1581 OPERATED ON BY TRANSFORMATION C004 RESIDUE 1592 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1598 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1599 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1603 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1606 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1607 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1609 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1611 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1612 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1613 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1614 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1615 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1616 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1618 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1626 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1627 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1633 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1638 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1641 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1644 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1647 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1649 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1650 OPERATED ON BY TRANSFORMATION C026 RESIDUE 1653 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1659 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1663 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1665 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1669 OPERATED ON BY TRANSFORMATION C025 RESIDUE 1671 OPERATED ON BY TRANSFORMATION C004 RESIDUE 1672 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1674 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1679 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1685 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1689 OPERATED ON BY TRANSFORMATION C025 RESIDUE 1690 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1691 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1702 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1707 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1708 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1711 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1713 OPERATED ON BY TRANSFORMATION C025 RESIDUE 1715 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1716 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1717 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1720 OPERATED ON BY TRANSFORMATION C023 RESIDUE 1721 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1723 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1724 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1728 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1729 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1745 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1746 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1747 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1750 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1752 OPERATED ON BY TRANSFORMATION C001 RESIDUE 1766 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1782 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1791 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1797 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1805 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1810 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1813 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1814 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1815 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1827 OPERATED ON BY TRANSFORMATION C004 RESIDUE 1830 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1834 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1835 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1837 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1841 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1846 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1853 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1855 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1858 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1862 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1863 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1864 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1866 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1867 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1868 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1869 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1870 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1872 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1876 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1878 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1880 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1881 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1882 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1886 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1892 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1895 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1900 OPERATED ON BY TRANSFORMATION C004 RESIDUE 1902 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1903 OPERATED ON BY TRANSFORMATION C002 RESIDUE 1906 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1912 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1916 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1918 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1920 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1924 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1926 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1927 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1929 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1930 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1935 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1939 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1940 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1941 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1943 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1947 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1951 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1963 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1969 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1970 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1978 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 579 193 193 0.00 2 C002 has 1122 374 374 0.00 3 C003 has 255 85 85 0.00 4 C004 has 978 326 326 0.00 5 C005 has 2487 829 829 0.00 6 C006 has 831 277 277 0.00 7 C007 has 1185 395 395 0.00 8 C008 has 2724 908 908 0.00 9 C009 has 888 296 296 0.00 10 C010 has 2628 876 876 0.00 12 C012 has 243 81 81 0.00 13 C013 has 858 286 286 0.00 14 C014 has 276 92 92 0.00 Total of21032 atoms and 7004 groups and 6999 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 1695 atoms have been selected out of 5978 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 565 residues deleted. DELTIC: 1695 bonds deleted DELTIC: 565 angles deleted DELTIC: 1130 donors deleted DELTIC: 565 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1416 Number of atoms = 4283 Number of groups = 1421 Number of bonds = 4276 Number of angles = 1520 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1418 Number of HB donors = 2814 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1416 Number of atoms = 4283 Number of groups = 1421 Number of bonds = 4276 Number of angles = 1520 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1418 Number of HB donors = 2814 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.998" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1416" Evaluating: 1416-7 Parameter: NUMWAT <- "1409" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1409" Comparing "1081" and "1409". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.998" Parameter: BOX -> "34.998" Parameter: BOX -> "34.998" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.99800 B = 34.99800 C = 34.99800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5105 2 1 -1 0 -1 4.0985 3 1 -1 1 -1 3.1330 4 1 0 -1 -1 2.0091 5 1 0 0 -1 2.6334 6 1 0 1 -1 3.1751 7 1 -1 -1 0 5.6405 8 1 -1 0 0 0.8865 9 1 -1 1 0 1.9150 10 1 0 -1 0 1.8331 11 1 0 1 0 1.8331 12 1 -1 -1 1 5.1739 13 1 -1 0 1 4.0082 14 1 -1 1 1 3.5969 15 1 0 -1 1 3.1751 16 1 0 0 1 2.6334 17 1 0 1 1 2.0091 18 1 1 1 1 4.5105 19 1 1 0 1 4.0985 20 1 1 -1 1 3.1330 21 1 1 1 0 5.6405 22 1 1 0 0 0.8865 23 1 1 -1 0 1.9150 24 1 1 1 -1 5.1739 25 1 1 0 -1 4.0082 26 1 1 -1 -1 3.5969 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4209 atoms have been selected out of 4283 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 175 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 723 241 241 0.00 3 C003 has 141 47 47 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1716 572 572 0.00 6 C006 has 495 165 165 0.00 7 C007 has 747 249 249 0.00 8 C008 has 1881 627 627 0.00 9 C009 has 516 172 172 0.00 10 C010 has 1800 600 600 0.00 12 C012 has 111 37 37 0.00 13 C013 has 489 163 163 0.00 14 C014 has 141 47 47 0.00 Total of14015 atoms and 4665 groups and 4660 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4283 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1415 Number of atoms = 4280 Number of groups = 1420 Number of bonds = 4273 Number of angles = 1519 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1417 Number of HB donors = 2812 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1415 Number of atoms = 4280 Number of groups = 1420 Number of bonds = 4273 Number of angles = 1519 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1417 Number of HB donors = 2812 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.996" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1415" Evaluating: 1415-7 Parameter: NUMWAT <- "1408" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1408" Comparing "1081" and "1408". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.996" Parameter: BOX -> "34.996" Parameter: BOX -> "34.996" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.99600 B = 34.99600 C = 34.99600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5124 2 1 -1 0 -1 4.0957 3 1 -1 1 -1 3.1299 4 1 0 -1 -1 2.0116 5 1 0 0 -1 2.6314 6 1 0 1 -1 3.1727 7 1 -1 -1 0 5.6384 8 1 -1 0 0 0.8867 9 1 -1 1 0 1.9122 10 1 0 -1 0 1.8328 11 1 0 1 0 1.8328 12 1 -1 -1 1 5.1704 13 1 -1 0 1 4.0061 14 1 -1 1 1 3.5937 15 1 0 -1 1 3.1727 16 1 0 0 1 2.6314 17 1 0 1 1 2.0116 18 1 1 1 1 4.5124 19 1 1 0 1 4.0957 20 1 1 -1 1 3.1299 21 1 1 1 0 5.6384 22 1 1 0 0 0.8867 23 1 1 -1 0 1.9122 24 1 1 1 -1 5.1704 25 1 1 0 -1 4.0061 26 1 1 -1 -1 3.5937 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4206 atoms have been selected out of 4280 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 723 241 241 0.00 3 C003 has 141 47 47 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1716 572 572 0.00 6 C006 has 495 165 165 0.00 7 C007 has 747 249 249 0.00 8 C008 has 1878 626 626 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1800 600 600 0.00 12 C012 has 111 37 37 0.00 13 C013 has 489 163 163 0.00 14 C014 has 141 47 47 0.00 Total of14006 atoms and 4662 groups and 4657 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4280 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1415 Number of atoms = 4280 Number of groups = 1420 Number of bonds = 4273 Number of angles = 1519 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1417 Number of HB donors = 2812 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1415 Number of atoms = 4280 Number of groups = 1420 Number of bonds = 4273 Number of angles = 1519 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1417 Number of HB donors = 2812 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.994" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1415" Evaluating: 1415-7 Parameter: NUMWAT <- "1408" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1408" Comparing "1081" and "1408". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.994" Parameter: BOX -> "34.994" Parameter: BOX -> "34.994" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.99400 B = 34.99400 C = 34.99400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5143 2 1 -1 0 -1 4.0929 3 1 -1 1 -1 3.1268 4 1 0 -1 -1 2.0141 5 1 0 0 -1 2.6295 6 1 0 1 -1 3.1703 7 1 -1 -1 0 5.6363 8 1 -1 0 0 0.8868 9 1 -1 1 0 1.9094 10 1 0 -1 0 1.8325 11 1 0 1 0 1.8325 12 1 -1 -1 1 5.1669 13 1 -1 0 1 4.0039 14 1 -1 1 1 3.5906 15 1 0 -1 1 3.1703 16 1 0 0 1 2.6295 17 1 0 1 1 2.0141 18 1 1 1 1 4.5143 19 1 1 0 1 4.0929 20 1 1 -1 1 3.1268 21 1 1 1 0 5.6363 22 1 1 0 0 0.8868 23 1 1 -1 0 1.9094 24 1 1 1 -1 5.1669 25 1 1 0 -1 4.0039 26 1 1 -1 -1 3.5906 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4206 atoms have been selected out of 4280 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 723 241 241 0.00 3 C003 has 141 47 47 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1716 572 572 0.00 6 C006 has 495 165 165 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1878 626 626 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1800 600 600 0.00 12 C012 has 111 37 37 0.00 13 C013 has 489 163 163 0.00 14 C014 has 141 47 47 0.00 Total of14009 atoms and 4663 groups and 4658 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4280 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1415 Number of atoms = 4280 Number of groups = 1420 Number of bonds = 4273 Number of angles = 1519 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1417 Number of HB donors = 2812 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1415 Number of atoms = 4280 Number of groups = 1420 Number of bonds = 4273 Number of angles = 1519 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1417 Number of HB donors = 2812 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.992" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1415" Evaluating: 1415-7 Parameter: NUMWAT <- "1408" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1408" Comparing "1081" and "1408". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.992" Parameter: BOX -> "34.992" Parameter: BOX -> "34.992" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.99200 B = 34.99200 C = 34.99200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5162 2 1 -1 0 -1 4.0901 3 1 -1 1 -1 3.1238 4 1 0 -1 -1 2.0166 5 1 0 0 -1 2.6276 6 1 0 1 -1 3.1679 7 1 -1 -1 0 5.6342 8 1 -1 0 0 0.8869 9 1 -1 1 0 1.9066 10 1 0 -1 0 1.8321 11 1 0 1 0 1.8321 12 1 -1 -1 1 5.1635 13 1 -1 0 1 4.0018 14 1 -1 1 1 3.5874 15 1 0 -1 1 3.1679 16 1 0 0 1 2.6276 17 1 0 1 1 2.0166 18 1 1 1 1 4.5162 19 1 1 0 1 4.0901 20 1 1 -1 1 3.1238 21 1 1 1 0 5.6342 22 1 1 0 0 0.8869 23 1 1 -1 0 1.9066 24 1 1 1 -1 5.1635 25 1 1 0 -1 4.0018 26 1 1 -1 -1 3.5874 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4206 atoms have been selected out of 4280 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 723 241 241 0.00 3 C003 has 141 47 47 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1716 572 572 0.00 6 C006 has 495 165 165 0.00 7 C007 has 753 251 251 0.00 8 C008 has 1878 626 626 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1800 600 600 0.00 12 C012 has 114 38 38 0.00 13 C013 has 489 163 163 0.00 14 C014 has 141 47 47 0.00 Total of14018 atoms and 4666 groups and 4661 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4280 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1415 Number of atoms = 4280 Number of groups = 1420 Number of bonds = 4273 Number of angles = 1519 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1417 Number of HB donors = 2812 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1415 Number of atoms = 4280 Number of groups = 1420 Number of bonds = 4273 Number of angles = 1519 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1417 Number of HB donors = 2812 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.99" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1415" Evaluating: 1415-7 Parameter: NUMWAT <- "1408" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1408" Comparing "1081" and "1408". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.99" Parameter: BOX -> "34.99" Parameter: BOX -> "34.99" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.99000 B = 34.99000 C = 34.99000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5182 2 1 -1 0 -1 4.0873 3 1 -1 1 -1 3.1207 4 1 0 -1 -1 2.0191 5 1 0 0 -1 2.6257 6 1 0 1 -1 3.1655 7 1 -1 -1 0 5.6321 8 1 -1 0 0 0.8870 9 1 -1 1 0 1.9038 10 1 0 -1 0 1.8318 11 1 0 1 0 1.8318 12 1 -1 -1 1 5.1600 13 1 -1 0 1 3.9997 14 1 -1 1 1 3.5842 15 1 0 -1 1 3.1655 16 1 0 0 1 2.6257 17 1 0 1 1 2.0191 18 1 1 1 1 4.5182 19 1 1 0 1 4.0873 20 1 1 -1 1 3.1207 21 1 1 1 0 5.6321 22 1 1 0 0 0.8870 23 1 1 -1 0 1.9038 24 1 1 1 -1 5.1600 25 1 1 0 -1 3.9997 26 1 1 -1 -1 3.5842 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4206 atoms have been selected out of 4280 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1140 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 726 242 242 0.00 3 C003 has 141 47 47 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1716 572 572 0.00 6 C006 has 495 165 165 0.00 7 C007 has 756 252 252 0.00 8 C008 has 1881 627 627 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1800 600 600 0.00 12 C012 has 114 38 38 0.00 13 C013 has 489 163 163 0.00 14 C014 has 141 47 47 0.00 Total of14027 atoms and 4669 groups and 4664 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4280 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1414 Number of atoms = 4277 Number of groups = 1419 Number of bonds = 4270 Number of angles = 1518 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1416 Number of HB donors = 2810 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1414 Number of atoms = 4277 Number of groups = 1419 Number of bonds = 4270 Number of angles = 1518 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1416 Number of HB donors = 2810 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.988" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1414" Evaluating: 1414-7 Parameter: NUMWAT <- "1407" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1407" Comparing "1081" and "1407". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.988" Parameter: BOX -> "34.988" Parameter: BOX -> "34.988" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.98800 B = 34.98800 C = 34.98800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5201 2 1 -1 0 -1 4.0845 3 1 -1 1 -1 3.1176 4 1 0 -1 -1 2.0217 5 1 0 0 -1 2.6238 6 1 0 1 -1 3.1631 7 1 -1 -1 0 5.6300 8 1 -1 0 0 0.8871 9 1 -1 1 0 1.9010 10 1 0 -1 0 1.8315 11 1 0 1 0 1.8315 12 1 -1 -1 1 5.1566 13 1 -1 0 1 3.9976 14 1 -1 1 1 3.5810 15 1 0 -1 1 3.1631 16 1 0 0 1 2.6238 17 1 0 1 1 2.0217 18 1 1 1 1 4.5201 19 1 1 0 1 4.0845 20 1 1 -1 1 3.1176 21 1 1 1 0 5.6300 22 1 1 0 0 0.8871 23 1 1 -1 0 1.9010 24 1 1 1 -1 5.1566 25 1 1 0 -1 3.9976 26 1 1 -1 -1 3.5810 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4203 atoms have been selected out of 4277 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 723 241 241 0.00 3 C003 has 141 47 47 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1713 571 571 0.00 6 C006 has 495 165 165 0.00 7 C007 has 753 251 251 0.00 8 C008 has 1878 626 626 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1800 600 600 0.00 12 C012 has 114 38 38 0.00 13 C013 has 492 164 164 0.00 14 C014 has 141 47 47 0.00 Total of14015 atoms and 4665 groups and 4660 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4277 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1414 Number of atoms = 4277 Number of groups = 1419 Number of bonds = 4270 Number of angles = 1518 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1416 Number of HB donors = 2810 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1414 Number of atoms = 4277 Number of groups = 1419 Number of bonds = 4270 Number of angles = 1518 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1416 Number of HB donors = 2810 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.986" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1414" Evaluating: 1414-7 Parameter: NUMWAT <- "1407" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1407" Comparing "1081" and "1407". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.986" Parameter: BOX -> "34.986" Parameter: BOX -> "34.986" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.98600 B = 34.98600 C = 34.98600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5220 2 1 -1 0 -1 4.0817 3 1 -1 1 -1 3.1145 4 1 0 -1 -1 2.0242 5 1 0 0 -1 2.6219 6 1 0 1 -1 3.1607 7 1 -1 -1 0 5.6279 8 1 -1 0 0 0.8873 9 1 -1 1 0 1.8983 10 1 0 -1 0 1.8311 11 1 0 1 0 1.8311 12 1 -1 -1 1 5.1531 13 1 -1 0 1 3.9954 14 1 -1 1 1 3.5779 15 1 0 -1 1 3.1607 16 1 0 0 1 2.6219 17 1 0 1 1 2.0242 18 1 1 1 1 4.5220 19 1 1 0 1 4.0817 20 1 1 -1 1 3.1145 21 1 1 1 0 5.6279 22 1 1 0 0 0.8873 23 1 1 -1 0 1.8983 24 1 1 1 -1 5.1531 25 1 1 0 -1 3.9954 26 1 1 -1 -1 3.5779 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4203 atoms have been selected out of 4277 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 723 241 241 0.00 3 C003 has 141 47 47 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1713 571 571 0.00 6 C006 has 495 165 165 0.00 7 C007 has 756 252 252 0.00 8 C008 has 1878 626 626 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1800 600 600 0.00 12 C012 has 114 38 38 0.00 13 C013 has 492 164 164 0.00 14 C014 has 141 47 47 0.00 Total of14018 atoms and 4666 groups and 4661 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4277 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1414 Number of atoms = 4277 Number of groups = 1419 Number of bonds = 4270 Number of angles = 1518 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1416 Number of HB donors = 2810 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1414 Number of atoms = 4277 Number of groups = 1419 Number of bonds = 4270 Number of angles = 1518 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1416 Number of HB donors = 2810 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.984" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1414" Evaluating: 1414-7 Parameter: NUMWAT <- "1407" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1407" Comparing "1081" and "1407". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.984" Parameter: BOX -> "34.984" Parameter: BOX -> "34.984" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.98400 B = 34.98400 C = 34.98400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5239 2 1 -1 0 -1 4.0789 3 1 -1 1 -1 3.1114 4 1 0 -1 -1 2.0267 5 1 0 0 -1 2.6199 6 1 0 1 -1 3.1583 7 1 -1 -1 0 5.6258 8 1 -1 0 0 0.8874 9 1 -1 1 0 1.8955 10 1 0 -1 0 1.8308 11 1 0 1 0 1.8308 12 1 -1 -1 1 5.1497 13 1 -1 0 1 3.9933 14 1 -1 1 1 3.5747 15 1 0 -1 1 3.1583 16 1 0 0 1 2.6199 17 1 0 1 1 2.0267 18 1 1 1 1 4.5239 19 1 1 0 1 4.0789 20 1 1 -1 1 3.1114 21 1 1 1 0 5.6258 22 1 1 0 0 0.8874 23 1 1 -1 0 1.8955 24 1 1 1 -1 5.1497 25 1 1 0 -1 3.9933 26 1 1 -1 -1 3.5747 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4203 atoms have been selected out of 4277 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 404 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 723 241 241 0.00 3 C003 has 141 47 47 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1713 571 571 0.00 6 C006 has 495 165 165 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1881 627 627 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1800 600 600 0.00 12 C012 has 114 38 38 0.00 13 C013 has 492 164 164 0.00 14 C014 has 141 47 47 0.00 Total of14030 atoms and 4670 groups and 4665 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4277 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1413 Number of atoms = 4274 Number of groups = 1418 Number of bonds = 4267 Number of angles = 1517 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1415 Number of HB donors = 2808 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1413 Number of atoms = 4274 Number of groups = 1418 Number of bonds = 4267 Number of angles = 1517 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1415 Number of HB donors = 2808 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.982" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1413" Evaluating: 1413-7 Parameter: NUMWAT <- "1406" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1406" Comparing "1081" and "1406". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.982" Parameter: BOX -> "34.982" Parameter: BOX -> "34.982" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.98200 B = 34.98200 C = 34.98200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5258 2 1 -1 0 -1 4.0761 3 1 -1 1 -1 3.1083 4 1 0 -1 -1 2.0293 5 1 0 0 -1 2.6180 6 1 0 1 -1 3.1559 7 1 -1 -1 0 5.6237 8 1 -1 0 0 0.8876 9 1 -1 1 0 1.8927 10 1 0 -1 0 1.8305 11 1 0 1 0 1.8305 12 1 -1 -1 1 5.1462 13 1 -1 0 1 3.9912 14 1 -1 1 1 3.5715 15 1 0 -1 1 3.1559 16 1 0 0 1 2.6180 17 1 0 1 1 2.0293 18 1 1 1 1 4.5258 19 1 1 0 1 4.0761 20 1 1 -1 1 3.1083 21 1 1 1 0 5.6237 22 1 1 0 0 0.8876 23 1 1 -1 0 1.8927 24 1 1 1 -1 5.1462 25 1 1 0 -1 3.9912 26 1 1 -1 -1 3.5715 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4200 atoms have been selected out of 4274 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 723 241 241 0.00 3 C003 has 141 47 47 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1713 571 571 0.00 6 C006 has 495 165 165 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1878 626 626 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1797 599 599 0.00 12 C012 has 114 38 38 0.00 13 C013 has 492 164 164 0.00 14 C014 has 141 47 47 0.00 Total of14018 atoms and 4666 groups and 4661 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4274 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1413 Number of atoms = 4274 Number of groups = 1418 Number of bonds = 4267 Number of angles = 1517 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1415 Number of HB donors = 2808 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1413 Number of atoms = 4274 Number of groups = 1418 Number of bonds = 4267 Number of angles = 1517 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1415 Number of HB donors = 2808 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.98" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1413" Evaluating: 1413-7 Parameter: NUMWAT <- "1406" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1406" Comparing "1081" and "1406". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.98" Parameter: BOX -> "34.98" Parameter: BOX -> "34.98" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.98000 B = 34.98000 C = 34.98000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5277 2 1 -1 0 -1 4.0733 3 1 -1 1 -1 3.1052 4 1 0 -1 -1 2.0318 5 1 0 0 -1 2.6161 6 1 0 1 -1 3.1535 7 1 -1 -1 0 5.6216 8 1 -1 0 0 0.8877 9 1 -1 1 0 1.8899 10 1 0 -1 0 1.8301 11 1 0 1 0 1.8301 12 1 -1 -1 1 5.1427 13 1 -1 0 1 3.9891 14 1 -1 1 1 3.5684 15 1 0 -1 1 3.1535 16 1 0 0 1 2.6161 17 1 0 1 1 2.0318 18 1 1 1 1 4.5277 19 1 1 0 1 4.0733 20 1 1 -1 1 3.1052 21 1 1 1 0 5.6216 22 1 1 0 0 0.8877 23 1 1 -1 0 1.8899 24 1 1 1 -1 5.1427 25 1 1 0 -1 3.9891 26 1 1 -1 -1 3.5684 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4200 atoms have been selected out of 4274 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 723 241 241 0.00 3 C003 has 141 47 47 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1713 571 571 0.00 6 C006 has 495 165 165 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1878 626 626 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1797 599 599 0.00 12 C012 has 114 38 38 0.00 13 C013 has 492 164 164 0.00 14 C014 has 141 47 47 0.00 Total of14018 atoms and 4666 groups and 4661 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4274 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1413 Number of atoms = 4274 Number of groups = 1418 Number of bonds = 4267 Number of angles = 1517 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1415 Number of HB donors = 2808 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1413 Number of atoms = 4274 Number of groups = 1418 Number of bonds = 4267 Number of angles = 1517 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1415 Number of HB donors = 2808 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.978" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1413" Evaluating: 1413-7 Parameter: NUMWAT <- "1406" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1406" Comparing "1081" and "1406". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.978" Parameter: BOX -> "34.978" Parameter: BOX -> "34.978" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.97800 B = 34.97800 C = 34.97800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5296 2 1 -1 0 -1 4.0705 3 1 -1 1 -1 3.1021 4 1 0 -1 -1 2.0343 5 1 0 0 -1 2.6142 6 1 0 1 -1 3.1511 7 1 -1 -1 0 5.6195 8 1 -1 0 0 0.8879 9 1 -1 1 0 1.8871 10 1 0 -1 0 1.8298 11 1 0 1 0 1.8298 12 1 -1 -1 1 5.1393 13 1 -1 0 1 3.9870 14 1 -1 1 1 3.5652 15 1 0 -1 1 3.1511 16 1 0 0 1 2.6142 17 1 0 1 1 2.0343 18 1 1 1 1 4.5296 19 1 1 0 1 4.0705 20 1 1 -1 1 3.1021 21 1 1 1 0 5.6195 22 1 1 0 0 0.8879 23 1 1 -1 0 1.8871 24 1 1 1 -1 5.1393 25 1 1 0 -1 3.9870 26 1 1 -1 -1 3.5652 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4200 atoms have been selected out of 4274 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 168 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 723 241 241 0.00 3 C003 has 141 47 47 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1713 571 571 0.00 6 C006 has 495 165 165 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1881 627 627 0.00 9 C009 has 516 172 172 0.00 10 C010 has 1797 599 599 0.00 12 C012 has 114 38 38 0.00 13 C013 has 495 165 165 0.00 14 C014 has 144 48 48 0.00 Total of14030 atoms and 4670 groups and 4665 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4274 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1412 Number of atoms = 4271 Number of groups = 1417 Number of bonds = 4264 Number of angles = 1516 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1414 Number of HB donors = 2806 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1412 Number of atoms = 4271 Number of groups = 1417 Number of bonds = 4264 Number of angles = 1516 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1414 Number of HB donors = 2806 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.976" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1412" Evaluating: 1412-7 Parameter: NUMWAT <- "1405" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1405" Comparing "1081" and "1405". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.976" Parameter: BOX -> "34.976" Parameter: BOX -> "34.976" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.97600 B = 34.97600 C = 34.97600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5316 2 1 -1 0 -1 4.0677 3 1 -1 1 -1 3.0991 4 1 0 -1 -1 2.0368 5 1 0 0 -1 2.6123 6 1 0 1 -1 3.1487 7 1 -1 -1 0 5.6174 8 1 -1 0 0 0.8880 9 1 -1 1 0 1.8844 10 1 0 -1 0 1.8295 11 1 0 1 0 1.8295 12 1 -1 -1 1 5.1358 13 1 -1 0 1 3.9848 14 1 -1 1 1 3.5620 15 1 0 -1 1 3.1487 16 1 0 0 1 2.6123 17 1 0 1 1 2.0368 18 1 1 1 1 4.5316 19 1 1 0 1 4.0677 20 1 1 -1 1 3.0991 21 1 1 1 0 5.6174 22 1 1 0 0 0.8880 23 1 1 -1 0 1.8844 24 1 1 1 -1 5.1358 25 1 1 0 -1 3.9848 26 1 1 -1 -1 3.5620 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4197 atoms have been selected out of 4271 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 445 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1143 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 723 241 241 0.00 3 C003 has 141 47 47 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1713 571 571 0.00 6 C006 has 498 166 166 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1878 626 626 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1791 597 597 0.00 12 C012 has 114 38 38 0.00 13 C013 has 495 165 165 0.00 14 C014 has 141 47 47 0.00 Total of14012 atoms and 4664 groups and 4659 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 4271 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1410 Number of atoms = 4265 Number of groups = 1415 Number of bonds = 4258 Number of angles = 1514 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1412 Number of HB donors = 2802 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1410 Number of atoms = 4265 Number of groups = 1415 Number of bonds = 4258 Number of angles = 1514 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1412 Number of HB donors = 2802 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.974" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1410" Evaluating: 1410-7 Parameter: NUMWAT <- "1403" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1403" Comparing "1081" and "1403". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.974" Parameter: BOX -> "34.974" Parameter: BOX -> "34.974" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.97400 B = 34.97400 C = 34.97400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5335 2 1 -1 0 -1 4.0649 3 1 -1 1 -1 3.0960 4 1 0 -1 -1 3.4248 5 1 0 0 -1 2.4494 6 1 0 1 -1 3.1463 7 1 -1 -1 0 5.6153 8 1 -1 0 0 0.8882 9 1 -1 1 0 1.8816 10 1 0 -1 0 0.8049 11 1 0 1 0 0.8049 12 1 -1 -1 1 5.1324 13 1 -1 0 1 3.9827 14 1 -1 1 1 3.5588 15 1 0 -1 1 3.1463 16 1 0 0 1 2.4494 17 1 0 1 1 3.4248 18 1 1 1 1 4.5335 19 1 1 0 1 4.0649 20 1 1 -1 1 3.0960 21 1 1 1 0 5.6153 22 1 1 0 0 0.8882 23 1 1 -1 0 1.8816 24 1 1 1 -1 5.1324 25 1 1 0 -1 3.9827 26 1 1 -1 -1 3.5588 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4191 atoms have been selected out of 4265 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 723 241 241 0.00 3 C003 has 141 47 47 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1710 570 570 0.00 6 C006 has 495 165 165 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1881 627 627 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1791 597 597 0.00 12 C012 has 114 38 38 0.00 13 C013 has 495 165 165 0.00 14 C014 has 141 47 47 0.00 Total of14003 atoms and 4661 groups and 4656 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4265 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1410 Number of atoms = 4265 Number of groups = 1415 Number of bonds = 4258 Number of angles = 1514 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1412 Number of HB donors = 2802 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1410 Number of atoms = 4265 Number of groups = 1415 Number of bonds = 4258 Number of angles = 1514 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1412 Number of HB donors = 2802 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.972" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1410" Evaluating: 1410-7 Parameter: NUMWAT <- "1403" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1403" Comparing "1081" and "1403". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.972" Parameter: BOX -> "34.972" Parameter: BOX -> "34.972" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.97200 B = 34.97200 C = 34.97200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5354 2 1 -1 0 -1 4.0622 3 1 -1 1 -1 3.0929 4 1 0 -1 -1 3.4227 5 1 0 0 -1 2.4475 6 1 0 1 -1 3.1439 7 1 -1 -1 0 5.6132 8 1 -1 0 0 0.8883 9 1 -1 1 0 1.8788 10 1 0 -1 0 0.8044 11 1 0 1 0 0.8044 12 1 -1 -1 1 5.1289 13 1 -1 0 1 3.9806 14 1 -1 1 1 3.5557 15 1 0 -1 1 3.1439 16 1 0 0 1 2.4475 17 1 0 1 1 3.4227 18 1 1 1 1 4.5354 19 1 1 0 1 4.0622 20 1 1 -1 1 3.0929 21 1 1 1 0 5.6132 22 1 1 0 0 0.8883 23 1 1 -1 0 1.8788 24 1 1 1 -1 5.1289 25 1 1 0 -1 3.9806 26 1 1 -1 -1 3.5557 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4191 atoms have been selected out of 4265 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 723 241 241 0.00 3 C003 has 141 47 47 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1710 570 570 0.00 6 C006 has 495 165 165 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1881 627 627 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1791 597 597 0.00 12 C012 has 114 38 38 0.00 13 C013 has 495 165 165 0.00 14 C014 has 141 47 47 0.00 Total of14003 atoms and 4661 groups and 4656 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4265 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1410 Number of atoms = 4265 Number of groups = 1415 Number of bonds = 4258 Number of angles = 1514 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1412 Number of HB donors = 2802 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1410 Number of atoms = 4265 Number of groups = 1415 Number of bonds = 4258 Number of angles = 1514 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1412 Number of HB donors = 2802 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.97" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1410" Evaluating: 1410-7 Parameter: NUMWAT <- "1403" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1403" Comparing "1081" and "1403". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.97" Parameter: BOX -> "34.97" Parameter: BOX -> "34.97" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.97000 B = 34.97000 C = 34.97000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5373 2 1 -1 0 -1 4.0594 3 1 -1 1 -1 3.0898 4 1 0 -1 -1 3.4206 5 1 0 0 -1 2.4455 6 1 0 1 -1 3.1415 7 1 -1 -1 0 5.6111 8 1 -1 0 0 0.8885 9 1 -1 1 0 1.8760 10 1 0 -1 0 0.8038 11 1 0 1 0 0.8038 12 1 -1 -1 1 5.1255 13 1 -1 0 1 3.9785 14 1 -1 1 1 3.5525 15 1 0 -1 1 3.1415 16 1 0 0 1 2.4455 17 1 0 1 1 3.4206 18 1 1 1 1 4.5373 19 1 1 0 1 4.0594 20 1 1 -1 1 3.0898 21 1 1 1 0 5.6111 22 1 1 0 0 0.8885 23 1 1 -1 0 1.8760 24 1 1 1 -1 5.1255 25 1 1 0 -1 3.9785 26 1 1 -1 -1 3.5525 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4191 atoms have been selected out of 4265 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 723 241 241 0.00 3 C003 has 141 47 47 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1710 570 570 0.00 6 C006 has 498 166 166 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1881 627 627 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1791 597 597 0.00 12 C012 has 114 38 38 0.00 13 C013 has 495 165 165 0.00 14 C014 has 141 47 47 0.00 Total of14006 atoms and 4662 groups and 4657 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4265 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1410 Number of atoms = 4265 Number of groups = 1415 Number of bonds = 4258 Number of angles = 1514 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1412 Number of HB donors = 2802 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1410 Number of atoms = 4265 Number of groups = 1415 Number of bonds = 4258 Number of angles = 1514 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1412 Number of HB donors = 2802 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.968" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1410" Evaluating: 1410-7 Parameter: NUMWAT <- "1403" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1403" Comparing "1081" and "1403". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.968" Parameter: BOX -> "34.968" Parameter: BOX -> "34.968" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.96800 B = 34.96800 C = 34.96800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5393 2 1 -1 0 -1 4.0566 3 1 -1 1 -1 3.0867 4 1 0 -1 -1 3.4185 5 1 0 0 -1 2.4436 6 1 0 1 -1 3.1391 7 1 -1 -1 0 5.6090 8 1 -1 0 0 0.8887 9 1 -1 1 0 1.8732 10 1 0 -1 0 0.8033 11 1 0 1 0 0.8033 12 1 -1 -1 1 5.1220 13 1 -1 0 1 3.9764 14 1 -1 1 1 3.5493 15 1 0 -1 1 3.1391 16 1 0 0 1 2.4436 17 1 0 1 1 3.4185 18 1 1 1 1 4.5393 19 1 1 0 1 4.0566 20 1 1 -1 1 3.0867 21 1 1 1 0 5.6090 22 1 1 0 0 0.8887 23 1 1 -1 0 1.8732 24 1 1 1 -1 5.1220 25 1 1 0 -1 3.9764 26 1 1 -1 -1 3.5493 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4191 atoms have been selected out of 4265 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1276 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 723 241 241 0.00 3 C003 has 144 48 48 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1710 570 570 0.00 6 C006 has 501 167 167 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1884 628 628 0.00 9 C009 has 516 172 172 0.00 10 C010 has 1788 596 596 0.00 12 C012 has 114 38 38 0.00 13 C013 has 495 165 165 0.00 14 C014 has 141 47 47 0.00 Total of14012 atoms and 4664 groups and 4659 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4265 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1409 Number of atoms = 4262 Number of groups = 1414 Number of bonds = 4255 Number of angles = 1513 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1411 Number of HB donors = 2800 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1409 Number of atoms = 4262 Number of groups = 1414 Number of bonds = 4255 Number of angles = 1513 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1411 Number of HB donors = 2800 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.966" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1409" Evaluating: 1409-7 Parameter: NUMWAT <- "1402" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1402" Comparing "1081" and "1402". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.966" Parameter: BOX -> "34.966" Parameter: BOX -> "34.966" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.96600 B = 34.96600 C = 34.96600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5412 2 1 -1 0 -1 4.0538 3 1 -1 1 -1 3.0836 4 1 0 -1 -1 3.4163 5 1 0 0 -1 2.4416 6 1 0 1 -1 3.1367 7 1 -1 -1 0 5.6069 8 1 -1 0 0 0.8889 9 1 -1 1 0 1.8704 10 1 0 -1 0 0.8028 11 1 0 1 0 0.8028 12 1 -1 -1 1 5.1186 13 1 -1 0 1 3.9743 14 1 -1 1 1 3.5462 15 1 0 -1 1 3.1367 16 1 0 0 1 2.4416 17 1 0 1 1 3.4163 18 1 1 1 1 4.5412 19 1 1 0 1 4.0538 20 1 1 -1 1 3.0836 21 1 1 1 0 5.6069 22 1 1 0 0 0.8889 23 1 1 -1 0 1.8704 24 1 1 1 -1 5.1186 25 1 1 0 -1 3.9743 26 1 1 -1 -1 3.5462 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4188 atoms have been selected out of 4262 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 720 240 240 0.00 3 C003 has 141 47 47 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1707 569 569 0.00 6 C006 has 498 166 166 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1881 627 627 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1788 596 596 0.00 12 C012 has 114 38 38 0.00 13 C013 has 498 166 166 0.00 14 C014 has 141 47 47 0.00 Total of13994 atoms and 4658 groups and 4653 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4262 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1409 Number of atoms = 4262 Number of groups = 1414 Number of bonds = 4255 Number of angles = 1513 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1411 Number of HB donors = 2800 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1409 Number of atoms = 4262 Number of groups = 1414 Number of bonds = 4255 Number of angles = 1513 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1411 Number of HB donors = 2800 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.964" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1409" Evaluating: 1409-7 Parameter: NUMWAT <- "1402" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1402" Comparing "1081" and "1402". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.964" Parameter: BOX -> "34.964" Parameter: BOX -> "34.964" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.96400 B = 34.96400 C = 34.96400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5431 2 1 -1 0 -1 4.0510 3 1 -1 1 -1 3.0806 4 1 0 -1 -1 3.4142 5 1 0 0 -1 2.4397 6 1 0 1 -1 3.1343 7 1 -1 -1 0 5.6048 8 1 -1 0 0 0.8890 9 1 -1 1 0 1.8677 10 1 0 -1 0 0.8023 11 1 0 1 0 0.8023 12 1 -1 -1 1 5.1151 13 1 -1 0 1 3.9721 14 1 -1 1 1 3.5430 15 1 0 -1 1 3.1343 16 1 0 0 1 2.4397 17 1 0 1 1 3.4142 18 1 1 1 1 4.5431 19 1 1 0 1 4.0510 20 1 1 -1 1 3.0806 21 1 1 1 0 5.6048 22 1 1 0 0 0.8890 23 1 1 -1 0 1.8677 24 1 1 1 -1 5.1151 25 1 1 0 -1 3.9721 26 1 1 -1 -1 3.5430 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4188 atoms have been selected out of 4262 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 720 240 240 0.00 3 C003 has 141 47 47 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1707 569 569 0.00 6 C006 has 498 166 166 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1881 627 627 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1788 596 596 0.00 12 C012 has 114 38 38 0.00 13 C013 has 498 166 166 0.00 14 C014 has 141 47 47 0.00 Total of13994 atoms and 4658 groups and 4653 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4262 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1409 Number of atoms = 4262 Number of groups = 1414 Number of bonds = 4255 Number of angles = 1513 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1411 Number of HB donors = 2800 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1409 Number of atoms = 4262 Number of groups = 1414 Number of bonds = 4255 Number of angles = 1513 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1411 Number of HB donors = 2800 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.962" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1409" Evaluating: 1409-7 Parameter: NUMWAT <- "1402" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1402" Comparing "1081" and "1402". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.962" Parameter: BOX -> "34.962" Parameter: BOX -> "34.962" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.96200 B = 34.96200 C = 34.96200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5451 2 1 -1 0 -1 4.0482 3 1 -1 1 -1 3.0775 4 1 0 -1 -1 3.4121 5 1 0 0 -1 2.4377 6 1 0 1 -1 3.1319 7 1 -1 -1 0 5.6027 8 1 -1 0 0 0.8892 9 1 -1 1 0 1.8649 10 1 0 -1 0 0.8018 11 1 0 1 0 0.8018 12 1 -1 -1 1 5.1116 13 1 -1 0 1 3.9700 14 1 -1 1 1 3.5399 15 1 0 -1 1 3.1319 16 1 0 0 1 2.4377 17 1 0 1 1 3.4121 18 1 1 1 1 4.5451 19 1 1 0 1 4.0482 20 1 1 -1 1 3.0775 21 1 1 1 0 5.6027 22 1 1 0 0 0.8892 23 1 1 -1 0 1.8649 24 1 1 1 -1 5.1116 25 1 1 0 -1 3.9700 26 1 1 -1 -1 3.5399 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4188 atoms have been selected out of 4262 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 736 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 720 240 240 0.00 3 C003 has 141 47 47 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1707 569 569 0.00 6 C006 has 495 165 165 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1884 628 628 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1791 597 597 0.00 12 C012 has 114 38 38 0.00 13 C013 has 498 166 166 0.00 14 C014 has 141 47 47 0.00 Total of14000 atoms and 4660 groups and 4655 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4262 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1408 Number of atoms = 4259 Number of groups = 1413 Number of bonds = 4252 Number of angles = 1512 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1410 Number of HB donors = 2798 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1408 Number of atoms = 4259 Number of groups = 1413 Number of bonds = 4252 Number of angles = 1512 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1410 Number of HB donors = 2798 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.96" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1408" Evaluating: 1408-7 Parameter: NUMWAT <- "1401" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1401" Comparing "1081" and "1401". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.96" Parameter: BOX -> "34.96" Parameter: BOX -> "34.96" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.96000 B = 34.96000 C = 34.96000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5470 2 1 -1 0 -1 4.0454 3 1 -1 1 -1 3.0744 4 1 0 -1 -1 3.4100 5 1 0 0 -1 2.4358 6 1 0 1 -1 3.1295 7 1 -1 -1 0 5.6006 8 1 -1 0 0 0.8894 9 1 -1 1 0 1.8621 10 1 0 -1 0 0.8013 11 1 0 1 0 0.8013 12 1 -1 -1 1 5.1082 13 1 -1 0 1 3.9679 14 1 -1 1 1 3.5367 15 1 0 -1 1 3.1295 16 1 0 0 1 2.4358 17 1 0 1 1 3.4100 18 1 1 1 1 4.5470 19 1 1 0 1 4.0454 20 1 1 -1 1 3.0744 21 1 1 1 0 5.6006 22 1 1 0 0 0.8894 23 1 1 -1 0 1.8621 24 1 1 1 -1 5.1082 25 1 1 0 -1 3.9679 26 1 1 -1 -1 3.5367 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4185 atoms have been selected out of 4259 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 720 240 240 0.00 3 C003 has 141 47 47 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1704 568 568 0.00 6 C006 has 495 165 165 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1884 628 628 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1788 596 596 0.00 12 C012 has 114 38 38 0.00 13 C013 has 498 166 166 0.00 14 C014 has 141 47 47 0.00 Total of13988 atoms and 4656 groups and 4651 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4259 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1408 Number of atoms = 4259 Number of groups = 1413 Number of bonds = 4252 Number of angles = 1512 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1410 Number of HB donors = 2798 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1408 Number of atoms = 4259 Number of groups = 1413 Number of bonds = 4252 Number of angles = 1512 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1410 Number of HB donors = 2798 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.958" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1408" Evaluating: 1408-7 Parameter: NUMWAT <- "1401" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1401" Comparing "1081" and "1401". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.958" Parameter: BOX -> "34.958" Parameter: BOX -> "34.958" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.95800 B = 34.95800 C = 34.95800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5489 2 1 -1 0 -1 4.0426 3 1 -1 1 -1 3.0713 4 1 0 -1 -1 3.4079 5 1 0 0 -1 2.4338 6 1 0 1 -1 3.1272 7 1 -1 -1 0 5.5985 8 1 -1 0 0 0.8896 9 1 -1 1 0 1.8593 10 1 0 -1 0 0.8008 11 1 0 1 0 0.8008 12 1 -1 -1 1 5.1047 13 1 -1 0 1 3.9658 14 1 -1 1 1 3.5335 15 1 0 -1 1 3.1272 16 1 0 0 1 2.4338 17 1 0 1 1 3.4079 18 1 1 1 1 4.5489 19 1 1 0 1 4.0426 20 1 1 -1 1 3.0713 21 1 1 1 0 5.5985 22 1 1 0 0 0.8896 23 1 1 -1 0 1.8593 24 1 1 1 -1 5.1047 25 1 1 0 -1 3.9658 26 1 1 -1 -1 3.5335 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4185 atoms have been selected out of 4259 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 720 240 240 0.00 3 C003 has 141 47 47 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1704 568 568 0.00 6 C006 has 495 165 165 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1884 628 628 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1788 596 596 0.00 12 C012 has 114 38 38 0.00 13 C013 has 498 166 166 0.00 14 C014 has 141 47 47 0.00 Total of13988 atoms and 4656 groups and 4651 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4259 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1408 Number of atoms = 4259 Number of groups = 1413 Number of bonds = 4252 Number of angles = 1512 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1410 Number of HB donors = 2798 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1408 Number of atoms = 4259 Number of groups = 1413 Number of bonds = 4252 Number of angles = 1512 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1410 Number of HB donors = 2798 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.956" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1408" Evaluating: 1408-7 Parameter: NUMWAT <- "1401" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1401" Comparing "1081" and "1401". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.956" Parameter: BOX -> "34.956" Parameter: BOX -> "34.956" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.95600 B = 34.95600 C = 34.95600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5509 2 1 -1 0 -1 4.0398 3 1 -1 1 -1 3.0683 4 1 0 -1 -1 3.4058 5 1 0 0 -1 2.4319 6 1 0 1 -1 3.1248 7 1 -1 -1 0 5.5964 8 1 -1 0 0 0.8898 9 1 -1 1 0 1.8565 10 1 0 -1 0 0.8003 11 1 0 1 0 0.8003 12 1 -1 -1 1 5.1013 13 1 -1 0 1 3.9637 14 1 -1 1 1 3.5304 15 1 0 -1 1 3.1248 16 1 0 0 1 2.4319 17 1 0 1 1 3.4058 18 1 1 1 1 4.5509 19 1 1 0 1 4.0398 20 1 1 -1 1 3.0683 21 1 1 1 0 5.5964 22 1 1 0 0 0.8898 23 1 1 -1 0 1.8565 24 1 1 1 -1 5.1013 25 1 1 0 -1 3.9637 26 1 1 -1 -1 3.5304 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4185 atoms have been selected out of 4259 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 720 240 240 0.00 3 C003 has 141 47 47 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1704 568 568 0.00 6 C006 has 495 165 165 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1884 628 628 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1788 596 596 0.00 12 C012 has 114 38 38 0.00 13 C013 has 498 166 166 0.00 14 C014 has 141 47 47 0.00 Total of13988 atoms and 4656 groups and 4651 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4259 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1408 Number of atoms = 4259 Number of groups = 1413 Number of bonds = 4252 Number of angles = 1512 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1410 Number of HB donors = 2798 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1408 Number of atoms = 4259 Number of groups = 1413 Number of bonds = 4252 Number of angles = 1512 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1410 Number of HB donors = 2798 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.954" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1408" Evaluating: 1408-7 Parameter: NUMWAT <- "1401" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1401" Comparing "1081" and "1401". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.954" Parameter: BOX -> "34.954" Parameter: BOX -> "34.954" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.95400 B = 34.95400 C = 34.95400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5528 2 1 -1 0 -1 4.0370 3 1 -1 1 -1 3.0652 4 1 0 -1 -1 3.4037 5 1 0 0 -1 2.4299 6 1 0 1 -1 3.1224 7 1 -1 -1 0 5.5943 8 1 -1 0 0 0.8900 9 1 -1 1 0 1.8538 10 1 0 -1 0 0.7998 11 1 0 1 0 0.7998 12 1 -1 -1 1 5.0978 13 1 -1 0 1 3.9616 14 1 -1 1 1 3.5272 15 1 0 -1 1 3.1224 16 1 0 0 1 2.4299 17 1 0 1 1 3.4037 18 1 1 1 1 4.5528 19 1 1 0 1 4.0370 20 1 1 -1 1 3.0652 21 1 1 1 0 5.5943 22 1 1 0 0 0.8900 23 1 1 -1 0 1.8538 24 1 1 1 -1 5.0978 25 1 1 0 -1 3.9616 26 1 1 -1 -1 3.5272 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4185 atoms have been selected out of 4259 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 726 242 242 0.00 3 C003 has 141 47 47 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1704 568 568 0.00 6 C006 has 495 165 165 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1884 628 628 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1788 596 596 0.00 12 C012 has 114 38 38 0.00 13 C013 has 498 166 166 0.00 14 C014 has 141 47 47 0.00 Total of13994 atoms and 4658 groups and 4653 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4259 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1408 Number of atoms = 4259 Number of groups = 1413 Number of bonds = 4252 Number of angles = 1512 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1410 Number of HB donors = 2798 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1408 Number of atoms = 4259 Number of groups = 1413 Number of bonds = 4252 Number of angles = 1512 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1410 Number of HB donors = 2798 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.952" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1408" Evaluating: 1408-7 Parameter: NUMWAT <- "1401" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1401" Comparing "1081" and "1401". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.952" Parameter: BOX -> "34.952" Parameter: BOX -> "34.952" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.95200 B = 34.95200 C = 34.95200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5548 2 1 -1 0 -1 4.0342 3 1 -1 1 -1 3.0621 4 1 0 -1 -1 3.4016 5 1 0 0 -1 2.4280 6 1 0 1 -1 3.1200 7 1 -1 -1 0 5.5922 8 1 -1 0 0 0.8902 9 1 -1 1 0 1.8510 10 1 0 -1 0 0.7993 11 1 0 1 0 0.7993 12 1 -1 -1 1 5.0944 13 1 -1 0 1 3.9595 14 1 -1 1 1 3.5240 15 1 0 -1 1 3.1200 16 1 0 0 1 2.4280 17 1 0 1 1 3.4016 18 1 1 1 1 4.5548 19 1 1 0 1 4.0342 20 1 1 -1 1 3.0621 21 1 1 1 0 5.5922 22 1 1 0 0 0.8902 23 1 1 -1 0 1.8510 24 1 1 1 -1 5.0944 25 1 1 0 -1 3.9595 26 1 1 -1 -1 3.5240 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4185 atoms have been selected out of 4259 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 586 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 726 242 242 0.00 3 C003 has 141 47 47 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1704 568 568 0.00 6 C006 has 495 165 165 0.00 7 C007 has 756 252 252 0.00 8 C008 has 1884 628 628 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1788 596 596 0.00 12 C012 has 114 38 38 0.00 13 C013 has 498 166 166 0.00 14 C014 has 141 47 47 0.00 Total of13991 atoms and 4657 groups and 4652 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4259 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1407 Number of atoms = 4256 Number of groups = 1412 Number of bonds = 4249 Number of angles = 1511 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1409 Number of HB donors = 2796 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1407 Number of atoms = 4256 Number of groups = 1412 Number of bonds = 4249 Number of angles = 1511 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1409 Number of HB donors = 2796 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.95" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1407" Evaluating: 1407-7 Parameter: NUMWAT <- "1400" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1400" Comparing "1081" and "1400". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.95" Parameter: BOX -> "34.95" Parameter: BOX -> "34.95" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.95000 B = 34.95000 C = 34.95000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5567 2 1 -1 0 -1 4.0314 3 1 -1 1 -1 3.0590 4 1 0 -1 -1 3.3995 5 1 0 0 -1 2.4260 6 1 0 1 -1 3.1176 7 1 -1 -1 0 5.5901 8 1 -1 0 0 0.8904 9 1 -1 1 0 1.8482 10 1 0 -1 0 0.7988 11 1 0 1 0 0.7988 12 1 -1 -1 1 5.0909 13 1 -1 0 1 3.9574 14 1 -1 1 1 3.5209 15 1 0 -1 1 3.1176 16 1 0 0 1 2.4260 17 1 0 1 1 3.3995 18 1 1 1 1 4.5567 19 1 1 0 1 4.0314 20 1 1 -1 1 3.0590 21 1 1 1 0 5.5901 22 1 1 0 0 0.8904 23 1 1 -1 0 1.8482 24 1 1 1 -1 5.0909 25 1 1 0 -1 3.9574 26 1 1 -1 -1 3.5209 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4182 atoms have been selected out of 4256 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 726 242 242 0.00 3 C003 has 141 47 47 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1704 568 568 0.00 6 C006 has 495 165 165 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1881 627 627 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1785 595 595 0.00 12 C012 has 114 38 38 0.00 13 C013 has 498 166 166 0.00 14 C014 has 141 47 47 0.00 Total of13985 atoms and 4655 groups and 4650 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4256 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1407 Number of atoms = 4256 Number of groups = 1412 Number of bonds = 4249 Number of angles = 1511 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1409 Number of HB donors = 2796 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1407 Number of atoms = 4256 Number of groups = 1412 Number of bonds = 4249 Number of angles = 1511 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1409 Number of HB donors = 2796 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.948" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1407" Evaluating: 1407-7 Parameter: NUMWAT <- "1400" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1400" Comparing "1081" and "1400". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.948" Parameter: BOX -> "34.948" Parameter: BOX -> "34.948" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.94800 B = 34.94800 C = 34.94800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5586 2 1 -1 0 -1 4.0286 3 1 -1 1 -1 3.0560 4 1 0 -1 -1 3.3974 5 1 0 0 -1 2.4241 6 1 0 1 -1 3.1152 7 1 -1 -1 0 5.5881 8 1 -1 0 0 0.8907 9 1 -1 1 0 1.8454 10 1 0 -1 0 0.7984 11 1 0 1 0 0.7984 12 1 -1 -1 1 5.0874 13 1 -1 0 1 3.9553 14 1 -1 1 1 3.5177 15 1 0 -1 1 3.1152 16 1 0 0 1 2.4241 17 1 0 1 1 3.3974 18 1 1 1 1 4.5586 19 1 1 0 1 4.0286 20 1 1 -1 1 3.0560 21 1 1 1 0 5.5881 22 1 1 0 0 0.8907 23 1 1 -1 0 1.8454 24 1 1 1 -1 5.0874 25 1 1 0 -1 3.9553 26 1 1 -1 -1 3.5177 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4182 atoms have been selected out of 4256 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 726 242 242 0.00 3 C003 has 141 47 47 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1704 568 568 0.00 6 C006 has 495 165 165 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1881 627 627 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1785 595 595 0.00 12 C012 has 114 38 38 0.00 13 C013 has 498 166 166 0.00 14 C014 has 144 48 48 0.00 Total of13988 atoms and 4656 groups and 4651 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4256 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1407 Number of atoms = 4256 Number of groups = 1412 Number of bonds = 4249 Number of angles = 1511 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1409 Number of HB donors = 2796 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1407 Number of atoms = 4256 Number of groups = 1412 Number of bonds = 4249 Number of angles = 1511 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1409 Number of HB donors = 2796 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.946" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1407" Evaluating: 1407-7 Parameter: NUMWAT <- "1400" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1400" Comparing "1081" and "1400". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.946" Parameter: BOX -> "34.946" Parameter: BOX -> "34.946" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.94600 B = 34.94600 C = 34.94600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5606 2 1 -1 0 -1 4.0259 3 1 -1 1 -1 3.0529 4 1 0 -1 -1 3.3954 5 1 0 0 -1 2.4221 6 1 0 1 -1 3.1128 7 1 -1 -1 0 5.5860 8 1 -1 0 0 0.8909 9 1 -1 1 0 1.8426 10 1 0 -1 0 0.7979 11 1 0 1 0 0.7979 12 1 -1 -1 1 5.0840 13 1 -1 0 1 3.9532 14 1 -1 1 1 3.5145 15 1 0 -1 1 3.1128 16 1 0 0 1 2.4221 17 1 0 1 1 3.3954 18 1 1 1 1 4.5606 19 1 1 0 1 4.0259 20 1 1 -1 1 3.0529 21 1 1 1 0 5.5860 22 1 1 0 0 0.8909 23 1 1 -1 0 1.8426 24 1 1 1 -1 5.0840 25 1 1 0 -1 3.9532 26 1 1 -1 -1 3.5145 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4182 atoms have been selected out of 4256 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 726 242 242 0.00 3 C003 has 141 47 47 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1704 568 568 0.00 6 C006 has 495 165 165 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1881 627 627 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1785 595 595 0.00 12 C012 has 114 38 38 0.00 13 C013 has 498 166 166 0.00 14 C014 has 144 48 48 0.00 Total of13988 atoms and 4656 groups and 4651 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4256 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1407 Number of atoms = 4256 Number of groups = 1412 Number of bonds = 4249 Number of angles = 1511 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1409 Number of HB donors = 2796 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1407 Number of atoms = 4256 Number of groups = 1412 Number of bonds = 4249 Number of angles = 1511 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1409 Number of HB donors = 2796 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.944" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1407" Evaluating: 1407-7 Parameter: NUMWAT <- "1400" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1400" Comparing "1081" and "1400". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.944" Parameter: BOX -> "34.944" Parameter: BOX -> "34.944" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.94400 B = 34.94400 C = 34.94400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5625 2 1 -1 0 -1 4.0231 3 1 -1 1 -1 3.0498 4 1 0 -1 -1 3.3933 5 1 0 0 -1 2.4201 6 1 0 1 -1 3.1104 7 1 -1 -1 0 5.5839 8 1 -1 0 0 0.8911 9 1 -1 1 0 1.8399 10 1 0 -1 0 0.7974 11 1 0 1 0 0.7974 12 1 -1 -1 1 5.0805 13 1 -1 0 1 3.9511 14 1 -1 1 1 3.5114 15 1 0 -1 1 3.1104 16 1 0 0 1 2.4201 17 1 0 1 1 3.3933 18 1 1 1 1 4.5625 19 1 1 0 1 4.0231 20 1 1 -1 1 3.0498 21 1 1 1 0 5.5839 22 1 1 0 0 0.8911 23 1 1 -1 0 1.8399 24 1 1 1 -1 5.0805 25 1 1 0 -1 3.9511 26 1 1 -1 -1 3.5114 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4182 atoms have been selected out of 4256 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1360 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 357 119 119 0.00 2 C002 has 729 243 243 0.00 3 C003 has 141 47 47 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1704 568 568 0.00 6 C006 has 498 166 166 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1881 627 627 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1785 595 595 0.00 12 C012 has 114 38 38 0.00 13 C013 has 498 166 166 0.00 14 C014 has 144 48 48 0.00 Total of13988 atoms and 4656 groups and 4651 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4256 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1406 Number of atoms = 4253 Number of groups = 1411 Number of bonds = 4246 Number of angles = 1510 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1408 Number of HB donors = 2794 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1406 Number of atoms = 4253 Number of groups = 1411 Number of bonds = 4246 Number of angles = 1510 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1408 Number of HB donors = 2794 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.942" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1406" Evaluating: 1406-7 Parameter: NUMWAT <- "1399" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1399" Comparing "1081" and "1399". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.942" Parameter: BOX -> "34.942" Parameter: BOX -> "34.942" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.94200 B = 34.94200 C = 34.94200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5645 2 1 -1 0 -1 4.0203 3 1 -1 1 -1 3.0468 4 1 0 -1 -1 3.3912 5 1 0 0 -1 2.4182 6 1 0 1 -1 3.1080 7 1 -1 -1 0 5.5818 8 1 -1 0 0 0.8913 9 1 -1 1 0 1.8371 10 1 0 -1 0 0.7970 11 1 0 1 0 0.7970 12 1 -1 -1 1 5.0771 13 1 -1 0 1 3.9490 14 1 -1 1 1 3.5082 15 1 0 -1 1 3.1080 16 1 0 0 1 2.4182 17 1 0 1 1 3.3912 18 1 1 1 1 4.5645 19 1 1 0 1 4.0203 20 1 1 -1 1 3.0468 21 1 1 1 0 5.5818 22 1 1 0 0 0.8913 23 1 1 -1 0 1.8371 24 1 1 1 -1 5.0771 25 1 1 0 -1 3.9490 26 1 1 -1 -1 3.5082 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4179 atoms have been selected out of 4253 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 357 119 119 0.00 2 C002 has 726 242 242 0.00 3 C003 has 141 47 47 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1707 569 569 0.00 6 C006 has 495 165 165 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1881 627 627 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1782 594 594 0.00 12 C012 has 114 38 38 0.00 13 C013 has 498 166 166 0.00 14 C014 has 144 48 48 0.00 Total of13979 atoms and 4653 groups and 4648 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4253 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1406 Number of atoms = 4253 Number of groups = 1411 Number of bonds = 4246 Number of angles = 1510 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1408 Number of HB donors = 2794 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1406 Number of atoms = 4253 Number of groups = 1411 Number of bonds = 4246 Number of angles = 1510 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1408 Number of HB donors = 2794 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.94" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1406" Evaluating: 1406-7 Parameter: NUMWAT <- "1399" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1399" Comparing "1081" and "1399". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.94" Parameter: BOX -> "34.94" Parameter: BOX -> "34.94" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.94000 B = 34.94000 C = 34.94000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5665 2 1 -1 0 -1 4.0175 3 1 -1 1 -1 3.0437 4 1 0 -1 -1 3.3891 5 1 0 0 -1 2.4162 6 1 0 1 -1 3.1057 7 1 -1 -1 0 5.5797 8 1 -1 0 0 0.8916 9 1 -1 1 0 1.8343 10 1 0 -1 0 0.7965 11 1 0 1 0 0.7965 12 1 -1 -1 1 5.0736 13 1 -1 0 1 3.9469 14 1 -1 1 1 3.5051 15 1 0 -1 1 3.1057 16 1 0 0 1 2.4162 17 1 0 1 1 3.3891 18 1 1 1 1 4.5665 19 1 1 0 1 4.0175 20 1 1 -1 1 3.0437 21 1 1 1 0 5.5797 22 1 1 0 0 0.8916 23 1 1 -1 0 1.8343 24 1 1 1 -1 5.0736 25 1 1 0 -1 3.9469 26 1 1 -1 -1 3.5051 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4179 atoms have been selected out of 4253 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 357 119 119 0.00 2 C002 has 726 242 242 0.00 3 C003 has 141 47 47 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1707 569 569 0.00 6 C006 has 495 165 165 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1884 628 628 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1782 594 594 0.00 12 C012 has 114 38 38 0.00 13 C013 has 498 166 166 0.00 14 C014 has 144 48 48 0.00 Total of13982 atoms and 4654 groups and 4649 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4253 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1406 Number of atoms = 4253 Number of groups = 1411 Number of bonds = 4246 Number of angles = 1510 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1408 Number of HB donors = 2794 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1406 Number of atoms = 4253 Number of groups = 1411 Number of bonds = 4246 Number of angles = 1510 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1408 Number of HB donors = 2794 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.938" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1406" Evaluating: 1406-7 Parameter: NUMWAT <- "1399" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1399" Comparing "1081" and "1399". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.938" Parameter: BOX -> "34.938" Parameter: BOX -> "34.938" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.93800 B = 34.93800 C = 34.93800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5684 2 1 -1 0 -1 4.0147 3 1 -1 1 -1 3.0406 4 1 0 -1 -1 3.3870 5 1 0 0 -1 2.4143 6 1 0 1 -1 3.1033 7 1 -1 -1 0 5.5776 8 1 -1 0 0 0.8918 9 1 -1 1 0 1.8315 10 1 0 -1 0 0.7961 11 1 0 1 0 0.7961 12 1 -1 -1 1 5.0702 13 1 -1 0 1 3.9448 14 1 -1 1 1 3.5019 15 1 0 -1 1 3.1033 16 1 0 0 1 2.4143 17 1 0 1 1 3.3870 18 1 1 1 1 4.5684 19 1 1 0 1 4.0147 20 1 1 -1 1 3.0406 21 1 1 1 0 5.5776 22 1 1 0 0 0.8918 23 1 1 -1 0 1.8315 24 1 1 1 -1 5.0702 25 1 1 0 -1 3.9448 26 1 1 -1 -1 3.5019 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4179 atoms have been selected out of 4253 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 357 119 119 0.00 2 C002 has 726 242 242 0.00 3 C003 has 141 47 47 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1707 569 569 0.00 6 C006 has 495 165 165 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1884 628 628 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1782 594 594 0.00 12 C012 has 114 38 38 0.00 13 C013 has 498 166 166 0.00 14 C014 has 144 48 48 0.00 Total of13982 atoms and 4654 groups and 4649 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4253 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1406 Number of atoms = 4253 Number of groups = 1411 Number of bonds = 4246 Number of angles = 1510 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1408 Number of HB donors = 2794 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1406 Number of atoms = 4253 Number of groups = 1411 Number of bonds = 4246 Number of angles = 1510 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1408 Number of HB donors = 2794 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.936" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1406" Evaluating: 1406-7 Parameter: NUMWAT <- "1399" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1399" Comparing "1081" and "1399". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.936" Parameter: BOX -> "34.936" Parameter: BOX -> "34.936" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.93600 B = 34.93600 C = 34.93600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5704 2 1 -1 0 -1 4.0119 3 1 -1 1 -1 3.0375 4 1 0 -1 -1 3.3849 5 1 0 0 -1 2.4123 6 1 0 1 -1 3.1009 7 1 -1 -1 0 5.5755 8 1 -1 0 0 0.8921 9 1 -1 1 0 1.8288 10 1 0 -1 0 0.7956 11 1 0 1 0 0.7956 12 1 -1 -1 1 5.0667 13 1 -1 0 1 3.9426 14 1 -1 1 1 3.4988 15 1 0 -1 1 3.1009 16 1 0 0 1 2.4123 17 1 0 1 1 3.3849 18 1 1 1 1 4.5704 19 1 1 0 1 4.0119 20 1 1 -1 1 3.0375 21 1 1 1 0 5.5755 22 1 1 0 0 0.8921 23 1 1 -1 0 1.8288 24 1 1 1 -1 5.0667 25 1 1 0 -1 3.9426 26 1 1 -1 -1 3.4988 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4179 atoms have been selected out of 4253 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 357 119 119 0.00 2 C002 has 726 242 242 0.00 3 C003 has 141 47 47 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1707 569 569 0.00 6 C006 has 495 165 165 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1884 628 628 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1782 594 594 0.00 12 C012 has 114 38 38 0.00 13 C013 has 498 166 166 0.00 14 C014 has 144 48 48 0.00 Total of13982 atoms and 4654 groups and 4649 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4253 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1406 Number of atoms = 4253 Number of groups = 1411 Number of bonds = 4246 Number of angles = 1510 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1408 Number of HB donors = 2794 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1406 Number of atoms = 4253 Number of groups = 1411 Number of bonds = 4246 Number of angles = 1510 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1408 Number of HB donors = 2794 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.934" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1406" Evaluating: 1406-7 Parameter: NUMWAT <- "1399" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1399" Comparing "1081" and "1399". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.934" Parameter: BOX -> "34.934" Parameter: BOX -> "34.934" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.93400 B = 34.93400 C = 34.93400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5723 2 1 -1 0 -1 4.0091 3 1 -1 1 -1 3.0345 4 1 0 -1 -1 3.3828 5 1 0 0 -1 2.4104 6 1 0 1 -1 3.0985 7 1 -1 -1 0 5.5734 8 1 -1 0 0 0.8923 9 1 -1 1 0 1.8260 10 1 0 -1 0 0.7952 11 1 0 1 0 0.7952 12 1 -1 -1 1 5.0633 13 1 -1 0 1 3.9405 14 1 -1 1 1 3.4956 15 1 0 -1 1 3.0985 16 1 0 0 1 2.4104 17 1 0 1 1 3.3828 18 1 1 1 1 4.5723 19 1 1 0 1 4.0091 20 1 1 -1 1 3.0345 21 1 1 1 0 5.5734 22 1 1 0 0 0.8923 23 1 1 -1 0 1.8260 24 1 1 1 -1 5.0633 25 1 1 0 -1 3.9405 26 1 1 -1 -1 3.4956 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4179 atoms have been selected out of 4253 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 726 242 242 0.00 3 C003 has 141 47 47 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1710 570 570 0.00 6 C006 has 495 165 165 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1884 628 628 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1782 594 594 0.00 12 C012 has 114 38 38 0.00 13 C013 has 498 166 166 0.00 14 C014 has 144 48 48 0.00 Total of13988 atoms and 4656 groups and 4651 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4253 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1406 Number of atoms = 4253 Number of groups = 1411 Number of bonds = 4246 Number of angles = 1510 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1408 Number of HB donors = 2794 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1406 Number of atoms = 4253 Number of groups = 1411 Number of bonds = 4246 Number of angles = 1510 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1408 Number of HB donors = 2794 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.932" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1406" Evaluating: 1406-7 Parameter: NUMWAT <- "1399" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1399" Comparing "1081" and "1399". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.932" Parameter: BOX -> "34.932" Parameter: BOX -> "34.932" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.93200 B = 34.93200 C = 34.93200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5743 2 1 -1 0 -1 4.0063 3 1 -1 1 -1 3.0314 4 1 0 -1 -1 3.3807 5 1 0 0 -1 2.4084 6 1 0 1 -1 3.0961 7 1 -1 -1 0 5.5713 8 1 -1 0 0 0.8926 9 1 -1 1 0 1.8232 10 1 0 -1 0 0.7947 11 1 0 1 0 0.7947 12 1 -1 -1 1 5.0598 13 1 -1 0 1 3.9385 14 1 -1 1 1 3.4924 15 1 0 -1 1 3.0961 16 1 0 0 1 2.4084 17 1 0 1 1 3.3807 18 1 1 1 1 4.5743 19 1 1 0 1 4.0063 20 1 1 -1 1 3.0314 21 1 1 1 0 5.5713 22 1 1 0 0 0.8926 23 1 1 -1 0 1.8232 24 1 1 1 -1 5.0598 25 1 1 0 -1 3.9385 26 1 1 -1 -1 3.4924 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4179 atoms have been selected out of 4253 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 127 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 726 242 242 0.00 3 C003 has 141 47 47 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1713 571 571 0.00 6 C006 has 498 166 166 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1892 629 629 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1782 594 594 0.00 12 C012 has 114 38 38 0.00 13 C013 has 501 167 167 0.00 14 C014 has 144 48 48 0.00 Total of14005 atoms and 4660 groups and 4655 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4253 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1405 Number of atoms = 4250 Number of groups = 1410 Number of bonds = 4243 Number of angles = 1509 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1407 Number of HB donors = 2792 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1405 Number of atoms = 4250 Number of groups = 1410 Number of bonds = 4243 Number of angles = 1509 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1407 Number of HB donors = 2792 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.93" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1405" Evaluating: 1405-7 Parameter: NUMWAT <- "1398" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1398" Comparing "1081" and "1398". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.93" Parameter: BOX -> "34.93" Parameter: BOX -> "34.93" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.93000 B = 34.93000 C = 34.93000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5762 2 1 -1 0 -1 4.0035 3 1 -1 1 -1 3.0283 4 1 0 -1 -1 3.3786 5 1 0 0 -1 2.4065 6 1 0 1 -1 3.0937 7 1 -1 -1 0 5.5693 8 1 -1 0 0 0.8928 9 1 -1 1 0 1.8204 10 1 0 -1 0 0.7943 11 1 0 1 0 0.7943 12 1 -1 -1 1 5.0563 13 1 -1 0 1 3.9364 14 1 -1 1 1 3.4893 15 1 0 -1 1 3.0937 16 1 0 0 1 2.4065 17 1 0 1 1 3.3786 18 1 1 1 1 4.5762 19 1 1 0 1 4.0035 20 1 1 -1 1 3.0283 21 1 1 1 0 5.5693 22 1 1 0 0 0.8928 23 1 1 -1 0 1.8204 24 1 1 1 -1 5.0563 25 1 1 0 -1 3.9364 26 1 1 -1 -1 3.4893 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4176 atoms have been selected out of 4250 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 729 243 243 0.00 3 C003 has 141 47 47 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1710 570 570 0.00 6 C006 has 495 165 165 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1895 630 630 0.00 9 C009 has 513 171 171 0.00 10 C010 has 1782 594 594 0.00 12 C012 has 114 38 38 0.00 13 C013 has 501 167 167 0.00 14 C014 has 144 48 48 0.00 Total of14002 atoms and 4659 groups and 4654 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4250 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1405 Number of atoms = 4250 Number of groups = 1410 Number of bonds = 4243 Number of angles = 1509 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1407 Number of HB donors = 2792 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1405 Number of atoms = 4250 Number of groups = 1410 Number of bonds = 4243 Number of angles = 1509 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1407 Number of HB donors = 2792 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.928" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1405" Evaluating: 1405-7 Parameter: NUMWAT <- "1398" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1398" Comparing "1081" and "1398". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.928" Parameter: BOX -> "34.928" Parameter: BOX -> "34.928" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.92800 B = 34.92800 C = 34.92800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5782 2 1 -1 0 -1 4.0007 3 1 -1 1 -1 3.0253 4 1 0 -1 -1 3.3766 5 1 0 0 -1 2.4045 6 1 0 1 -1 3.0913 7 1 -1 -1 0 5.5672 8 1 -1 0 0 0.8931 9 1 -1 1 0 1.8176 10 1 0 -1 0 0.7939 11 1 0 1 0 0.7939 12 1 -1 -1 1 5.0529 13 1 -1 0 1 3.9343 14 1 -1 1 1 3.4861 15 1 0 -1 1 3.0913 16 1 0 0 1 2.4045 17 1 0 1 1 3.3766 18 1 1 1 1 4.5782 19 1 1 0 1 4.0007 20 1 1 -1 1 3.0253 21 1 1 1 0 5.5672 22 1 1 0 0 0.8931 23 1 1 -1 0 1.8176 24 1 1 1 -1 5.0529 25 1 1 0 -1 3.9343 26 1 1 -1 -1 3.4861 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4176 atoms have been selected out of 4250 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 150 OPERATED ON BY TRANSFORMATION C022 RESIDUE 492 OPERATED ON BY TRANSFORMATION C022 RESIDUE 841 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1186 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 729 243 243 0.00 3 C003 has 78 26 26 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1710 570 570 0.00 6 C006 has 486 162 162 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1898 631 631 0.00 9 C009 has 462 154 154 0.00 10 C010 has 1782 594 594 0.00 12 C012 has 111 37 37 0.00 13 C013 has 480 160 160 0.00 14 C014 has 105 35 35 0.00 Total of13825 atoms and 4600 groups and 4595 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 12 atoms have been selected out of 4250 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 4 residues deleted. DELTIC: 12 bonds deleted DELTIC: 4 angles deleted DELTIC: 8 donors deleted DELTIC: 4 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1401 Number of atoms = 4238 Number of groups = 1406 Number of bonds = 4231 Number of angles = 1505 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1403 Number of HB donors = 2784 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1401 Number of atoms = 4238 Number of groups = 1406 Number of bonds = 4231 Number of angles = 1505 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1403 Number of HB donors = 2784 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.926" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1401" Evaluating: 1401-7 Parameter: NUMWAT <- "1394" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1394" Comparing "1081" and "1394". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.926" Parameter: BOX -> "34.926" Parameter: BOX -> "34.926" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.92600 B = 34.92600 C = 34.92600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5802 2 1 -1 0 -1 6.1382 3 1 -1 1 -1 5.7697 4 1 0 -1 -1 3.3745 5 1 0 0 -1 2.4026 6 1 0 1 -1 3.0890 7 1 -1 -1 0 5.5651 8 1 -1 0 0 0.8934 9 1 -1 1 0 4.8178 10 1 0 -1 0 0.7934 11 1 0 1 0 0.7934 12 1 -1 -1 1 5.0494 13 1 -1 0 1 4.8157 14 1 -1 1 1 5.5989 15 1 0 -1 1 3.0890 16 1 0 0 1 2.4026 17 1 0 1 1 3.3745 18 1 1 1 1 4.5802 19 1 1 0 1 6.1382 20 1 1 -1 1 5.7697 21 1 1 1 0 5.5651 22 1 1 0 0 0.8934 23 1 1 -1 0 4.8178 24 1 1 1 -1 5.0494 25 1 1 0 -1 4.8157 26 1 1 -1 -1 5.5989 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4164 atoms have been selected out of 4238 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 723 241 241 0.00 3 C003 has 75 25 25 0.00 4 C004 has 606 202 202 0.00 5 C005 has 1704 568 568 0.00 6 C006 has 483 161 161 0.00 7 C007 has 756 252 252 0.00 8 C008 has 1886 627 627 0.00 9 C009 has 456 152 152 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 108 36 36 0.00 13 C013 has 474 158 158 0.00 14 C014 has 102 34 34 0.00 Total of13747 atoms and 4574 groups and 4569 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4238 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1401 Number of atoms = 4238 Number of groups = 1406 Number of bonds = 4231 Number of angles = 1505 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1403 Number of HB donors = 2784 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1401 Number of atoms = 4238 Number of groups = 1406 Number of bonds = 4231 Number of angles = 1505 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1403 Number of HB donors = 2784 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.924" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1401" Evaluating: 1401-7 Parameter: NUMWAT <- "1394" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1394" Comparing "1081" and "1394". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.924" Parameter: BOX -> "34.924" Parameter: BOX -> "34.924" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.92400 B = 34.92400 C = 34.92400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5821 2 1 -1 0 -1 6.1393 3 1 -1 1 -1 5.7663 4 1 0 -1 -1 3.3724 5 1 0 0 -1 2.4006 6 1 0 1 -1 3.0866 7 1 -1 -1 0 5.5630 8 1 -1 0 0 0.8936 9 1 -1 1 0 4.8169 10 1 0 -1 0 0.7930 11 1 0 1 0 0.7930 12 1 -1 -1 1 5.0460 13 1 -1 0 1 4.8129 14 1 -1 1 1 5.5958 15 1 0 -1 1 3.0866 16 1 0 0 1 2.4006 17 1 0 1 1 3.3724 18 1 1 1 1 4.5821 19 1 1 0 1 6.1393 20 1 1 -1 1 5.7663 21 1 1 1 0 5.5630 22 1 1 0 0 0.8936 23 1 1 -1 0 4.8169 24 1 1 1 -1 5.0460 25 1 1 0 -1 4.8129 26 1 1 -1 -1 5.5958 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4164 atoms have been selected out of 4238 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 723 241 241 0.00 3 C003 has 75 25 25 0.00 4 C004 has 606 202 202 0.00 5 C005 has 1704 568 568 0.00 6 C006 has 483 161 161 0.00 7 C007 has 756 252 252 0.00 8 C008 has 1886 627 627 0.00 9 C009 has 456 152 152 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 108 36 36 0.00 13 C013 has 474 158 158 0.00 14 C014 has 102 34 34 0.00 Total of13747 atoms and 4574 groups and 4569 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4238 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1401 Number of atoms = 4238 Number of groups = 1406 Number of bonds = 4231 Number of angles = 1505 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1403 Number of HB donors = 2784 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1401 Number of atoms = 4238 Number of groups = 1406 Number of bonds = 4231 Number of angles = 1505 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1403 Number of HB donors = 2784 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.922" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1401" Evaluating: 1401-7 Parameter: NUMWAT <- "1394" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1394" Comparing "1081" and "1394". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.922" Parameter: BOX -> "34.922" Parameter: BOX -> "34.922" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.92200 B = 34.92200 C = 34.92200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5841 2 1 -1 0 -1 6.1403 3 1 -1 1 -1 5.7628 4 1 0 -1 -1 3.3703 5 1 0 0 -1 2.3987 6 1 0 1 -1 3.0842 7 1 -1 -1 0 5.5609 8 1 -1 0 0 0.8939 9 1 -1 1 0 4.8161 10 1 0 -1 0 0.7926 11 1 0 1 0 0.7926 12 1 -1 -1 1 5.0425 13 1 -1 0 1 4.8101 14 1 -1 1 1 5.5927 15 1 0 -1 1 3.0842 16 1 0 0 1 2.3987 17 1 0 1 1 3.3703 18 1 1 1 1 4.5841 19 1 1 0 1 6.1403 20 1 1 -1 1 5.7628 21 1 1 1 0 5.5609 22 1 1 0 0 0.8939 23 1 1 -1 0 4.8161 24 1 1 1 -1 5.0425 25 1 1 0 -1 4.8101 26 1 1 -1 -1 5.5927 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4164 atoms have been selected out of 4238 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 907 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 720 240 240 0.00 3 C003 has 75 25 25 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1704 568 568 0.00 6 C006 has 483 161 161 0.00 7 C007 has 756 252 252 0.00 8 C008 has 1889 628 628 0.00 9 C009 has 456 152 152 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 108 36 36 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13753 atoms and 4576 groups and 4571 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4238 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1400 Number of atoms = 4235 Number of groups = 1405 Number of bonds = 4228 Number of angles = 1504 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1402 Number of HB donors = 2782 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1400 Number of atoms = 4235 Number of groups = 1405 Number of bonds = 4228 Number of angles = 1504 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1402 Number of HB donors = 2782 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.92" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1400" Evaluating: 1400-7 Parameter: NUMWAT <- "1393" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1393" Comparing "1081" and "1393". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.92" Parameter: BOX -> "34.92" Parameter: BOX -> "34.92" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.92000 B = 34.92000 C = 34.92000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5861 2 1 -1 0 -1 6.1414 3 1 -1 1 -1 5.7594 4 1 0 -1 -1 3.3682 5 1 0 0 -1 2.3967 6 1 0 1 -1 3.0818 7 1 -1 -1 0 5.5588 8 1 -1 0 0 0.8942 9 1 -1 1 0 4.8153 10 1 0 -1 0 0.7922 11 1 0 1 0 0.7922 12 1 -1 -1 1 5.0391 13 1 -1 0 1 4.8073 14 1 -1 1 1 5.5896 15 1 0 -1 1 3.0818 16 1 0 0 1 2.3967 17 1 0 1 1 3.3682 18 1 1 1 1 4.5861 19 1 1 0 1 6.1414 20 1 1 -1 1 5.7594 21 1 1 1 0 5.5588 22 1 1 0 0 0.8942 23 1 1 -1 0 4.8153 24 1 1 1 -1 5.0391 25 1 1 0 -1 4.8073 26 1 1 -1 -1 5.5896 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4161 atoms have been selected out of 4235 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 71 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 720 240 240 0.00 3 C003 has 75 25 25 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1704 568 568 0.00 6 C006 has 483 161 161 0.00 7 C007 has 756 252 252 0.00 8 C008 has 1886 627 627 0.00 9 C009 has 459 153 153 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 108 36 36 0.00 13 C013 has 474 158 158 0.00 14 C014 has 102 34 34 0.00 Total of13747 atoms and 4574 groups and 4569 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4235 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1399 Number of atoms = 4232 Number of groups = 1404 Number of bonds = 4225 Number of angles = 1503 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1401 Number of HB donors = 2780 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1399 Number of atoms = 4232 Number of groups = 1404 Number of bonds = 4225 Number of angles = 1503 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1401 Number of HB donors = 2780 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.918" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1399" Evaluating: 1399-7 Parameter: NUMWAT <- "1392" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1392" Comparing "1081" and "1392". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.918" Parameter: BOX -> "34.918" Parameter: BOX -> "34.918" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.91800 B = 34.91800 C = 34.91800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5881 2 1 -1 0 -1 6.1424 3 1 -1 1 -1 5.7559 4 1 0 -1 -1 3.3661 5 1 0 0 -1 2.3948 6 1 0 1 -1 3.0795 7 1 -1 -1 0 5.5568 8 1 -1 0 0 0.8945 9 1 -1 1 0 4.8145 10 1 0 -1 0 0.7918 11 1 0 1 0 0.7918 12 1 -1 -1 1 5.0356 13 1 -1 0 1 4.8045 14 1 -1 1 1 5.5864 15 1 0 -1 1 3.0795 16 1 0 0 1 2.3948 17 1 0 1 1 3.3661 18 1 1 1 1 4.5881 19 1 1 0 1 6.1424 20 1 1 -1 1 5.7559 21 1 1 1 0 5.5568 22 1 1 0 0 0.8945 23 1 1 -1 0 4.8145 24 1 1 1 -1 5.0356 25 1 1 0 -1 4.8045 26 1 1 -1 -1 5.5864 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4158 atoms have been selected out of 4232 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 720 240 240 0.00 3 C003 has 75 25 25 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1701 567 567 0.00 6 C006 has 483 161 161 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1886 627 627 0.00 9 C009 has 459 153 153 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 108 36 36 0.00 13 C013 has 474 158 158 0.00 14 C014 has 102 34 34 0.00 Total of13744 atoms and 4573 groups and 4568 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4232 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1399 Number of atoms = 4232 Number of groups = 1404 Number of bonds = 4225 Number of angles = 1503 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1401 Number of HB donors = 2780 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1399 Number of atoms = 4232 Number of groups = 1404 Number of bonds = 4225 Number of angles = 1503 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1401 Number of HB donors = 2780 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.916" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1399" Evaluating: 1399-7 Parameter: NUMWAT <- "1392" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1392" Comparing "1081" and "1392". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.916" Parameter: BOX -> "34.916" Parameter: BOX -> "34.916" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.91600 B = 34.91600 C = 34.91600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5900 2 1 -1 0 -1 6.1435 3 1 -1 1 -1 5.7525 4 1 0 -1 -1 3.3641 5 1 0 0 -1 2.3928 6 1 0 1 -1 3.0771 7 1 -1 -1 0 5.5547 8 1 -1 0 0 0.8948 9 1 -1 1 0 4.8137 10 1 0 -1 0 0.7914 11 1 0 1 0 0.7914 12 1 -1 -1 1 5.0321 13 1 -1 0 1 4.8017 14 1 -1 1 1 5.5833 15 1 0 -1 1 3.0771 16 1 0 0 1 2.3928 17 1 0 1 1 3.3641 18 1 1 1 1 4.5900 19 1 1 0 1 6.1435 20 1 1 -1 1 5.7525 21 1 1 1 0 5.5547 22 1 1 0 0 0.8948 23 1 1 -1 0 4.8137 24 1 1 1 -1 5.0321 25 1 1 0 -1 4.8017 26 1 1 -1 -1 5.5833 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4158 atoms have been selected out of 4232 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1185 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 720 240 240 0.00 3 C003 has 75 25 25 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1701 567 567 0.00 6 C006 has 483 161 161 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1889 628 628 0.00 9 C009 has 459 153 153 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 108 36 36 0.00 13 C013 has 474 158 158 0.00 14 C014 has 102 34 34 0.00 Total of13750 atoms and 4575 groups and 4570 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4232 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1398 Number of atoms = 4229 Number of groups = 1403 Number of bonds = 4222 Number of angles = 1502 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1400 Number of HB donors = 2778 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1398 Number of atoms = 4229 Number of groups = 1403 Number of bonds = 4222 Number of angles = 1502 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1400 Number of HB donors = 2778 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.914" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1398" Evaluating: 1398-7 Parameter: NUMWAT <- "1391" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1391" Comparing "1081" and "1391". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.914" Parameter: BOX -> "34.914" Parameter: BOX -> "34.914" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.91400 B = 34.91400 C = 34.91400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5920 2 1 -1 0 -1 6.1445 3 1 -1 1 -1 5.7490 4 1 0 -1 -1 3.3620 5 1 0 0 -1 2.3909 6 1 0 1 -1 3.0747 7 1 -1 -1 0 5.5526 8 1 -1 0 0 0.8950 9 1 -1 1 0 4.8128 10 1 0 -1 0 0.7910 11 1 0 1 0 0.7910 12 1 -1 -1 1 5.0287 13 1 -1 0 1 4.7989 14 1 -1 1 1 5.5802 15 1 0 -1 1 3.0747 16 1 0 0 1 2.3909 17 1 0 1 1 3.3620 18 1 1 1 1 4.5920 19 1 1 0 1 6.1445 20 1 1 -1 1 5.7490 21 1 1 1 0 5.5526 22 1 1 0 0 0.8950 23 1 1 -1 0 4.8128 24 1 1 1 -1 5.0287 25 1 1 0 -1 4.7989 26 1 1 -1 -1 5.5802 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4155 atoms have been selected out of 4229 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 720 240 240 0.00 3 C003 has 75 25 25 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1701 567 567 0.00 6 C006 has 483 161 161 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1889 628 628 0.00 9 C009 has 459 153 153 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 108 36 36 0.00 13 C013 has 474 158 158 0.00 14 C014 has 102 34 34 0.00 Total of13741 atoms and 4572 groups and 4567 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4229 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1398 Number of atoms = 4229 Number of groups = 1403 Number of bonds = 4222 Number of angles = 1502 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1400 Number of HB donors = 2778 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1398 Number of atoms = 4229 Number of groups = 1403 Number of bonds = 4222 Number of angles = 1502 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1400 Number of HB donors = 2778 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.912" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1398" Evaluating: 1398-7 Parameter: NUMWAT <- "1391" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1391" Comparing "1081" and "1391". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.912" Parameter: BOX -> "34.912" Parameter: BOX -> "34.912" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.91200 B = 34.91200 C = 34.91200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5940 2 1 -1 0 -1 6.1456 3 1 -1 1 -1 5.7456 4 1 0 -1 -1 3.3599 5 1 0 0 -1 2.3889 6 1 0 1 -1 3.0723 7 1 -1 -1 0 5.5505 8 1 -1 0 0 0.8953 9 1 -1 1 0 4.8120 10 1 0 -1 0 0.7906 11 1 0 1 0 0.7906 12 1 -1 -1 1 5.0252 13 1 -1 0 1 4.7961 14 1 -1 1 1 5.5771 15 1 0 -1 1 3.0723 16 1 0 0 1 2.3889 17 1 0 1 1 3.3599 18 1 1 1 1 4.5940 19 1 1 0 1 6.1456 20 1 1 -1 1 5.7456 21 1 1 1 0 5.5505 22 1 1 0 0 0.8953 23 1 1 -1 0 4.8120 24 1 1 1 -1 5.0252 25 1 1 0 -1 4.7961 26 1 1 -1 -1 5.5771 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4155 atoms have been selected out of 4229 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 720 240 240 0.00 3 C003 has 75 25 25 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1701 567 567 0.00 6 C006 has 483 161 161 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1889 628 628 0.00 9 C009 has 459 153 153 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 108 36 36 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13744 atoms and 4573 groups and 4568 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4229 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1398 Number of atoms = 4229 Number of groups = 1403 Number of bonds = 4222 Number of angles = 1502 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1400 Number of HB donors = 2778 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1398 Number of atoms = 4229 Number of groups = 1403 Number of bonds = 4222 Number of angles = 1502 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1400 Number of HB donors = 2778 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.91" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1398" Evaluating: 1398-7 Parameter: NUMWAT <- "1391" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1391" Comparing "1081" and "1391". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.91" Parameter: BOX -> "34.91" Parameter: BOX -> "34.91" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.91000 B = 34.91000 C = 34.91000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5960 2 1 -1 0 -1 6.1466 3 1 -1 1 -1 5.7421 4 1 0 -1 -1 3.3578 5 1 0 0 -1 2.3870 6 1 0 1 -1 3.0699 7 1 -1 -1 0 5.5484 8 1 -1 0 0 0.8956 9 1 -1 1 0 4.8112 10 1 0 -1 0 0.7902 11 1 0 1 0 0.7902 12 1 -1 -1 1 5.0218 13 1 -1 0 1 4.7933 14 1 -1 1 1 5.5740 15 1 0 -1 1 3.0699 16 1 0 0 1 2.3870 17 1 0 1 1 3.3578 18 1 1 1 1 4.5960 19 1 1 0 1 6.1466 20 1 1 -1 1 5.7421 21 1 1 1 0 5.5484 22 1 1 0 0 0.8956 23 1 1 -1 0 4.8112 24 1 1 1 -1 5.0218 25 1 1 0 -1 4.7933 26 1 1 -1 -1 5.5740 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4155 atoms have been selected out of 4229 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 720 240 240 0.00 3 C003 has 75 25 25 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1701 567 567 0.00 6 C006 has 483 161 161 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1889 628 628 0.00 9 C009 has 459 153 153 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 108 36 36 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13747 atoms and 4574 groups and 4569 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4229 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1398 Number of atoms = 4229 Number of groups = 1403 Number of bonds = 4222 Number of angles = 1502 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1400 Number of HB donors = 2778 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1398 Number of atoms = 4229 Number of groups = 1403 Number of bonds = 4222 Number of angles = 1502 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1400 Number of HB donors = 2778 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.908" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1398" Evaluating: 1398-7 Parameter: NUMWAT <- "1391" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1391" Comparing "1081" and "1391". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.908" Parameter: BOX -> "34.908" Parameter: BOX -> "34.908" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.90800 B = 34.90800 C = 34.90800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5979 2 1 -1 0 -1 6.1477 3 1 -1 1 -1 5.7387 4 1 0 -1 -1 3.3558 5 1 0 0 -1 2.3850 6 1 0 1 -1 3.0676 7 1 -1 -1 0 5.5464 8 1 -1 0 0 0.8959 9 1 -1 1 0 4.8104 10 1 0 -1 0 0.7899 11 1 0 1 0 0.7899 12 1 -1 -1 1 5.0183 13 1 -1 0 1 4.7906 14 1 -1 1 1 5.5708 15 1 0 -1 1 3.0676 16 1 0 0 1 2.3850 17 1 0 1 1 3.3558 18 1 1 1 1 4.5979 19 1 1 0 1 6.1477 20 1 1 -1 1 5.7387 21 1 1 1 0 5.5464 22 1 1 0 0 0.8959 23 1 1 -1 0 4.8104 24 1 1 1 -1 5.0183 25 1 1 0 -1 4.7906 26 1 1 -1 -1 5.5708 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4155 atoms have been selected out of 4229 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 720 240 240 0.00 3 C003 has 75 25 25 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1701 567 567 0.00 6 C006 has 483 161 161 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1889 628 628 0.00 9 C009 has 459 153 153 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 108 36 36 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13747 atoms and 4574 groups and 4569 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4229 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1398 Number of atoms = 4229 Number of groups = 1403 Number of bonds = 4222 Number of angles = 1502 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1400 Number of HB donors = 2778 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1398 Number of atoms = 4229 Number of groups = 1403 Number of bonds = 4222 Number of angles = 1502 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1400 Number of HB donors = 2778 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.906" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1398" Evaluating: 1398-7 Parameter: NUMWAT <- "1391" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1391" Comparing "1081" and "1391". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.906" Parameter: BOX -> "34.906" Parameter: BOX -> "34.906" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.90600 B = 34.90600 C = 34.90600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.5999 2 1 -1 0 -1 6.1488 3 1 -1 1 -1 5.7352 4 1 0 -1 -1 3.3537 5 1 0 0 -1 2.3831 6 1 0 1 -1 3.0652 7 1 -1 -1 0 5.5443 8 1 -1 0 0 0.8963 9 1 -1 1 0 4.8096 10 1 0 -1 0 0.7895 11 1 0 1 0 0.7895 12 1 -1 -1 1 5.0149 13 1 -1 0 1 4.7878 14 1 -1 1 1 5.5677 15 1 0 -1 1 3.0652 16 1 0 0 1 2.3831 17 1 0 1 1 3.3537 18 1 1 1 1 4.5999 19 1 1 0 1 6.1488 20 1 1 -1 1 5.7352 21 1 1 1 0 5.5443 22 1 1 0 0 0.8963 23 1 1 -1 0 4.8096 24 1 1 1 -1 5.0149 25 1 1 0 -1 4.7878 26 1 1 -1 -1 5.5677 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4155 atoms have been selected out of 4229 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 720 240 240 0.00 3 C003 has 75 25 25 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1701 567 567 0.00 6 C006 has 486 162 162 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1889 628 628 0.00 9 C009 has 462 154 154 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 108 36 36 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13753 atoms and 4576 groups and 4571 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4229 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1398 Number of atoms = 4229 Number of groups = 1403 Number of bonds = 4222 Number of angles = 1502 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1400 Number of HB donors = 2778 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1398 Number of atoms = 4229 Number of groups = 1403 Number of bonds = 4222 Number of angles = 1502 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1400 Number of HB donors = 2778 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.904" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1398" Evaluating: 1398-7 Parameter: NUMWAT <- "1391" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1391" Comparing "1081" and "1391". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.904" Parameter: BOX -> "34.904" Parameter: BOX -> "34.904" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.90400 B = 34.90400 C = 34.90400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6019 2 1 -1 0 -1 6.1498 3 1 -1 1 -1 5.7318 4 1 0 -1 -1 3.3516 5 1 0 0 -1 2.3811 6 1 0 1 -1 3.0628 7 1 -1 -1 0 5.5422 8 1 -1 0 0 0.8966 9 1 -1 1 0 4.8088 10 1 0 -1 0 0.7891 11 1 0 1 0 0.7891 12 1 -1 -1 1 5.0114 13 1 -1 0 1 4.7850 14 1 -1 1 1 5.5646 15 1 0 -1 1 3.0628 16 1 0 0 1 2.3811 17 1 0 1 1 3.3516 18 1 1 1 1 4.6019 19 1 1 0 1 6.1498 20 1 1 -1 1 5.7318 21 1 1 1 0 5.5422 22 1 1 0 0 0.8966 23 1 1 -1 0 4.8088 24 1 1 1 -1 5.0114 25 1 1 0 -1 4.7850 26 1 1 -1 -1 5.5646 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4155 atoms have been selected out of 4229 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 262 OPERATED ON BY TRANSFORMATION C008 RESIDUE 957 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 717 239 239 0.00 3 C003 has 78 26 26 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1701 567 567 0.00 6 C006 has 483 161 161 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1889 628 628 0.00 9 C009 has 459 153 153 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 108 36 36 0.00 13 C013 has 501 167 167 0.00 14 C014 has 102 34 34 0.00 Total of13771 atoms and 4582 groups and 4577 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 4229 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1396 Number of atoms = 4223 Number of groups = 1401 Number of bonds = 4216 Number of angles = 1500 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1398 Number of HB donors = 2774 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1396 Number of atoms = 4223 Number of groups = 1401 Number of bonds = 4216 Number of angles = 1500 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1398 Number of HB donors = 2774 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.902" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1396" Evaluating: 1396-7 Parameter: NUMWAT <- "1389" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1389" Comparing "1081" and "1389". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.902" Parameter: BOX -> "34.902" Parameter: BOX -> "34.902" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.90200 B = 34.90200 C = 34.90200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6039 2 1 -1 0 -1 6.1509 3 1 -1 1 -1 5.7283 4 1 0 -1 -1 3.3495 5 1 0 0 -1 2.3792 6 1 0 1 -1 3.0605 7 1 -1 -1 0 5.5401 8 1 -1 0 0 2.8142 9 1 -1 1 0 4.8080 10 1 0 -1 0 0.7887 11 1 0 1 0 0.7887 12 1 -1 -1 1 5.0080 13 1 -1 0 1 4.7822 14 1 -1 1 1 5.5615 15 1 0 -1 1 3.0605 16 1 0 0 1 2.3792 17 1 0 1 1 3.3495 18 1 1 1 1 4.6039 19 1 1 0 1 6.1509 20 1 1 -1 1 5.7283 21 1 1 1 0 5.5401 22 1 1 0 0 2.8142 23 1 1 -1 0 4.8080 24 1 1 1 -1 5.0080 25 1 1 0 -1 4.7822 26 1 1 -1 -1 5.5615 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4149 atoms have been selected out of 4223 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 717 239 239 0.00 3 C003 has 78 26 26 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 483 161 161 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 462 154 154 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 108 36 36 0.00 13 C013 has 474 158 158 0.00 14 C014 has 102 34 34 0.00 Total of13732 atoms and 4569 groups and 4564 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4223 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1396 Number of atoms = 4223 Number of groups = 1401 Number of bonds = 4216 Number of angles = 1500 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1398 Number of HB donors = 2774 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1396 Number of atoms = 4223 Number of groups = 1401 Number of bonds = 4216 Number of angles = 1500 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1398 Number of HB donors = 2774 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.9" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1396" Evaluating: 1396-7 Parameter: NUMWAT <- "1389" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1389" Comparing "1081" and "1389". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.9" Parameter: BOX -> "34.9" Parameter: BOX -> "34.9" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.90000 B = 34.90000 C = 34.90000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6059 2 1 -1 0 -1 6.1519 3 1 -1 1 -1 5.7249 4 1 0 -1 -1 3.3475 5 1 0 0 -1 2.3772 6 1 0 1 -1 3.0581 7 1 -1 -1 0 5.5380 8 1 -1 0 0 2.8134 9 1 -1 1 0 4.8072 10 1 0 -1 0 0.7884 11 1 0 1 0 0.7884 12 1 -1 -1 1 5.0045 13 1 -1 0 1 4.7794 14 1 -1 1 1 5.5584 15 1 0 -1 1 3.0581 16 1 0 0 1 2.3772 17 1 0 1 1 3.3475 18 1 1 1 1 4.6059 19 1 1 0 1 6.1519 20 1 1 -1 1 5.7249 21 1 1 1 0 5.5380 22 1 1 0 0 2.8134 23 1 1 -1 0 4.8072 24 1 1 1 -1 5.0045 25 1 1 0 -1 4.7794 26 1 1 -1 -1 5.5584 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4149 atoms have been selected out of 4223 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 717 239 239 0.00 3 C003 has 78 26 26 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 483 161 161 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 462 154 154 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 108 36 36 0.00 13 C013 has 474 158 158 0.00 14 C014 has 102 34 34 0.00 Total of13732 atoms and 4569 groups and 4564 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4223 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1396 Number of atoms = 4223 Number of groups = 1401 Number of bonds = 4216 Number of angles = 1500 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1398 Number of HB donors = 2774 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1396 Number of atoms = 4223 Number of groups = 1401 Number of bonds = 4216 Number of angles = 1500 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1398 Number of HB donors = 2774 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.898" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1396" Evaluating: 1396-7 Parameter: NUMWAT <- "1389" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1389" Comparing "1081" and "1389". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.898" Parameter: BOX -> "34.898" Parameter: BOX -> "34.898" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.89800 B = 34.89800 C = 34.89800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6079 2 1 -1 0 -1 6.1530 3 1 -1 1 -1 5.7214 4 1 0 -1 -1 3.3454 5 1 0 0 -1 2.3753 6 1 0 1 -1 3.0557 7 1 -1 -1 0 5.5360 8 1 -1 0 0 2.8125 9 1 -1 1 0 4.8064 10 1 0 -1 0 0.7880 11 1 0 1 0 0.7880 12 1 -1 -1 1 5.0010 13 1 -1 0 1 4.7766 14 1 -1 1 1 5.5552 15 1 0 -1 1 3.0557 16 1 0 0 1 2.3753 17 1 0 1 1 3.3454 18 1 1 1 1 4.6079 19 1 1 0 1 6.1530 20 1 1 -1 1 5.7214 21 1 1 1 0 5.5360 22 1 1 0 0 2.8125 23 1 1 -1 0 4.8064 24 1 1 1 -1 5.0010 25 1 1 0 -1 4.7766 26 1 1 -1 -1 5.5552 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4149 atoms have been selected out of 4223 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 717 239 239 0.00 3 C003 has 78 26 26 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 483 161 161 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 462 154 154 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 108 36 36 0.00 13 C013 has 474 158 158 0.00 14 C014 has 102 34 34 0.00 Total of13732 atoms and 4569 groups and 4564 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4223 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1396 Number of atoms = 4223 Number of groups = 1401 Number of bonds = 4216 Number of angles = 1500 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1398 Number of HB donors = 2774 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1396 Number of atoms = 4223 Number of groups = 1401 Number of bonds = 4216 Number of angles = 1500 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1398 Number of HB donors = 2774 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.896" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1396" Evaluating: 1396-7 Parameter: NUMWAT <- "1389" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1389" Comparing "1081" and "1389". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.896" Parameter: BOX -> "34.896" Parameter: BOX -> "34.896" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.89600 B = 34.89600 C = 34.89600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6099 2 1 -1 0 -1 6.1541 3 1 -1 1 -1 5.7180 4 1 0 -1 -1 3.3433 5 1 0 0 -1 2.3733 6 1 0 1 -1 3.0533 7 1 -1 -1 0 5.5339 8 1 -1 0 0 2.8117 9 1 -1 1 0 4.8056 10 1 0 -1 0 0.7877 11 1 0 1 0 0.7877 12 1 -1 -1 1 4.9976 13 1 -1 0 1 4.7738 14 1 -1 1 1 5.5521 15 1 0 -1 1 3.0533 16 1 0 0 1 2.3733 17 1 0 1 1 3.3433 18 1 1 1 1 4.6099 19 1 1 0 1 6.1541 20 1 1 -1 1 5.7180 21 1 1 1 0 5.5339 22 1 1 0 0 2.8117 23 1 1 -1 0 4.8056 24 1 1 1 -1 4.9976 25 1 1 0 -1 4.7738 26 1 1 -1 -1 5.5521 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4149 atoms have been selected out of 4223 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 717 239 239 0.00 3 C003 has 78 26 26 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 483 161 161 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 462 154 154 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 108 36 36 0.00 13 C013 has 474 158 158 0.00 14 C014 has 102 34 34 0.00 Total of13732 atoms and 4569 groups and 4564 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4223 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1396 Number of atoms = 4223 Number of groups = 1401 Number of bonds = 4216 Number of angles = 1500 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1398 Number of HB donors = 2774 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1396 Number of atoms = 4223 Number of groups = 1401 Number of bonds = 4216 Number of angles = 1500 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1398 Number of HB donors = 2774 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.894" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1396" Evaluating: 1396-7 Parameter: NUMWAT <- "1389" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1389" Comparing "1081" and "1389". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.894" Parameter: BOX -> "34.894" Parameter: BOX -> "34.894" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.89400 B = 34.89400 C = 34.89400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6119 2 1 -1 0 -1 6.1551 3 1 -1 1 -1 5.7145 4 1 0 -1 -1 3.3413 5 1 0 0 -1 2.3714 6 1 0 1 -1 3.0510 7 1 -1 -1 0 5.5318 8 1 -1 0 0 2.8108 9 1 -1 1 0 4.8048 10 1 0 -1 0 0.7873 11 1 0 1 0 0.7873 12 1 -1 -1 1 4.9941 13 1 -1 0 1 4.7710 14 1 -1 1 1 5.5490 15 1 0 -1 1 3.0510 16 1 0 0 1 2.3714 17 1 0 1 1 3.3413 18 1 1 1 1 4.6119 19 1 1 0 1 6.1551 20 1 1 -1 1 5.7145 21 1 1 1 0 5.5318 22 1 1 0 0 2.8108 23 1 1 -1 0 4.8048 24 1 1 1 -1 4.9941 25 1 1 0 -1 4.7710 26 1 1 -1 -1 5.5490 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4149 atoms have been selected out of 4223 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 717 239 239 0.00 3 C003 has 78 26 26 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 483 161 161 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 462 154 154 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 111 37 37 0.00 13 C013 has 474 158 158 0.00 14 C014 has 102 34 34 0.00 Total of13735 atoms and 4570 groups and 4565 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4223 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1396 Number of atoms = 4223 Number of groups = 1401 Number of bonds = 4216 Number of angles = 1500 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1398 Number of HB donors = 2774 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1396 Number of atoms = 4223 Number of groups = 1401 Number of bonds = 4216 Number of angles = 1500 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1398 Number of HB donors = 2774 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.892" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1396" Evaluating: 1396-7 Parameter: NUMWAT <- "1389" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1389" Comparing "1081" and "1389". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.892" Parameter: BOX -> "34.892" Parameter: BOX -> "34.892" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.89200 B = 34.89200 C = 34.89200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6139 2 1 -1 0 -1 6.1562 3 1 -1 1 -1 5.7111 4 1 0 -1 -1 3.3392 5 1 0 0 -1 2.3694 6 1 0 1 -1 3.0486 7 1 -1 -1 0 5.5297 8 1 -1 0 0 2.8100 9 1 -1 1 0 4.8040 10 1 0 -1 0 0.7870 11 1 0 1 0 0.7870 12 1 -1 -1 1 4.9907 13 1 -1 0 1 4.7682 14 1 -1 1 1 5.5459 15 1 0 -1 1 3.0486 16 1 0 0 1 2.3694 17 1 0 1 1 3.3392 18 1 1 1 1 4.6139 19 1 1 0 1 6.1562 20 1 1 -1 1 5.7111 21 1 1 1 0 5.5297 22 1 1 0 0 2.8100 23 1 1 -1 0 4.8040 24 1 1 1 -1 4.9907 25 1 1 0 -1 4.7682 26 1 1 -1 -1 5.5459 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4149 atoms have been selected out of 4223 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 717 239 239 0.00 3 C003 has 78 26 26 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 483 161 161 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1886 627 627 0.00 9 C009 has 462 154 154 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13741 atoms and 4572 groups and 4567 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4223 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1396 Number of atoms = 4223 Number of groups = 1401 Number of bonds = 4216 Number of angles = 1500 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1398 Number of HB donors = 2774 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1396 Number of atoms = 4223 Number of groups = 1401 Number of bonds = 4216 Number of angles = 1500 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1398 Number of HB donors = 2774 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.89" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1396" Evaluating: 1396-7 Parameter: NUMWAT <- "1389" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1389" Comparing "1081" and "1389". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.89" Parameter: BOX -> "34.89" Parameter: BOX -> "34.89" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.89000 B = 34.89000 C = 34.89000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6159 2 1 -1 0 -1 6.1573 3 1 -1 1 -1 5.7077 4 1 0 -1 -1 3.3371 5 1 0 0 -1 2.3675 6 1 0 1 -1 3.0462 7 1 -1 -1 0 5.5277 8 1 -1 0 0 2.8091 9 1 -1 1 0 4.8032 10 1 0 -1 0 0.7867 11 1 0 1 0 0.7867 12 1 -1 -1 1 4.9872 13 1 -1 0 1 4.7654 14 1 -1 1 1 5.5428 15 1 0 -1 1 3.0462 16 1 0 0 1 2.3675 17 1 0 1 1 3.3371 18 1 1 1 1 4.6159 19 1 1 0 1 6.1573 20 1 1 -1 1 5.7077 21 1 1 1 0 5.5277 22 1 1 0 0 2.8091 23 1 1 -1 0 4.8032 24 1 1 1 -1 4.9872 25 1 1 0 -1 4.7654 26 1 1 -1 -1 5.5428 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4149 atoms have been selected out of 4223 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 717 239 239 0.00 3 C003 has 81 27 27 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 483 161 161 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1886 627 627 0.00 9 C009 has 462 154 154 0.00 10 C010 has 1779 593 593 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13750 atoms and 4575 groups and 4570 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4223 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1396 Number of atoms = 4223 Number of groups = 1401 Number of bonds = 4216 Number of angles = 1500 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1398 Number of HB donors = 2774 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1396 Number of atoms = 4223 Number of groups = 1401 Number of bonds = 4216 Number of angles = 1500 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1398 Number of HB donors = 2774 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.888" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1396" Evaluating: 1396-7 Parameter: NUMWAT <- "1389" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1389" Comparing "1081" and "1389". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.888" Parameter: BOX -> "34.888" Parameter: BOX -> "34.888" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.88800 B = 34.88800 C = 34.88800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6179 2 1 -1 0 -1 6.1583 3 1 -1 1 -1 5.7042 4 1 0 -1 -1 3.3351 5 1 0 0 -1 2.3656 6 1 0 1 -1 3.0439 7 1 -1 -1 0 5.5256 8 1 -1 0 0 2.8083 9 1 -1 1 0 4.8024 10 1 0 -1 0 0.7863 11 1 0 1 0 0.7863 12 1 -1 -1 1 4.9838 13 1 -1 0 1 4.7626 14 1 -1 1 1 5.5397 15 1 0 -1 1 3.0439 16 1 0 0 1 2.3656 17 1 0 1 1 3.3351 18 1 1 1 1 4.6179 19 1 1 0 1 6.1583 20 1 1 -1 1 5.7042 21 1 1 1 0 5.5256 22 1 1 0 0 2.8083 23 1 1 -1 0 4.8024 24 1 1 1 -1 4.9838 25 1 1 0 -1 4.7626 26 1 1 -1 -1 5.5397 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4149 atoms have been selected out of 4223 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 717 239 239 0.00 3 C003 has 81 27 27 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 486 162 162 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1886 627 627 0.00 9 C009 has 462 154 154 0.00 10 C010 has 1779 593 593 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13753 atoms and 4576 groups and 4571 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4223 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1396 Number of atoms = 4223 Number of groups = 1401 Number of bonds = 4216 Number of angles = 1500 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1398 Number of HB donors = 2774 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1396 Number of atoms = 4223 Number of groups = 1401 Number of bonds = 4216 Number of angles = 1500 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1398 Number of HB donors = 2774 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.886" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1396" Evaluating: 1396-7 Parameter: NUMWAT <- "1389" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1389" Comparing "1081" and "1389". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.886" Parameter: BOX -> "34.886" Parameter: BOX -> "34.886" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.88600 B = 34.88600 C = 34.88600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6199 2 1 -1 0 -1 6.1594 3 1 -1 1 -1 5.7008 4 1 0 -1 -1 3.3330 5 1 0 0 -1 2.3636 6 1 0 1 -1 3.0415 7 1 -1 -1 0 5.5235 8 1 -1 0 0 2.8074 9 1 -1 1 0 4.8016 10 1 0 -1 0 0.7860 11 1 0 1 0 0.7860 12 1 -1 -1 1 4.9803 13 1 -1 0 1 4.7599 14 1 -1 1 1 5.5365 15 1 0 -1 1 3.0415 16 1 0 0 1 2.3636 17 1 0 1 1 3.3330 18 1 1 1 1 4.6199 19 1 1 0 1 6.1594 20 1 1 -1 1 5.7008 21 1 1 1 0 5.5235 22 1 1 0 0 2.8074 23 1 1 -1 0 4.8016 24 1 1 1 -1 4.9803 25 1 1 0 -1 4.7599 26 1 1 -1 -1 5.5365 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4149 atoms have been selected out of 4223 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1052 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 720 240 240 0.00 3 C003 has 81 27 27 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 486 162 162 0.00 7 C007 has 765 255 255 0.00 8 C008 has 1886 627 627 0.00 9 C009 has 462 154 154 0.00 10 C010 has 1779 593 593 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13762 atoms and 4579 groups and 4574 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4223 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1395 Number of atoms = 4220 Number of groups = 1400 Number of bonds = 4213 Number of angles = 1499 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1397 Number of HB donors = 2772 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1395 Number of atoms = 4220 Number of groups = 1400 Number of bonds = 4213 Number of angles = 1499 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1397 Number of HB donors = 2772 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.884" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1395" Evaluating: 1395-7 Parameter: NUMWAT <- "1388" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1388" Comparing "1081" and "1388". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.884" Parameter: BOX -> "34.884" Parameter: BOX -> "34.884" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.88400 B = 34.88400 C = 34.88400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6219 2 1 -1 0 -1 6.1605 3 1 -1 1 -1 5.6973 4 1 0 -1 -1 3.3310 5 1 0 0 -1 2.3617 6 1 0 1 -1 3.0391 7 1 -1 -1 0 5.5215 8 1 -1 0 0 2.8066 9 1 -1 1 0 4.8008 10 1 0 -1 0 0.7857 11 1 0 1 0 0.7857 12 1 -1 -1 1 4.9769 13 1 -1 0 1 4.7571 14 1 -1 1 1 5.5334 15 1 0 -1 1 3.0391 16 1 0 0 1 2.3617 17 1 0 1 1 3.3310 18 1 1 1 1 4.6219 19 1 1 0 1 6.1605 20 1 1 -1 1 5.6973 21 1 1 1 0 5.5215 22 1 1 0 0 2.8066 23 1 1 -1 0 4.8008 24 1 1 1 -1 4.9769 25 1 1 0 -1 4.7571 26 1 1 -1 -1 5.5334 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4146 atoms have been selected out of 4220 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 720 240 240 0.00 3 C003 has 81 27 27 0.00 4 C004 has 606 202 202 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 486 162 162 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 462 154 154 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13741 atoms and 4572 groups and 4567 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4220 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1395 Number of atoms = 4220 Number of groups = 1400 Number of bonds = 4213 Number of angles = 1499 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1397 Number of HB donors = 2772 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1395 Number of atoms = 4220 Number of groups = 1400 Number of bonds = 4213 Number of angles = 1499 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1397 Number of HB donors = 2772 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.882" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1395" Evaluating: 1395-7 Parameter: NUMWAT <- "1388" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1388" Comparing "1081" and "1388". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.882" Parameter: BOX -> "34.882" Parameter: BOX -> "34.882" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.88200 B = 34.88200 C = 34.88200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6239 2 1 -1 0 -1 6.1616 3 1 -1 1 -1 5.6939 4 1 0 -1 -1 3.3289 5 1 0 0 -1 2.3597 6 1 0 1 -1 3.0368 7 1 -1 -1 0 5.5194 8 1 -1 0 0 2.8057 9 1 -1 1 0 4.8000 10 1 0 -1 0 0.7854 11 1 0 1 0 0.7854 12 1 -1 -1 1 4.9734 13 1 -1 0 1 4.7543 14 1 -1 1 1 5.5303 15 1 0 -1 1 3.0368 16 1 0 0 1 2.3597 17 1 0 1 1 3.3289 18 1 1 1 1 4.6239 19 1 1 0 1 6.1616 20 1 1 -1 1 5.6939 21 1 1 1 0 5.5194 22 1 1 0 0 2.8057 23 1 1 -1 0 4.8000 24 1 1 1 -1 4.9734 25 1 1 0 -1 4.7543 26 1 1 -1 -1 5.5303 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4146 atoms have been selected out of 4220 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 720 240 240 0.00 3 C003 has 81 27 27 0.00 4 C004 has 606 202 202 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 486 162 162 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 462 154 154 0.00 10 C010 has 1779 593 593 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13744 atoms and 4573 groups and 4568 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4220 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1395 Number of atoms = 4220 Number of groups = 1400 Number of bonds = 4213 Number of angles = 1499 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1397 Number of HB donors = 2772 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1395 Number of atoms = 4220 Number of groups = 1400 Number of bonds = 4213 Number of angles = 1499 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1397 Number of HB donors = 2772 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.88" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1395" Evaluating: 1395-7 Parameter: NUMWAT <- "1388" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1388" Comparing "1081" and "1388". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.88" Parameter: BOX -> "34.88" Parameter: BOX -> "34.88" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.88000 B = 34.88000 C = 34.88000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6259 2 1 -1 0 -1 6.1626 3 1 -1 1 -1 5.6904 4 1 0 -1 -1 3.3268 5 1 0 0 -1 2.3578 6 1 0 1 -1 3.0344 7 1 -1 -1 0 5.5173 8 1 -1 0 0 2.8049 9 1 -1 1 0 4.7992 10 1 0 -1 0 0.7851 11 1 0 1 0 0.7851 12 1 -1 -1 1 4.9699 13 1 -1 0 1 4.7515 14 1 -1 1 1 5.5272 15 1 0 -1 1 3.0344 16 1 0 0 1 2.3578 17 1 0 1 1 3.3268 18 1 1 1 1 4.6259 19 1 1 0 1 6.1626 20 1 1 -1 1 5.6904 21 1 1 1 0 5.5173 22 1 1 0 0 2.8049 23 1 1 -1 0 4.7992 24 1 1 1 -1 4.9699 25 1 1 0 -1 4.7515 26 1 1 -1 -1 5.5272 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4146 atoms have been selected out of 4220 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 720 240 240 0.00 3 C003 has 81 27 27 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 486 162 162 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 465 155 155 0.00 10 C010 has 1779 593 593 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13750 atoms and 4575 groups and 4570 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4220 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1395 Number of atoms = 4220 Number of groups = 1400 Number of bonds = 4213 Number of angles = 1499 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1397 Number of HB donors = 2772 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1395 Number of atoms = 4220 Number of groups = 1400 Number of bonds = 4213 Number of angles = 1499 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1397 Number of HB donors = 2772 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.878" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1395" Evaluating: 1395-7 Parameter: NUMWAT <- "1388" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1388" Comparing "1081" and "1388". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.878" Parameter: BOX -> "34.878" Parameter: BOX -> "34.878" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.87800 B = 34.87800 C = 34.87800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6279 2 1 -1 0 -1 6.1637 3 1 -1 1 -1 5.6870 4 1 0 -1 -1 3.3248 5 1 0 0 -1 2.3558 6 1 0 1 -1 3.0321 7 1 -1 -1 0 5.5152 8 1 -1 0 0 2.8040 9 1 -1 1 0 4.7984 10 1 0 -1 0 0.7848 11 1 0 1 0 0.7848 12 1 -1 -1 1 4.9665 13 1 -1 0 1 4.7487 14 1 -1 1 1 5.5241 15 1 0 -1 1 3.0321 16 1 0 0 1 2.3558 17 1 0 1 1 3.3248 18 1 1 1 1 4.6279 19 1 1 0 1 6.1637 20 1 1 -1 1 5.6870 21 1 1 1 0 5.5152 22 1 1 0 0 2.8040 23 1 1 -1 0 4.7984 24 1 1 1 -1 4.9665 25 1 1 0 -1 4.7487 26 1 1 -1 -1 5.5241 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4146 atoms have been selected out of 4220 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 720 240 240 0.00 3 C003 has 81 27 27 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 486 162 162 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 465 155 155 0.00 10 C010 has 1779 593 593 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13750 atoms and 4575 groups and 4570 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4220 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1395 Number of atoms = 4220 Number of groups = 1400 Number of bonds = 4213 Number of angles = 1499 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1397 Number of HB donors = 2772 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1395 Number of atoms = 4220 Number of groups = 1400 Number of bonds = 4213 Number of angles = 1499 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1397 Number of HB donors = 2772 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.876" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1395" Evaluating: 1395-7 Parameter: NUMWAT <- "1388" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1388" Comparing "1081" and "1388". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.876" Parameter: BOX -> "34.876" Parameter: BOX -> "34.876" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.87600 B = 34.87600 C = 34.87600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6299 2 1 -1 0 -1 6.1648 3 1 -1 1 -1 5.6835 4 1 0 -1 -1 3.3227 5 1 0 0 -1 2.3539 6 1 0 1 -1 3.0297 7 1 -1 -1 0 5.5132 8 1 -1 0 0 2.8032 9 1 -1 1 0 4.7976 10 1 0 -1 0 0.7845 11 1 0 1 0 0.7845 12 1 -1 -1 1 4.9630 13 1 -1 0 1 4.7459 14 1 -1 1 1 5.5210 15 1 0 -1 1 3.0297 16 1 0 0 1 2.3539 17 1 0 1 1 3.3227 18 1 1 1 1 4.6299 19 1 1 0 1 6.1648 20 1 1 -1 1 5.6835 21 1 1 1 0 5.5132 22 1 1 0 0 2.8032 23 1 1 -1 0 4.7976 24 1 1 1 -1 4.9630 25 1 1 0 -1 4.7459 26 1 1 -1 -1 5.5210 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4146 atoms have been selected out of 4220 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 720 240 240 0.00 3 C003 has 81 27 27 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 486 162 162 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 465 155 155 0.00 10 C010 has 1779 593 593 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13750 atoms and 4575 groups and 4570 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4220 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1395 Number of atoms = 4220 Number of groups = 1400 Number of bonds = 4213 Number of angles = 1499 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1397 Number of HB donors = 2772 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1395 Number of atoms = 4220 Number of groups = 1400 Number of bonds = 4213 Number of angles = 1499 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1397 Number of HB donors = 2772 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.874" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1395" Evaluating: 1395-7 Parameter: NUMWAT <- "1388" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1388" Comparing "1081" and "1388". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.874" Parameter: BOX -> "34.874" Parameter: BOX -> "34.874" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.87400 B = 34.87400 C = 34.87400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6319 2 1 -1 0 -1 6.1659 3 1 -1 1 -1 5.6801 4 1 0 -1 -1 3.3207 5 1 0 0 -1 2.3519 6 1 0 1 -1 3.0273 7 1 -1 -1 0 5.5111 8 1 -1 0 0 2.8024 9 1 -1 1 0 4.7968 10 1 0 -1 0 0.7842 11 1 0 1 0 0.7842 12 1 -1 -1 1 4.9596 13 1 -1 0 1 4.7431 14 1 -1 1 1 5.5178 15 1 0 -1 1 3.0273 16 1 0 0 1 2.3519 17 1 0 1 1 3.3207 18 1 1 1 1 4.6319 19 1 1 0 1 6.1659 20 1 1 -1 1 5.6801 21 1 1 1 0 5.5111 22 1 1 0 0 2.8024 23 1 1 -1 0 4.7968 24 1 1 1 -1 4.9596 25 1 1 0 -1 4.7431 26 1 1 -1 -1 5.5178 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4146 atoms have been selected out of 4220 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 720 240 240 0.00 3 C003 has 81 27 27 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 486 162 162 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 465 155 155 0.00 10 C010 has 1779 593 593 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13750 atoms and 4575 groups and 4570 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4220 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1395 Number of atoms = 4220 Number of groups = 1400 Number of bonds = 4213 Number of angles = 1499 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1397 Number of HB donors = 2772 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1395 Number of atoms = 4220 Number of groups = 1400 Number of bonds = 4213 Number of angles = 1499 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1397 Number of HB donors = 2772 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.872" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1395" Evaluating: 1395-7 Parameter: NUMWAT <- "1388" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1388" Comparing "1081" and "1388". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.872" Parameter: BOX -> "34.872" Parameter: BOX -> "34.872" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.87200 B = 34.87200 C = 34.87200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6339 2 1 -1 0 -1 6.1669 3 1 -1 1 -1 5.6766 4 1 0 -1 -1 3.3186 5 1 0 0 -1 2.3500 6 1 0 1 -1 3.0250 7 1 -1 -1 0 5.5090 8 1 -1 0 0 2.8015 9 1 -1 1 0 4.7961 10 1 0 -1 0 0.7839 11 1 0 1 0 0.7839 12 1 -1 -1 1 4.9561 13 1 -1 0 1 4.7403 14 1 -1 1 1 5.5147 15 1 0 -1 1 3.0250 16 1 0 0 1 2.3500 17 1 0 1 1 3.3186 18 1 1 1 1 4.6339 19 1 1 0 1 6.1669 20 1 1 -1 1 5.6766 21 1 1 1 0 5.5090 22 1 1 0 0 2.8015 23 1 1 -1 0 4.7961 24 1 1 1 -1 4.9561 25 1 1 0 -1 4.7403 26 1 1 -1 -1 5.5147 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4146 atoms have been selected out of 4220 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 720 240 240 0.00 3 C003 has 81 27 27 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 486 162 162 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 465 155 155 0.00 10 C010 has 1779 593 593 0.00 12 C012 has 111 37 37 0.00 13 C013 has 480 160 160 0.00 14 C014 has 102 34 34 0.00 Total of13753 atoms and 4576 groups and 4571 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4220 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1395 Number of atoms = 4220 Number of groups = 1400 Number of bonds = 4213 Number of angles = 1499 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1397 Number of HB donors = 2772 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1395 Number of atoms = 4220 Number of groups = 1400 Number of bonds = 4213 Number of angles = 1499 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1397 Number of HB donors = 2772 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.87" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1395" Evaluating: 1395-7 Parameter: NUMWAT <- "1388" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1388" Comparing "1081" and "1388". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.87" Parameter: BOX -> "34.87" Parameter: BOX -> "34.87" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.87000 B = 34.87000 C = 34.87000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6359 2 1 -1 0 -1 6.1680 3 1 -1 1 -1 5.6732 4 1 0 -1 -1 3.3166 5 1 0 0 -1 2.3480 6 1 0 1 -1 3.0226 7 1 -1 -1 0 5.5070 8 1 -1 0 0 2.8007 9 1 -1 1 0 4.7953 10 1 0 -1 0 0.7836 11 1 0 1 0 0.7836 12 1 -1 -1 1 4.9527 13 1 -1 0 1 4.7375 14 1 -1 1 1 5.5116 15 1 0 -1 1 3.0226 16 1 0 0 1 2.3480 17 1 0 1 1 3.3166 18 1 1 1 1 4.6359 19 1 1 0 1 6.1680 20 1 1 -1 1 5.6732 21 1 1 1 0 5.5070 22 1 1 0 0 2.8007 23 1 1 -1 0 4.7953 24 1 1 1 -1 4.9527 25 1 1 0 -1 4.7375 26 1 1 -1 -1 5.5116 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4146 atoms have been selected out of 4220 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 720 240 240 0.00 3 C003 has 81 27 27 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 486 162 162 0.00 7 C007 has 765 255 255 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 465 155 155 0.00 10 C010 has 1779 593 593 0.00 12 C012 has 111 37 37 0.00 13 C013 has 480 160 160 0.00 14 C014 has 102 34 34 0.00 Total of13756 atoms and 4577 groups and 4572 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4220 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1395 Number of atoms = 4220 Number of groups = 1400 Number of bonds = 4213 Number of angles = 1499 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1397 Number of HB donors = 2772 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1395 Number of atoms = 4220 Number of groups = 1400 Number of bonds = 4213 Number of angles = 1499 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1397 Number of HB donors = 2772 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.868" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1395" Evaluating: 1395-7 Parameter: NUMWAT <- "1388" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1388" Comparing "1081" and "1388". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.868" Parameter: BOX -> "34.868" Parameter: BOX -> "34.868" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.86800 B = 34.86800 C = 34.86800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6380 2 1 -1 0 -1 6.1691 3 1 -1 1 -1 5.6697 4 1 0 -1 -1 3.3145 5 1 0 0 -1 2.3461 6 1 0 1 -1 3.0203 7 1 -1 -1 0 5.5049 8 1 -1 0 0 2.7998 9 1 -1 1 0 4.7945 10 1 0 -1 0 0.7833 11 1 0 1 0 0.7833 12 1 -1 -1 1 4.9492 13 1 -1 0 1 4.7347 14 1 -1 1 1 5.5085 15 1 0 -1 1 3.0203 16 1 0 0 1 2.3461 17 1 0 1 1 3.3145 18 1 1 1 1 4.6380 19 1 1 0 1 6.1691 20 1 1 -1 1 5.6697 21 1 1 1 0 5.5049 22 1 1 0 0 2.7998 23 1 1 -1 0 4.7945 24 1 1 1 -1 4.9492 25 1 1 0 -1 4.7347 26 1 1 -1 -1 5.5085 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4146 atoms have been selected out of 4220 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 720 240 240 0.00 3 C003 has 81 27 27 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 486 162 162 0.00 7 C007 has 765 255 255 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 465 155 155 0.00 10 C010 has 1779 593 593 0.00 12 C012 has 111 37 37 0.00 13 C013 has 480 160 160 0.00 14 C014 has 102 34 34 0.00 Total of13756 atoms and 4577 groups and 4572 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4220 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1395 Number of atoms = 4220 Number of groups = 1400 Number of bonds = 4213 Number of angles = 1499 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1397 Number of HB donors = 2772 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1395 Number of atoms = 4220 Number of groups = 1400 Number of bonds = 4213 Number of angles = 1499 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1397 Number of HB donors = 2772 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.866" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1395" Evaluating: 1395-7 Parameter: NUMWAT <- "1388" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1388" Comparing "1081" and "1388". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.866" Parameter: BOX -> "34.866" Parameter: BOX -> "34.866" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.86600 B = 34.86600 C = 34.86600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6400 2 1 -1 0 -1 6.1702 3 1 -1 1 -1 5.6663 4 1 0 -1 -1 3.3125 5 1 0 0 -1 2.3441 6 1 0 1 -1 3.0179 7 1 -1 -1 0 5.5029 8 1 -1 0 0 2.7990 9 1 -1 1 0 4.7937 10 1 0 -1 0 0.7830 11 1 0 1 0 0.7830 12 1 -1 -1 1 4.9458 13 1 -1 0 1 4.7319 14 1 -1 1 1 5.5054 15 1 0 -1 1 3.0179 16 1 0 0 1 2.3441 17 1 0 1 1 3.3125 18 1 1 1 1 4.6400 19 1 1 0 1 6.1702 20 1 1 -1 1 5.6663 21 1 1 1 0 5.5029 22 1 1 0 0 2.7990 23 1 1 -1 0 4.7937 24 1 1 1 -1 4.9458 25 1 1 0 -1 4.7319 26 1 1 -1 -1 5.5054 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4146 atoms have been selected out of 4220 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 720 240 240 0.00 3 C003 has 81 27 27 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 489 163 163 0.00 7 C007 has 765 255 255 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 465 155 155 0.00 10 C010 has 1779 593 593 0.00 12 C012 has 111 37 37 0.00 13 C013 has 480 160 160 0.00 14 C014 has 102 34 34 0.00 Total of13762 atoms and 4579 groups and 4574 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4220 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1395 Number of atoms = 4220 Number of groups = 1400 Number of bonds = 4213 Number of angles = 1499 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1397 Number of HB donors = 2772 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1395 Number of atoms = 4220 Number of groups = 1400 Number of bonds = 4213 Number of angles = 1499 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1397 Number of HB donors = 2772 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.864" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1395" Evaluating: 1395-7 Parameter: NUMWAT <- "1388" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1388" Comparing "1081" and "1388". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.864" Parameter: BOX -> "34.864" Parameter: BOX -> "34.864" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.86400 B = 34.86400 C = 34.86400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6420 2 1 -1 0 -1 6.1713 3 1 -1 1 -1 5.6628 4 1 0 -1 -1 3.3104 5 1 0 0 -1 2.3422 6 1 0 1 -1 3.0155 7 1 -1 -1 0 5.5008 8 1 -1 0 0 2.7982 9 1 -1 1 0 4.7929 10 1 0 -1 0 0.7828 11 1 0 1 0 0.7828 12 1 -1 -1 1 4.9423 13 1 -1 0 1 4.7292 14 1 -1 1 1 5.5023 15 1 0 -1 1 3.0155 16 1 0 0 1 2.3422 17 1 0 1 1 3.3104 18 1 1 1 1 4.6420 19 1 1 0 1 6.1713 20 1 1 -1 1 5.6628 21 1 1 1 0 5.5008 22 1 1 0 0 2.7982 23 1 1 -1 0 4.7929 24 1 1 1 -1 4.9423 25 1 1 0 -1 4.7292 26 1 1 -1 -1 5.5023 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4146 atoms have been selected out of 4220 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 239 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 723 241 241 0.00 3 C003 has 81 27 27 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 489 163 163 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 465 155 155 0.00 10 C010 has 1779 593 593 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13771 atoms and 4582 groups and 4577 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4220 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.862" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1394" Evaluating: 1394-7 Parameter: NUMWAT <- "1387" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1387" Comparing "1081" and "1387". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.862" Parameter: BOX -> "34.862" Parameter: BOX -> "34.862" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.86200 B = 34.86200 C = 34.86200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6440 2 1 -1 0 -1 6.1723 3 1 -1 1 -1 5.6594 4 1 0 -1 -1 3.3084 5 1 0 0 -1 2.3402 6 1 0 1 -1 3.0132 7 1 -1 -1 0 5.4987 8 1 -1 0 0 2.7973 9 1 -1 1 0 4.7922 10 1 0 -1 0 0.7825 11 1 0 1 0 0.7825 12 1 -1 -1 1 4.9388 13 1 -1 0 1 4.7264 14 1 -1 1 1 5.4992 15 1 0 -1 1 3.0132 16 1 0 0 1 2.3402 17 1 0 1 1 3.3084 18 1 1 1 1 4.6440 19 1 1 0 1 6.1723 20 1 1 -1 1 5.6594 21 1 1 1 0 5.4987 22 1 1 0 0 2.7973 23 1 1 -1 0 4.7922 24 1 1 1 -1 4.9388 25 1 1 0 -1 4.7264 26 1 1 -1 -1 5.4992 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4143 atoms have been selected out of 4217 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 723 241 241 0.00 3 C003 has 81 27 27 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 489 163 163 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1880 625 625 0.00 9 C009 has 465 155 155 0.00 10 C010 has 1779 593 593 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13759 atoms and 4578 groups and 4573 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4217 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.86" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1394" Evaluating: 1394-7 Parameter: NUMWAT <- "1387" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1387" Comparing "1081" and "1387". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.86" Parameter: BOX -> "34.86" Parameter: BOX -> "34.86" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.86000 B = 34.86000 C = 34.86000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6460 2 1 -1 0 -1 6.1734 3 1 -1 1 -1 5.6560 4 1 0 -1 -1 3.3063 5 1 0 0 -1 2.3383 6 1 0 1 -1 3.0108 7 1 -1 -1 0 5.4967 8 1 -1 0 0 2.7965 9 1 -1 1 0 4.7914 10 1 0 -1 0 0.7822 11 1 0 1 0 0.7822 12 1 -1 -1 1 4.9354 13 1 -1 0 1 4.7236 14 1 -1 1 1 5.4961 15 1 0 -1 1 3.0108 16 1 0 0 1 2.3383 17 1 0 1 1 3.3063 18 1 1 1 1 4.6460 19 1 1 0 1 6.1734 20 1 1 -1 1 5.6560 21 1 1 1 0 5.4967 22 1 1 0 0 2.7965 23 1 1 -1 0 4.7914 24 1 1 1 -1 4.9354 25 1 1 0 -1 4.7236 26 1 1 -1 -1 5.4961 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4143 atoms have been selected out of 4217 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 723 241 241 0.00 3 C003 has 81 27 27 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 492 164 164 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 465 155 155 0.00 10 C010 has 1779 593 593 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13765 atoms and 4580 groups and 4575 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4217 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.858" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1394" Evaluating: 1394-7 Parameter: NUMWAT <- "1387" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1387" Comparing "1081" and "1387". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.858" Parameter: BOX -> "34.858" Parameter: BOX -> "34.858" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.85800 B = 34.85800 C = 34.85800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6481 2 1 -1 0 -1 6.1745 3 1 -1 1 -1 5.6525 4 1 0 -1 -1 3.3043 5 1 0 0 -1 2.3363 6 1 0 1 -1 3.0085 7 1 -1 -1 0 5.4946 8 1 -1 0 0 2.7957 9 1 -1 1 0 4.7906 10 1 0 -1 0 0.7820 11 1 0 1 0 0.7820 12 1 -1 -1 1 4.9319 13 1 -1 0 1 4.7208 14 1 -1 1 1 5.4930 15 1 0 -1 1 3.0085 16 1 0 0 1 2.3363 17 1 0 1 1 3.3043 18 1 1 1 1 4.6481 19 1 1 0 1 6.1745 20 1 1 -1 1 5.6525 21 1 1 1 0 5.4946 22 1 1 0 0 2.7957 23 1 1 -1 0 4.7906 24 1 1 1 -1 4.9319 25 1 1 0 -1 4.7208 26 1 1 -1 -1 5.4930 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4143 atoms have been selected out of 4217 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 723 241 241 0.00 3 C003 has 81 27 27 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 492 164 164 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 465 155 155 0.00 10 C010 has 1779 593 593 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13765 atoms and 4580 groups and 4575 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4217 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.856" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1394" Evaluating: 1394-7 Parameter: NUMWAT <- "1387" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1387" Comparing "1081" and "1387". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.856" Parameter: BOX -> "34.856" Parameter: BOX -> "34.856" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.85600 B = 34.85600 C = 34.85600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6501 2 1 -1 0 -1 6.1756 3 1 -1 1 -1 5.6491 4 1 0 -1 -1 3.3022 5 1 0 0 -1 2.3344 6 1 0 1 -1 3.0061 7 1 -1 -1 0 5.4925 8 1 -1 0 0 2.7948 9 1 -1 1 0 4.7899 10 1 0 -1 0 0.7817 11 1 0 1 0 0.7817 12 1 -1 -1 1 4.9285 13 1 -1 0 1 4.7180 14 1 -1 1 1 5.4898 15 1 0 -1 1 3.0061 16 1 0 0 1 2.3344 17 1 0 1 1 3.3022 18 1 1 1 1 4.6501 19 1 1 0 1 6.1756 20 1 1 -1 1 5.6491 21 1 1 1 0 5.4925 22 1 1 0 0 2.7948 23 1 1 -1 0 4.7899 24 1 1 1 -1 4.9285 25 1 1 0 -1 4.7180 26 1 1 -1 -1 5.4898 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4143 atoms have been selected out of 4217 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 360 120 120 0.00 2 C002 has 723 241 241 0.00 3 C003 has 81 27 27 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 492 164 164 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 465 155 155 0.00 10 C010 has 1779 593 593 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13765 atoms and 4580 groups and 4575 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4217 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.854" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1394" Evaluating: 1394-7 Parameter: NUMWAT <- "1387" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1387" Comparing "1081" and "1387". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.854" Parameter: BOX -> "34.854" Parameter: BOX -> "34.854" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.85400 B = 34.85400 C = 34.85400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6521 2 1 -1 0 -1 6.1767 3 1 -1 1 -1 5.6456 4 1 0 -1 -1 3.3002 5 1 0 0 -1 2.3324 6 1 0 1 -1 3.0038 7 1 -1 -1 0 5.4905 8 1 -1 0 0 2.7940 9 1 -1 1 0 4.7891 10 1 0 -1 0 0.7815 11 1 0 1 0 0.7815 12 1 -1 -1 1 4.9250 13 1 -1 0 1 4.7152 14 1 -1 1 1 5.4867 15 1 0 -1 1 3.0038 16 1 0 0 1 2.3324 17 1 0 1 1 3.3002 18 1 1 1 1 4.6521 19 1 1 0 1 6.1767 20 1 1 -1 1 5.6456 21 1 1 1 0 5.4905 22 1 1 0 0 2.7940 23 1 1 -1 0 4.7891 24 1 1 1 -1 4.9250 25 1 1 0 -1 4.7152 26 1 1 -1 -1 5.4867 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4143 atoms have been selected out of 4217 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 723 241 241 0.00 3 C003 has 81 27 27 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 492 164 164 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 465 155 155 0.00 10 C010 has 1779 593 593 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13768 atoms and 4581 groups and 4576 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4217 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.852" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1394" Evaluating: 1394-7 Parameter: NUMWAT <- "1387" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1387" Comparing "1081" and "1387". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.852" Parameter: BOX -> "34.852" Parameter: BOX -> "34.852" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.85200 B = 34.85200 C = 34.85200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6541 2 1 -1 0 -1 6.1778 3 1 -1 1 -1 5.6422 4 1 0 -1 -1 3.2982 5 1 0 0 -1 2.3305 6 1 0 1 -1 3.0014 7 1 -1 -1 0 5.4884 8 1 -1 0 0 2.7932 9 1 -1 1 0 4.7883 10 1 0 -1 0 0.7812 11 1 0 1 0 0.7812 12 1 -1 -1 1 4.9216 13 1 -1 0 1 4.7124 14 1 -1 1 1 5.4836 15 1 0 -1 1 3.0014 16 1 0 0 1 2.3305 17 1 0 1 1 3.2982 18 1 1 1 1 4.6541 19 1 1 0 1 6.1778 20 1 1 -1 1 5.6422 21 1 1 1 0 5.4884 22 1 1 0 0 2.7932 23 1 1 -1 0 4.7883 24 1 1 1 -1 4.9216 25 1 1 0 -1 4.7124 26 1 1 -1 -1 5.4836 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4143 atoms have been selected out of 4217 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 723 241 241 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 492 164 164 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 465 155 155 0.00 10 C010 has 1779 593 593 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13771 atoms and 4582 groups and 4577 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4217 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.85" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1394" Evaluating: 1394-7 Parameter: NUMWAT <- "1387" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1387" Comparing "1081" and "1387". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.85" Parameter: BOX -> "34.85" Parameter: BOX -> "34.85" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.85000 B = 34.85000 C = 34.85000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6562 2 1 -1 0 -1 6.1789 3 1 -1 1 -1 5.6387 4 1 0 -1 -1 3.2961 5 1 0 0 -1 2.3285 6 1 0 1 -1 2.9991 7 1 -1 -1 0 5.4864 8 1 -1 0 0 2.7924 9 1 -1 1 0 4.7875 10 1 0 -1 0 0.7810 11 1 0 1 0 0.7810 12 1 -1 -1 1 4.9181 13 1 -1 0 1 4.7096 14 1 -1 1 1 5.4805 15 1 0 -1 1 2.9991 16 1 0 0 1 2.3285 17 1 0 1 1 3.2961 18 1 1 1 1 4.6562 19 1 1 0 1 6.1789 20 1 1 -1 1 5.6387 21 1 1 1 0 5.4864 22 1 1 0 0 2.7924 23 1 1 -1 0 4.7875 24 1 1 1 -1 4.9181 25 1 1 0 -1 4.7096 26 1 1 -1 -1 5.4805 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4143 atoms have been selected out of 4217 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 723 241 241 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 492 164 164 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 465 155 155 0.00 10 C010 has 1788 596 596 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13783 atoms and 4586 groups and 4581 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4217 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.848" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1394" Evaluating: 1394-7 Parameter: NUMWAT <- "1387" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1387" Comparing "1081" and "1387". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.848" Parameter: BOX -> "34.848" Parameter: BOX -> "34.848" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.84800 B = 34.84800 C = 34.84800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6582 2 1 -1 0 -1 6.1800 3 1 -1 1 -1 5.6353 4 1 0 -1 -1 3.2941 5 1 0 0 -1 2.3266 6 1 0 1 -1 2.9967 7 1 -1 -1 0 5.4843 8 1 -1 0 0 2.7915 9 1 -1 1 0 4.7868 10 1 0 -1 0 0.7808 11 1 0 1 0 0.7808 12 1 -1 -1 1 4.9146 13 1 -1 0 1 4.7068 14 1 -1 1 1 5.4774 15 1 0 -1 1 2.9967 16 1 0 0 1 2.3266 17 1 0 1 1 3.2941 18 1 1 1 1 4.6582 19 1 1 0 1 6.1800 20 1 1 -1 1 5.6353 21 1 1 1 0 5.4843 22 1 1 0 0 2.7915 23 1 1 -1 0 4.7868 24 1 1 1 -1 4.9146 25 1 1 0 -1 4.7068 26 1 1 -1 -1 5.4774 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4143 atoms have been selected out of 4217 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 723 241 241 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 492 164 164 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 465 155 155 0.00 10 C010 has 1788 596 596 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13783 atoms and 4586 groups and 4581 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4217 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.846" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1394" Evaluating: 1394-7 Parameter: NUMWAT <- "1387" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1387" Comparing "1081" and "1387". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.846" Parameter: BOX -> "34.846" Parameter: BOX -> "34.846" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.84600 B = 34.84600 C = 34.84600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6602 2 1 -1 0 -1 6.1811 3 1 -1 1 -1 5.6318 4 1 0 -1 -1 3.2920 5 1 0 0 -1 2.3246 6 1 0 1 -1 2.9944 7 1 -1 -1 0 5.4822 8 1 -1 0 0 2.7907 9 1 -1 1 0 4.7860 10 1 0 -1 0 0.7805 11 1 0 1 0 0.7805 12 1 -1 -1 1 4.9112 13 1 -1 0 1 4.7040 14 1 -1 1 1 5.4743 15 1 0 -1 1 2.9944 16 1 0 0 1 2.3246 17 1 0 1 1 3.2920 18 1 1 1 1 4.6602 19 1 1 0 1 6.1811 20 1 1 -1 1 5.6318 21 1 1 1 0 5.4822 22 1 1 0 0 2.7907 23 1 1 -1 0 4.7860 24 1 1 1 -1 4.9112 25 1 1 0 -1 4.7040 26 1 1 -1 -1 5.4743 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4143 atoms have been selected out of 4217 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 723 241 241 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 495 165 165 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 465 155 155 0.00 10 C010 has 1788 596 596 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13786 atoms and 4587 groups and 4582 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4217 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.844" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1394" Evaluating: 1394-7 Parameter: NUMWAT <- "1387" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1387" Comparing "1081" and "1387". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.844" Parameter: BOX -> "34.844" Parameter: BOX -> "34.844" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.84400 B = 34.84400 C = 34.84400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6623 2 1 -1 0 -1 6.1821 3 1 -1 1 -1 5.6284 4 1 0 -1 -1 3.2900 5 1 0 0 -1 2.3227 6 1 0 1 -1 2.9920 7 1 -1 -1 0 5.4802 8 1 -1 0 0 2.7899 9 1 -1 1 0 4.7853 10 1 0 -1 0 0.7803 11 1 0 1 0 0.7803 12 1 -1 -1 1 4.9077 13 1 -1 0 1 4.7013 14 1 -1 1 1 5.4712 15 1 0 -1 1 2.9920 16 1 0 0 1 2.3227 17 1 0 1 1 3.2900 18 1 1 1 1 4.6623 19 1 1 0 1 6.1821 20 1 1 -1 1 5.6284 21 1 1 1 0 5.4802 22 1 1 0 0 2.7899 23 1 1 -1 0 4.7853 24 1 1 1 -1 4.9077 25 1 1 0 -1 4.7013 26 1 1 -1 -1 5.4712 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4143 atoms have been selected out of 4217 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 723 241 241 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 495 165 165 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 465 155 155 0.00 10 C010 has 1788 596 596 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13789 atoms and 4588 groups and 4583 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4217 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.842" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1394" Evaluating: 1394-7 Parameter: NUMWAT <- "1387" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1387" Comparing "1081" and "1387". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.842" Parameter: BOX -> "34.842" Parameter: BOX -> "34.842" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.84200 B = 34.84200 C = 34.84200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6643 2 1 -1 0 -1 6.1832 3 1 -1 1 -1 5.6249 4 1 0 -1 -1 3.2880 5 1 0 0 -1 2.3208 6 1 0 1 -1 2.9897 7 1 -1 -1 0 5.4781 8 1 -1 0 0 2.7891 9 1 -1 1 0 4.7845 10 1 0 -1 0 0.7801 11 1 0 1 0 0.7801 12 1 -1 -1 1 4.9043 13 1 -1 0 1 4.6985 14 1 -1 1 1 5.4681 15 1 0 -1 1 2.9897 16 1 0 0 1 2.3208 17 1 0 1 1 3.2880 18 1 1 1 1 4.6643 19 1 1 0 1 6.1832 20 1 1 -1 1 5.6249 21 1 1 1 0 5.4781 22 1 1 0 0 2.7891 23 1 1 -1 0 4.7845 24 1 1 1 -1 4.9043 25 1 1 0 -1 4.6985 26 1 1 -1 -1 5.4681 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4143 atoms have been selected out of 4217 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 723 241 241 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 498 166 166 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 465 155 155 0.00 10 C010 has 1788 596 596 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13795 atoms and 4590 groups and 4585 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4217 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.84" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1394" Evaluating: 1394-7 Parameter: NUMWAT <- "1387" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1387" Comparing "1081" and "1387". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.84" Parameter: BOX -> "34.84" Parameter: BOX -> "34.84" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.84000 B = 34.84000 C = 34.84000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6664 2 1 -1 0 -1 6.1843 3 1 -1 1 -1 5.6215 4 1 0 -1 -1 3.2859 5 1 0 0 -1 2.3188 6 1 0 1 -1 2.9873 7 1 -1 -1 0 5.4761 8 1 -1 0 0 2.7883 9 1 -1 1 0 4.7837 10 1 0 -1 0 0.7799 11 1 0 1 0 0.7799 12 1 -1 -1 1 4.9008 13 1 -1 0 1 4.6957 14 1 -1 1 1 5.4650 15 1 0 -1 1 2.9873 16 1 0 0 1 2.3188 17 1 0 1 1 3.2859 18 1 1 1 1 4.6664 19 1 1 0 1 6.1843 20 1 1 -1 1 5.6215 21 1 1 1 0 5.4761 22 1 1 0 0 2.7883 23 1 1 -1 0 4.7837 24 1 1 1 -1 4.9008 25 1 1 0 -1 4.6957 26 1 1 -1 -1 5.4650 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4143 atoms have been selected out of 4217 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 723 241 241 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 498 166 166 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 465 155 155 0.00 10 C010 has 1788 596 596 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13798 atoms and 4591 groups and 4586 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4217 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.838" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1394" Evaluating: 1394-7 Parameter: NUMWAT <- "1387" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1387" Comparing "1081" and "1387". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.838" Parameter: BOX -> "34.838" Parameter: BOX -> "34.838" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.83800 B = 34.83800 C = 34.83800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6684 2 1 -1 0 -1 6.1854 3 1 -1 1 -1 5.6180 4 1 0 -1 -1 3.2839 5 1 0 0 -1 2.3169 6 1 0 1 -1 2.9850 7 1 -1 -1 0 5.4740 8 1 -1 0 0 2.7874 9 1 -1 1 0 4.7830 10 1 0 -1 0 0.7797 11 1 0 1 0 0.7797 12 1 -1 -1 1 4.8974 13 1 -1 0 1 4.6929 14 1 -1 1 1 5.4619 15 1 0 -1 1 2.9850 16 1 0 0 1 2.3169 17 1 0 1 1 3.2839 18 1 1 1 1 4.6684 19 1 1 0 1 6.1854 20 1 1 -1 1 5.6180 21 1 1 1 0 5.4740 22 1 1 0 0 2.7874 23 1 1 -1 0 4.7830 24 1 1 1 -1 4.8974 25 1 1 0 -1 4.6929 26 1 1 -1 -1 5.4619 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4143 atoms have been selected out of 4217 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 723 241 241 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 498 166 166 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 465 155 155 0.00 10 C010 has 1788 596 596 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13798 atoms and 4591 groups and 4586 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4217 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.836" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1394" Evaluating: 1394-7 Parameter: NUMWAT <- "1387" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1387" Comparing "1081" and "1387". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.836" Parameter: BOX -> "34.836" Parameter: BOX -> "34.836" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.83600 B = 34.83600 C = 34.83600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6704 2 1 -1 0 -1 6.1865 3 1 -1 1 -1 5.6146 4 1 0 -1 -1 3.2819 5 1 0 0 -1 2.3149 6 1 0 1 -1 2.9826 7 1 -1 -1 0 5.4720 8 1 -1 0 0 2.7866 9 1 -1 1 0 4.7822 10 1 0 -1 0 0.7795 11 1 0 1 0 0.7795 12 1 -1 -1 1 4.8939 13 1 -1 0 1 4.6901 14 1 -1 1 1 5.4588 15 1 0 -1 1 2.9826 16 1 0 0 1 2.3149 17 1 0 1 1 3.2819 18 1 1 1 1 4.6704 19 1 1 0 1 6.1865 20 1 1 -1 1 5.6146 21 1 1 1 0 5.4720 22 1 1 0 0 2.7866 23 1 1 -1 0 4.7822 24 1 1 1 -1 4.8939 25 1 1 0 -1 4.6901 26 1 1 -1 -1 5.4588 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4143 atoms have been selected out of 4217 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 723 241 241 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1701 567 567 0.00 6 C006 has 498 166 166 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 465 155 155 0.00 10 C010 has 1788 596 596 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13801 atoms and 4592 groups and 4587 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4217 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.834" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1394" Evaluating: 1394-7 Parameter: NUMWAT <- "1387" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1387" Comparing "1081" and "1387". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.834" Parameter: BOX -> "34.834" Parameter: BOX -> "34.834" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.83400 B = 34.83400 C = 34.83400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6725 2 1 -1 0 -1 6.1876 3 1 -1 1 -1 5.6111 4 1 0 -1 -1 3.2798 5 1 0 0 -1 2.3130 6 1 0 1 -1 2.9803 7 1 -1 -1 0 5.4699 8 1 -1 0 0 2.7858 9 1 -1 1 0 4.7815 10 1 0 -1 0 0.7793 11 1 0 1 0 0.7793 12 1 -1 -1 1 4.8905 13 1 -1 0 1 4.6873 14 1 -1 1 1 5.4557 15 1 0 -1 1 2.9803 16 1 0 0 1 2.3130 17 1 0 1 1 3.2798 18 1 1 1 1 4.6725 19 1 1 0 1 6.1876 20 1 1 -1 1 5.6111 21 1 1 1 0 5.4699 22 1 1 0 0 2.7858 23 1 1 -1 0 4.7815 24 1 1 1 -1 4.8905 25 1 1 0 -1 4.6873 26 1 1 -1 -1 5.4557 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4143 atoms have been selected out of 4217 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 723 241 241 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1701 567 567 0.00 6 C006 has 498 166 166 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 465 155 155 0.00 10 C010 has 1788 596 596 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13801 atoms and 4592 groups and 4587 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4217 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.832" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1394" Evaluating: 1394-7 Parameter: NUMWAT <- "1387" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1387" Comparing "1081" and "1387". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.832" Parameter: BOX -> "34.832" Parameter: BOX -> "34.832" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.83200 B = 34.83200 C = 34.83200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6745 2 1 -1 0 -1 6.1887 3 1 -1 1 -1 5.6077 4 1 0 -1 -1 3.2778 5 1 0 0 -1 2.3110 6 1 0 1 -1 2.9779 7 1 -1 -1 0 5.4679 8 1 -1 0 0 2.7850 9 1 -1 1 0 4.7807 10 1 0 -1 0 0.7791 11 1 0 1 0 0.7791 12 1 -1 -1 1 4.8870 13 1 -1 0 1 4.6845 14 1 -1 1 1 5.4526 15 1 0 -1 1 2.9779 16 1 0 0 1 2.3110 17 1 0 1 1 3.2778 18 1 1 1 1 4.6745 19 1 1 0 1 6.1887 20 1 1 -1 1 5.6077 21 1 1 1 0 5.4679 22 1 1 0 0 2.7850 23 1 1 -1 0 4.7807 24 1 1 1 -1 4.8870 25 1 1 0 -1 4.6845 26 1 1 -1 -1 5.4526 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4143 atoms have been selected out of 4217 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 723 241 241 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1701 567 567 0.00 6 C006 has 498 166 166 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1883 626 626 0.00 9 C009 has 468 156 156 0.00 10 C010 has 1788 596 596 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13804 atoms and 4593 groups and 4588 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4217 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1394 Number of atoms = 4217 Number of groups = 1399 Number of bonds = 4210 Number of angles = 1498 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1396 Number of HB donors = 2770 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.83" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1394" Evaluating: 1394-7 Parameter: NUMWAT <- "1387" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1387" Comparing "1081" and "1387". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.83" Parameter: BOX -> "34.83" Parameter: BOX -> "34.83" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.83000 B = 34.83000 C = 34.83000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6766 2 1 -1 0 -1 6.1898 3 1 -1 1 -1 5.6043 4 1 0 -1 -1 3.2758 5 1 0 0 -1 2.3091 6 1 0 1 -1 2.9756 7 1 -1 -1 0 5.4658 8 1 -1 0 0 2.7842 9 1 -1 1 0 4.7800 10 1 0 -1 0 0.7789 11 1 0 1 0 0.7789 12 1 -1 -1 1 4.8835 13 1 -1 0 1 4.6817 14 1 -1 1 1 5.4495 15 1 0 -1 1 2.9756 16 1 0 0 1 2.3091 17 1 0 1 1 3.2758 18 1 1 1 1 4.6766 19 1 1 0 1 6.1898 20 1 1 -1 1 5.6043 21 1 1 1 0 5.4658 22 1 1 0 0 2.7842 23 1 1 -1 0 4.7800 24 1 1 1 -1 4.8835 25 1 1 0 -1 4.6817 26 1 1 -1 -1 5.4495 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4143 atoms have been selected out of 4217 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 179 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 723 241 241 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1701 567 567 0.00 6 C006 has 498 166 166 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1880 625 625 0.00 9 C009 has 468 156 156 0.00 10 C010 has 1779 593 593 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13795 atoms and 4590 groups and 4585 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4217 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1393 Number of atoms = 4214 Number of groups = 1398 Number of bonds = 4207 Number of angles = 1497 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1395 Number of HB donors = 2768 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1393 Number of atoms = 4214 Number of groups = 1398 Number of bonds = 4207 Number of angles = 1497 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1395 Number of HB donors = 2768 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.828" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1393" Evaluating: 1393-7 Parameter: NUMWAT <- "1386" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1386" Comparing "1081" and "1386". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.828" Parameter: BOX -> "34.828" Parameter: BOX -> "34.828" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.82800 B = 34.82800 C = 34.82800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6786 2 1 -1 0 -1 6.1909 3 1 -1 1 -1 5.6008 4 1 0 -1 -1 3.2737 5 1 0 0 -1 2.3071 6 1 0 1 -1 2.9733 7 1 -1 -1 0 5.4638 8 1 -1 0 0 2.7834 9 1 -1 1 0 4.7792 10 1 0 -1 0 0.7787 11 1 0 1 0 0.7787 12 1 -1 -1 1 4.8801 13 1 -1 0 1 4.6789 14 1 -1 1 1 5.4463 15 1 0 -1 1 2.9733 16 1 0 0 1 2.3071 17 1 0 1 1 3.2737 18 1 1 1 1 4.6786 19 1 1 0 1 6.1909 20 1 1 -1 1 5.6008 21 1 1 1 0 5.4638 22 1 1 0 0 2.7834 23 1 1 -1 0 4.7792 24 1 1 1 -1 4.8801 25 1 1 0 -1 4.6789 26 1 1 -1 -1 5.4463 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4140 atoms have been selected out of 4214 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 723 241 241 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1701 567 567 0.00 6 C006 has 501 167 167 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1880 625 625 0.00 9 C009 has 468 156 156 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13792 atoms and 4589 groups and 4584 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4214 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1393 Number of atoms = 4214 Number of groups = 1398 Number of bonds = 4207 Number of angles = 1497 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1395 Number of HB donors = 2768 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1393 Number of atoms = 4214 Number of groups = 1398 Number of bonds = 4207 Number of angles = 1497 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1395 Number of HB donors = 2768 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.826" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1393" Evaluating: 1393-7 Parameter: NUMWAT <- "1386" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1386" Comparing "1081" and "1386". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.826" Parameter: BOX -> "34.826" Parameter: BOX -> "34.826" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.82600 B = 34.82600 C = 34.82600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6807 2 1 -1 0 -1 6.1920 3 1 -1 1 -1 5.5974 4 1 0 -1 -1 3.2717 5 1 0 0 -1 2.3052 6 1 0 1 -1 2.9709 7 1 -1 -1 0 5.4617 8 1 -1 0 0 2.7826 9 1 -1 1 0 4.7785 10 1 0 -1 0 0.7786 11 1 0 1 0 0.7786 12 1 -1 -1 1 4.8766 13 1 -1 0 1 4.6761 14 1 -1 1 1 5.4432 15 1 0 -1 1 2.9709 16 1 0 0 1 2.3052 17 1 0 1 1 3.2717 18 1 1 1 1 4.6807 19 1 1 0 1 6.1920 20 1 1 -1 1 5.5974 21 1 1 1 0 5.4617 22 1 1 0 0 2.7826 23 1 1 -1 0 4.7785 24 1 1 1 -1 4.8766 25 1 1 0 -1 4.6761 26 1 1 -1 -1 5.4432 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4140 atoms have been selected out of 4214 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 726 242 242 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1701 567 567 0.00 6 C006 has 501 167 167 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1880 625 625 0.00 9 C009 has 468 156 156 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13795 atoms and 4590 groups and 4585 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4214 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1393 Number of atoms = 4214 Number of groups = 1398 Number of bonds = 4207 Number of angles = 1497 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1395 Number of HB donors = 2768 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1393 Number of atoms = 4214 Number of groups = 1398 Number of bonds = 4207 Number of angles = 1497 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1395 Number of HB donors = 2768 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.824" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1393" Evaluating: 1393-7 Parameter: NUMWAT <- "1386" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1386" Comparing "1081" and "1386". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.824" Parameter: BOX -> "34.824" Parameter: BOX -> "34.824" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.82400 B = 34.82400 C = 34.82400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6827 2 1 -1 0 -1 6.1931 3 1 -1 1 -1 5.5939 4 1 0 -1 -1 3.2697 5 1 0 0 -1 2.3032 6 1 0 1 -1 2.9686 7 1 -1 -1 0 5.4597 8 1 -1 0 0 2.7817 9 1 -1 1 0 4.7777 10 1 0 -1 0 0.7784 11 1 0 1 0 0.7784 12 1 -1 -1 1 4.8732 13 1 -1 0 1 4.6734 14 1 -1 1 1 5.4401 15 1 0 -1 1 2.9686 16 1 0 0 1 2.3032 17 1 0 1 1 3.2697 18 1 1 1 1 4.6827 19 1 1 0 1 6.1931 20 1 1 -1 1 5.5939 21 1 1 1 0 5.4597 22 1 1 0 0 2.7817 23 1 1 -1 0 4.7777 24 1 1 1 -1 4.8732 25 1 1 0 -1 4.6734 26 1 1 -1 -1 5.4401 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4140 atoms have been selected out of 4214 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1056 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 729 243 243 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1701 567 567 0.00 6 C006 has 504 168 168 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1880 625 625 0.00 9 C009 has 468 156 156 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13798 atoms and 4591 groups and 4586 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4214 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1392 Number of atoms = 4211 Number of groups = 1397 Number of bonds = 4204 Number of angles = 1496 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1394 Number of HB donors = 2766 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1392 Number of atoms = 4211 Number of groups = 1397 Number of bonds = 4204 Number of angles = 1496 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1394 Number of HB donors = 2766 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.822" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1392" Evaluating: 1392-7 Parameter: NUMWAT <- "1385" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1385" Comparing "1081" and "1385". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.822" Parameter: BOX -> "34.822" Parameter: BOX -> "34.822" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.82200 B = 34.82200 C = 34.82200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6848 2 1 -1 0 -1 6.1943 3 1 -1 1 -1 5.5905 4 1 0 -1 -1 3.2677 5 1 0 0 -1 2.3013 6 1 0 1 -1 2.9662 7 1 -1 -1 0 5.4576 8 1 -1 0 0 2.7809 9 1 -1 1 0 4.7770 10 1 0 -1 0 0.7782 11 1 0 1 0 0.7782 12 1 -1 -1 1 4.8697 13 1 -1 0 1 4.6706 14 1 -1 1 1 5.4370 15 1 0 -1 1 2.9662 16 1 0 0 1 2.3013 17 1 0 1 1 3.2677 18 1 1 1 1 4.6848 19 1 1 0 1 6.1943 20 1 1 -1 1 5.5905 21 1 1 1 0 5.4576 22 1 1 0 0 2.7809 23 1 1 -1 0 4.7770 24 1 1 1 -1 4.8697 25 1 1 0 -1 4.6706 26 1 1 -1 -1 5.4370 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4137 atoms have been selected out of 4211 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 726 242 242 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1880 625 625 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13786 atoms and 4587 groups and 4582 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4211 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1392 Number of atoms = 4211 Number of groups = 1397 Number of bonds = 4204 Number of angles = 1496 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1394 Number of HB donors = 2766 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1392 Number of atoms = 4211 Number of groups = 1397 Number of bonds = 4204 Number of angles = 1496 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1394 Number of HB donors = 2766 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.82" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1392" Evaluating: 1392-7 Parameter: NUMWAT <- "1385" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1385" Comparing "1081" and "1385". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.82" Parameter: BOX -> "34.82" Parameter: BOX -> "34.82" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.82000 B = 34.82000 C = 34.82000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6869 2 1 -1 0 -1 6.1954 3 1 -1 1 -1 5.5870 4 1 0 -1 -1 3.2656 5 1 0 0 -1 2.2993 6 1 0 1 -1 2.9639 7 1 -1 -1 0 5.4556 8 1 -1 0 0 2.7801 9 1 -1 1 0 4.7762 10 1 0 -1 0 0.7781 11 1 0 1 0 0.7781 12 1 -1 -1 1 4.8663 13 1 -1 0 1 4.6678 14 1 -1 1 1 5.4339 15 1 0 -1 1 2.9639 16 1 0 0 1 2.2993 17 1 0 1 1 3.2656 18 1 1 1 1 4.6869 19 1 1 0 1 6.1954 20 1 1 -1 1 5.5870 21 1 1 1 0 5.4556 22 1 1 0 0 2.7801 23 1 1 -1 0 4.7762 24 1 1 1 -1 4.8663 25 1 1 0 -1 4.6678 26 1 1 -1 -1 5.4339 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4137 atoms have been selected out of 4211 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 726 242 242 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1880 625 625 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13786 atoms and 4587 groups and 4582 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4211 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1392 Number of atoms = 4211 Number of groups = 1397 Number of bonds = 4204 Number of angles = 1496 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1394 Number of HB donors = 2766 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1392 Number of atoms = 4211 Number of groups = 1397 Number of bonds = 4204 Number of angles = 1496 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1394 Number of HB donors = 2766 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.818" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1392" Evaluating: 1392-7 Parameter: NUMWAT <- "1385" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1385" Comparing "1081" and "1385". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.818" Parameter: BOX -> "34.818" Parameter: BOX -> "34.818" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.81800 B = 34.81800 C = 34.81800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6889 2 1 -1 0 -1 6.1965 3 1 -1 1 -1 5.5836 4 1 0 -1 -1 3.2636 5 1 0 0 -1 2.2974 6 1 0 1 -1 2.9616 7 1 -1 -1 0 5.4535 8 1 -1 0 0 2.7793 9 1 -1 1 0 4.7755 10 1 0 -1 0 0.7779 11 1 0 1 0 0.7779 12 1 -1 -1 1 4.8628 13 1 -1 0 1 4.6650 14 1 -1 1 1 5.4308 15 1 0 -1 1 2.9616 16 1 0 0 1 2.2974 17 1 0 1 1 3.2636 18 1 1 1 1 4.6889 19 1 1 0 1 6.1965 20 1 1 -1 1 5.5836 21 1 1 1 0 5.4535 22 1 1 0 0 2.7793 23 1 1 -1 0 4.7755 24 1 1 1 -1 4.8628 25 1 1 0 -1 4.6650 26 1 1 -1 -1 5.4308 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4137 atoms have been selected out of 4211 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 726 242 242 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1880 625 625 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13792 atoms and 4589 groups and 4584 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4211 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1392 Number of atoms = 4211 Number of groups = 1397 Number of bonds = 4204 Number of angles = 1496 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1394 Number of HB donors = 2766 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1392 Number of atoms = 4211 Number of groups = 1397 Number of bonds = 4204 Number of angles = 1496 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1394 Number of HB donors = 2766 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.816" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1392" Evaluating: 1392-7 Parameter: NUMWAT <- "1385" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1385" Comparing "1081" and "1385". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.816" Parameter: BOX -> "34.816" Parameter: BOX -> "34.816" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.81600 B = 34.81600 C = 34.81600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6910 2 1 -1 0 -1 6.1976 3 1 -1 1 -1 5.5801 4 1 0 -1 -1 3.2616 5 1 0 0 -1 2.2955 6 1 0 1 -1 2.9592 7 1 -1 -1 0 5.4515 8 1 -1 0 0 2.7785 9 1 -1 1 0 4.7748 10 1 0 -1 0 0.7778 11 1 0 1 0 0.7778 12 1 -1 -1 1 4.8594 13 1 -1 0 1 4.6622 14 1 -1 1 1 5.4277 15 1 0 -1 1 2.9592 16 1 0 0 1 2.2955 17 1 0 1 1 3.2616 18 1 1 1 1 4.6910 19 1 1 0 1 6.1976 20 1 1 -1 1 5.5801 21 1 1 1 0 5.4515 22 1 1 0 0 2.7785 23 1 1 -1 0 4.7748 24 1 1 1 -1 4.8594 25 1 1 0 -1 4.6622 26 1 1 -1 -1 5.4277 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4137 atoms have been selected out of 4211 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 726 242 242 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1880 625 625 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13795 atoms and 4590 groups and 4585 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4211 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1392 Number of atoms = 4211 Number of groups = 1397 Number of bonds = 4204 Number of angles = 1496 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1394 Number of HB donors = 2766 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1392 Number of atoms = 4211 Number of groups = 1397 Number of bonds = 4204 Number of angles = 1496 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1394 Number of HB donors = 2766 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.814" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1392" Evaluating: 1392-7 Parameter: NUMWAT <- "1385" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1385" Comparing "1081" and "1385". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.814" Parameter: BOX -> "34.814" Parameter: BOX -> "34.814" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.81400 B = 34.81400 C = 34.81400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6930 2 1 -1 0 -1 6.1987 3 1 -1 1 -1 5.5767 4 1 0 -1 -1 3.2596 5 1 0 0 -1 2.2935 6 1 0 1 -1 2.9569 7 1 -1 -1 0 5.4494 8 1 -1 0 0 2.7777 9 1 -1 1 0 4.7740 10 1 0 -1 0 0.7776 11 1 0 1 0 0.7776 12 1 -1 -1 1 4.8559 13 1 -1 0 1 4.6594 14 1 -1 1 1 5.4246 15 1 0 -1 1 2.9569 16 1 0 0 1 2.2935 17 1 0 1 1 3.2596 18 1 1 1 1 4.6930 19 1 1 0 1 6.1987 20 1 1 -1 1 5.5767 21 1 1 1 0 5.4494 22 1 1 0 0 2.7777 23 1 1 -1 0 4.7740 24 1 1 1 -1 4.8559 25 1 1 0 -1 4.6594 26 1 1 -1 -1 5.4246 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4137 atoms have been selected out of 4211 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 726 242 242 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1880 625 625 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13795 atoms and 4590 groups and 4585 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4211 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1392 Number of atoms = 4211 Number of groups = 1397 Number of bonds = 4204 Number of angles = 1496 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1394 Number of HB donors = 2766 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1392 Number of atoms = 4211 Number of groups = 1397 Number of bonds = 4204 Number of angles = 1496 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1394 Number of HB donors = 2766 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.812" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1392" Evaluating: 1392-7 Parameter: NUMWAT <- "1385" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1385" Comparing "1081" and "1385". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.812" Parameter: BOX -> "34.812" Parameter: BOX -> "34.812" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.81200 B = 34.81200 C = 34.81200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6951 2 1 -1 0 -1 6.1998 3 1 -1 1 -1 5.5732 4 1 0 -1 -1 3.2576 5 1 0 0 -1 2.2916 6 1 0 1 -1 2.9546 7 1 -1 -1 0 5.4474 8 1 -1 0 0 2.7769 9 1 -1 1 0 4.7733 10 1 0 -1 0 0.7775 11 1 0 1 0 0.7775 12 1 -1 -1 1 4.8524 13 1 -1 0 1 4.6566 14 1 -1 1 1 5.4215 15 1 0 -1 1 2.9546 16 1 0 0 1 2.2916 17 1 0 1 1 3.2576 18 1 1 1 1 4.6951 19 1 1 0 1 6.1998 20 1 1 -1 1 5.5732 21 1 1 1 0 5.4474 22 1 1 0 0 2.7769 23 1 1 -1 0 4.7733 24 1 1 1 -1 4.8524 25 1 1 0 -1 4.6566 26 1 1 -1 -1 5.4215 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4137 atoms have been selected out of 4211 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 726 242 242 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1880 625 625 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13795 atoms and 4590 groups and 4585 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4211 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1392 Number of atoms = 4211 Number of groups = 1397 Number of bonds = 4204 Number of angles = 1496 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1394 Number of HB donors = 2766 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1392 Number of atoms = 4211 Number of groups = 1397 Number of bonds = 4204 Number of angles = 1496 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1394 Number of HB donors = 2766 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.81" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1392" Evaluating: 1392-7 Parameter: NUMWAT <- "1385" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1385" Comparing "1081" and "1385". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.81" Parameter: BOX -> "34.81" Parameter: BOX -> "34.81" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.81000 B = 34.81000 C = 34.81000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6972 2 1 -1 0 -1 6.2009 3 1 -1 1 -1 5.5698 4 1 0 -1 -1 3.2555 5 1 0 0 -1 2.2896 6 1 0 1 -1 2.9522 7 1 -1 -1 0 5.4453 8 1 -1 0 0 2.7761 9 1 -1 1 0 4.7725 10 1 0 -1 0 0.7774 11 1 0 1 0 0.7774 12 1 -1 -1 1 4.8490 13 1 -1 0 1 4.6538 14 1 -1 1 1 5.4184 15 1 0 -1 1 2.9522 16 1 0 0 1 2.2896 17 1 0 1 1 3.2555 18 1 1 1 1 4.6972 19 1 1 0 1 6.2009 20 1 1 -1 1 5.5698 21 1 1 1 0 5.4453 22 1 1 0 0 2.7761 23 1 1 -1 0 4.7725 24 1 1 1 -1 4.8490 25 1 1 0 -1 4.6538 26 1 1 -1 -1 5.4184 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4137 atoms have been selected out of 4211 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 726 242 242 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1880 625 625 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13795 atoms and 4590 groups and 4585 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4211 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1392 Number of atoms = 4211 Number of groups = 1397 Number of bonds = 4204 Number of angles = 1496 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1394 Number of HB donors = 2766 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1392 Number of atoms = 4211 Number of groups = 1397 Number of bonds = 4204 Number of angles = 1496 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1394 Number of HB donors = 2766 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.808" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1392" Evaluating: 1392-7 Parameter: NUMWAT <- "1385" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1385" Comparing "1081" and "1385". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.808" Parameter: BOX -> "34.808" Parameter: BOX -> "34.808" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.80800 B = 34.80800 C = 34.80800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.6992 2 1 -1 0 -1 6.2020 3 1 -1 1 -1 5.5664 4 1 0 -1 -1 3.2535 5 1 0 0 -1 2.2877 6 1 0 1 -1 2.9499 7 1 -1 -1 0 5.4433 8 1 -1 0 0 2.7753 9 1 -1 1 0 4.7718 10 1 0 -1 0 0.7772 11 1 0 1 0 0.7772 12 1 -1 -1 1 4.8455 13 1 -1 0 1 4.6510 14 1 -1 1 1 5.4153 15 1 0 -1 1 2.9499 16 1 0 0 1 2.2877 17 1 0 1 1 3.2535 18 1 1 1 1 4.6992 19 1 1 0 1 6.2020 20 1 1 -1 1 5.5664 21 1 1 1 0 5.4433 22 1 1 0 0 2.7753 23 1 1 -1 0 4.7718 24 1 1 1 -1 4.8455 25 1 1 0 -1 4.6510 26 1 1 -1 -1 5.4153 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4137 atoms have been selected out of 4211 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1234 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 723 241 241 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1880 625 625 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13792 atoms and 4589 groups and 4584 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4211 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1391 Number of atoms = 4208 Number of groups = 1396 Number of bonds = 4201 Number of angles = 1495 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1393 Number of HB donors = 2764 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1391 Number of atoms = 4208 Number of groups = 1396 Number of bonds = 4201 Number of angles = 1495 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1393 Number of HB donors = 2764 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.806" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1391" Evaluating: 1391-7 Parameter: NUMWAT <- "1384" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1384" Comparing "1081" and "1384". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.806" Parameter: BOX -> "34.806" Parameter: BOX -> "34.806" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.80600 B = 34.80600 C = 34.80600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7013 2 1 -1 0 -1 6.2031 3 1 -1 1 -1 5.5629 4 1 0 -1 -1 3.2515 5 1 0 0 -1 2.2857 6 1 0 1 -1 2.9476 7 1 -1 -1 0 5.4412 8 1 -1 0 0 2.7745 9 1 -1 1 0 4.7711 10 1 0 -1 0 0.7771 11 1 0 1 0 0.7771 12 1 -1 -1 1 4.8421 13 1 -1 0 1 4.6483 14 1 -1 1 1 5.4122 15 1 0 -1 1 2.9476 16 1 0 0 1 2.2857 17 1 0 1 1 3.2515 18 1 1 1 1 4.7013 19 1 1 0 1 6.2031 20 1 1 -1 1 5.5629 21 1 1 1 0 5.4412 22 1 1 0 0 2.7745 23 1 1 -1 0 4.7711 24 1 1 1 -1 4.8421 25 1 1 0 -1 4.6483 26 1 1 -1 -1 5.4122 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4134 atoms have been selected out of 4208 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 723 241 241 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1877 624 624 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13780 atoms and 4585 groups and 4580 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4208 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1391 Number of atoms = 4208 Number of groups = 1396 Number of bonds = 4201 Number of angles = 1495 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1393 Number of HB donors = 2764 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1391 Number of atoms = 4208 Number of groups = 1396 Number of bonds = 4201 Number of angles = 1495 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1393 Number of HB donors = 2764 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.804" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1391" Evaluating: 1391-7 Parameter: NUMWAT <- "1384" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1384" Comparing "1081" and "1384". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.804" Parameter: BOX -> "34.804" Parameter: BOX -> "34.804" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.80400 B = 34.80400 C = 34.80400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7034 2 1 -1 0 -1 6.2043 3 1 -1 1 -1 5.5595 4 1 0 -1 -1 3.2495 5 1 0 0 -1 2.2838 6 1 0 1 -1 2.9452 7 1 -1 -1 0 5.4392 8 1 -1 0 0 2.7737 9 1 -1 1 0 4.7704 10 1 0 -1 0 0.7770 11 1 0 1 0 0.7770 12 1 -1 -1 1 4.8386 13 1 -1 0 1 4.6455 14 1 -1 1 1 5.4091 15 1 0 -1 1 2.9452 16 1 0 0 1 2.2838 17 1 0 1 1 3.2495 18 1 1 1 1 4.7034 19 1 1 0 1 6.2043 20 1 1 -1 1 5.5595 21 1 1 1 0 5.4392 22 1 1 0 0 2.7737 23 1 1 -1 0 4.7704 24 1 1 1 -1 4.8386 25 1 1 0 -1 4.6455 26 1 1 -1 -1 5.4091 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4134 atoms have been selected out of 4208 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 931 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 720 240 240 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1880 625 625 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13780 atoms and 4585 groups and 4580 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4208 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.802" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1390" Evaluating: 1390-7 Parameter: NUMWAT <- "1383" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1383" Comparing "1081" and "1383". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.802" Parameter: BOX -> "34.802" Parameter: BOX -> "34.802" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.80200 B = 34.80200 C = 34.80200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7054 2 1 -1 0 -1 6.2054 3 1 -1 1 -1 5.5560 4 1 0 -1 -1 3.2475 5 1 0 0 -1 2.2818 6 1 0 1 -1 2.9429 7 1 -1 -1 0 5.4371 8 1 -1 0 0 2.7729 9 1 -1 1 0 4.7696 10 1 0 -1 0 0.7769 11 1 0 1 0 0.7769 12 1 -1 -1 1 4.8352 13 1 -1 0 1 4.6427 14 1 -1 1 1 5.4060 15 1 0 -1 1 2.9429 16 1 0 0 1 2.2818 17 1 0 1 1 3.2475 18 1 1 1 1 4.7054 19 1 1 0 1 6.2054 20 1 1 -1 1 5.5560 21 1 1 1 0 5.4371 22 1 1 0 0 2.7729 23 1 1 -1 0 4.7696 24 1 1 1 -1 4.8352 25 1 1 0 -1 4.6427 26 1 1 -1 -1 5.4060 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4131 atoms have been selected out of 4205 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 720 240 240 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1877 624 624 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 111 37 37 0.00 13 C013 has 480 160 160 0.00 14 C014 has 102 34 34 0.00 Total of13777 atoms and 4584 groups and 4579 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4205 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.8" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1390" Evaluating: 1390-7 Parameter: NUMWAT <- "1383" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1383" Comparing "1081" and "1383". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.8" Parameter: BOX -> "34.8" Parameter: BOX -> "34.8" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.80000 B = 34.80000 C = 34.80000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7075 2 1 -1 0 -1 6.2065 3 1 -1 1 -1 5.5526 4 1 0 -1 -1 3.2455 5 1 0 0 -1 2.2799 6 1 0 1 -1 2.9406 7 1 -1 -1 0 5.4351 8 1 -1 0 0 2.7721 9 1 -1 1 0 4.7689 10 1 0 -1 0 0.7768 11 1 0 1 0 0.7768 12 1 -1 -1 1 4.8317 13 1 -1 0 1 4.6399 14 1 -1 1 1 5.4029 15 1 0 -1 1 2.9406 16 1 0 0 1 2.2799 17 1 0 1 1 3.2455 18 1 1 1 1 4.7075 19 1 1 0 1 6.2065 20 1 1 -1 1 5.5526 21 1 1 1 0 5.4351 22 1 1 0 0 2.7721 23 1 1 -1 0 4.7689 24 1 1 1 -1 4.8317 25 1 1 0 -1 4.6399 26 1 1 -1 -1 5.4029 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4131 atoms have been selected out of 4205 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 720 240 240 0.00 3 C003 has 87 29 29 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1877 624 624 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 111 37 37 0.00 13 C013 has 480 160 160 0.00 14 C014 has 102 34 34 0.00 Total of13780 atoms and 4585 groups and 4580 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4205 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.798" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1390" Evaluating: 1390-7 Parameter: NUMWAT <- "1383" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1383" Comparing "1081" and "1383". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.798" Parameter: BOX -> "34.798" Parameter: BOX -> "34.798" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.79800 B = 34.79800 C = 34.79800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7096 2 1 -1 0 -1 6.2076 3 1 -1 1 -1 5.5491 4 1 0 -1 -1 3.2435 5 1 0 0 -1 2.2779 6 1 0 1 -1 2.9382 7 1 -1 -1 0 5.4331 8 1 -1 0 0 2.7713 9 1 -1 1 0 4.7682 10 1 0 -1 0 0.7767 11 1 0 1 0 0.7767 12 1 -1 -1 1 4.8283 13 1 -1 0 1 4.6371 14 1 -1 1 1 5.3998 15 1 0 -1 1 2.9382 16 1 0 0 1 2.2779 17 1 0 1 1 3.2435 18 1 1 1 1 4.7096 19 1 1 0 1 6.2076 20 1 1 -1 1 5.5491 21 1 1 1 0 5.4331 22 1 1 0 0 2.7713 23 1 1 -1 0 4.7682 24 1 1 1 -1 4.8283 25 1 1 0 -1 4.6371 26 1 1 -1 -1 5.3998 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4131 atoms have been selected out of 4205 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 720 240 240 0.00 3 C003 has 87 29 29 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1877 624 624 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 111 37 37 0.00 13 C013 has 480 160 160 0.00 14 C014 has 102 34 34 0.00 Total of13780 atoms and 4585 groups and 4580 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4205 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.796" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1390" Evaluating: 1390-7 Parameter: NUMWAT <- "1383" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1383" Comparing "1081" and "1383". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.796" Parameter: BOX -> "34.796" Parameter: BOX -> "34.796" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.79600 B = 34.79600 C = 34.79600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7117 2 1 -1 0 -1 6.2087 3 1 -1 1 -1 5.5457 4 1 0 -1 -1 3.2414 5 1 0 0 -1 2.2760 6 1 0 1 -1 2.9359 7 1 -1 -1 0 5.4310 8 1 -1 0 0 2.7705 9 1 -1 1 0 4.7674 10 1 0 -1 0 0.7766 11 1 0 1 0 0.7766 12 1 -1 -1 1 4.8248 13 1 -1 0 1 4.6343 14 1 -1 1 1 5.3967 15 1 0 -1 1 2.9359 16 1 0 0 1 2.2760 17 1 0 1 1 3.2414 18 1 1 1 1 4.7117 19 1 1 0 1 6.2087 20 1 1 -1 1 5.5457 21 1 1 1 0 5.4310 22 1 1 0 0 2.7705 23 1 1 -1 0 4.7674 24 1 1 1 -1 4.8248 25 1 1 0 -1 4.6343 26 1 1 -1 -1 5.3967 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4131 atoms have been selected out of 4205 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 720 240 240 0.00 3 C003 has 87 29 29 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1877 624 624 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 111 37 37 0.00 13 C013 has 480 160 160 0.00 14 C014 has 102 34 34 0.00 Total of13780 atoms and 4585 groups and 4580 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4205 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.794" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1390" Evaluating: 1390-7 Parameter: NUMWAT <- "1383" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1383" Comparing "1081" and "1383". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.794" Parameter: BOX -> "34.794" Parameter: BOX -> "34.794" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.79400 B = 34.79400 C = 34.79400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7137 2 1 -1 0 -1 6.2098 3 1 -1 1 -1 5.5422 4 1 0 -1 -1 3.2394 5 1 0 0 -1 2.2741 6 1 0 1 -1 2.9336 7 1 -1 -1 0 5.4290 8 1 -1 0 0 2.7697 9 1 -1 1 0 4.7667 10 1 0 -1 0 0.7765 11 1 0 1 0 0.7765 12 1 -1 -1 1 4.8214 13 1 -1 0 1 4.6315 14 1 -1 1 1 5.3937 15 1 0 -1 1 2.9336 16 1 0 0 1 2.2741 17 1 0 1 1 3.2394 18 1 1 1 1 4.7137 19 1 1 0 1 6.2098 20 1 1 -1 1 5.5422 21 1 1 1 0 5.4290 22 1 1 0 0 2.7697 23 1 1 -1 0 4.7667 24 1 1 1 -1 4.8214 25 1 1 0 -1 4.6315 26 1 1 -1 -1 5.3937 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4131 atoms have been selected out of 4205 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1877 624 624 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13786 atoms and 4587 groups and 4582 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4205 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.792" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1390" Evaluating: 1390-7 Parameter: NUMWAT <- "1383" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1383" Comparing "1081" and "1383". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.792" Parameter: BOX -> "34.792" Parameter: BOX -> "34.792" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.79200 B = 34.79200 C = 34.79200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7158 2 1 -1 0 -1 6.2110 3 1 -1 1 -1 5.5388 4 1 0 -1 -1 3.2374 5 1 0 0 -1 2.2721 6 1 0 1 -1 2.9313 7 1 -1 -1 0 5.4269 8 1 -1 0 0 2.7689 9 1 -1 1 0 4.7660 10 1 0 -1 0 0.7764 11 1 0 1 0 0.7764 12 1 -1 -1 1 4.8179 13 1 -1 0 1 4.6287 14 1 -1 1 1 5.3906 15 1 0 -1 1 2.9313 16 1 0 0 1 2.2721 17 1 0 1 1 3.2374 18 1 1 1 1 4.7158 19 1 1 0 1 6.2110 20 1 1 -1 1 5.5388 21 1 1 1 0 5.4269 22 1 1 0 0 2.7689 23 1 1 -1 0 4.7660 24 1 1 1 -1 4.8179 25 1 1 0 -1 4.6287 26 1 1 -1 -1 5.3906 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4131 atoms have been selected out of 4205 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1877 624 624 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13786 atoms and 4587 groups and 4582 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4205 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.79" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1390" Evaluating: 1390-7 Parameter: NUMWAT <- "1383" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1383" Comparing "1081" and "1383". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.79" Parameter: BOX -> "34.79" Parameter: BOX -> "34.79" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.79000 B = 34.79000 C = 34.79000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7179 2 1 -1 0 -1 6.2121 3 1 -1 1 -1 5.5353 4 1 0 -1 -1 3.2354 5 1 0 0 -1 2.2702 6 1 0 1 -1 2.9289 7 1 -1 -1 0 5.4249 8 1 -1 0 0 2.7682 9 1 -1 1 0 4.7653 10 1 0 -1 0 0.7763 11 1 0 1 0 0.7763 12 1 -1 -1 1 4.8144 13 1 -1 0 1 4.6259 14 1 -1 1 1 5.3875 15 1 0 -1 1 2.9289 16 1 0 0 1 2.2702 17 1 0 1 1 3.2354 18 1 1 1 1 4.7179 19 1 1 0 1 6.2121 20 1 1 -1 1 5.5353 21 1 1 1 0 5.4249 22 1 1 0 0 2.7682 23 1 1 -1 0 4.7653 24 1 1 1 -1 4.8144 25 1 1 0 -1 4.6259 26 1 1 -1 -1 5.3875 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4131 atoms have been selected out of 4205 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1877 624 624 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13792 atoms and 4589 groups and 4584 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4205 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.788" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1390" Evaluating: 1390-7 Parameter: NUMWAT <- "1383" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1383" Comparing "1081" and "1383". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.788" Parameter: BOX -> "34.788" Parameter: BOX -> "34.788" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.78800 B = 34.78800 C = 34.78800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7200 2 1 -1 0 -1 6.2132 3 1 -1 1 -1 5.5319 4 1 0 -1 -1 3.2334 5 1 0 0 -1 2.2682 6 1 0 1 -1 2.9266 7 1 -1 -1 0 5.4229 8 1 -1 0 0 2.7674 9 1 -1 1 0 4.7646 10 1 0 -1 0 0.7762 11 1 0 1 0 0.7762 12 1 -1 -1 1 4.8110 13 1 -1 0 1 4.6232 14 1 -1 1 1 5.3844 15 1 0 -1 1 2.9266 16 1 0 0 1 2.2682 17 1 0 1 1 3.2334 18 1 1 1 1 4.7200 19 1 1 0 1 6.2132 20 1 1 -1 1 5.5319 21 1 1 1 0 5.4229 22 1 1 0 0 2.7674 23 1 1 -1 0 4.7646 24 1 1 1 -1 4.8110 25 1 1 0 -1 4.6232 26 1 1 -1 -1 5.3844 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4131 atoms have been selected out of 4205 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1877 624 624 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13792 atoms and 4589 groups and 4584 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4205 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.786" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1390" Evaluating: 1390-7 Parameter: NUMWAT <- "1383" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1383" Comparing "1081" and "1383". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.786" Parameter: BOX -> "34.786" Parameter: BOX -> "34.786" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.78600 B = 34.78600 C = 34.78600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7221 2 1 -1 0 -1 6.2143 3 1 -1 1 -1 5.5284 4 1 0 -1 -1 3.2314 5 1 0 0 -1 2.2663 6 1 0 1 -1 2.9243 7 1 -1 -1 0 5.4208 8 1 -1 0 0 2.7666 9 1 -1 1 0 4.7638 10 1 0 -1 0 0.7762 11 1 0 1 0 0.7762 12 1 -1 -1 1 4.8075 13 1 -1 0 1 4.6204 14 1 -1 1 1 5.3813 15 1 0 -1 1 2.9243 16 1 0 0 1 2.2663 17 1 0 1 1 3.2314 18 1 1 1 1 4.7221 19 1 1 0 1 6.2143 20 1 1 -1 1 5.5284 21 1 1 1 0 5.4208 22 1 1 0 0 2.7666 23 1 1 -1 0 4.7638 24 1 1 1 -1 4.8075 25 1 1 0 -1 4.6204 26 1 1 -1 -1 5.3813 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4131 atoms have been selected out of 4205 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1877 624 624 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13792 atoms and 4589 groups and 4584 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4205 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.784" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1390" Evaluating: 1390-7 Parameter: NUMWAT <- "1383" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1383" Comparing "1081" and "1383". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.784" Parameter: BOX -> "34.784" Parameter: BOX -> "34.784" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.78400 B = 34.78400 C = 34.78400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7242 2 1 -1 0 -1 6.2155 3 1 -1 1 -1 5.5250 4 1 0 -1 -1 3.2294 5 1 0 0 -1 2.2643 6 1 0 1 -1 2.9220 7 1 -1 -1 0 5.4188 8 1 -1 0 0 2.7658 9 1 -1 1 0 4.7631 10 1 0 -1 0 0.7761 11 1 0 1 0 0.7761 12 1 -1 -1 1 4.8041 13 1 -1 0 1 4.6176 14 1 -1 1 1 5.3782 15 1 0 -1 1 2.9220 16 1 0 0 1 2.2643 17 1 0 1 1 3.2294 18 1 1 1 1 4.7242 19 1 1 0 1 6.2155 20 1 1 -1 1 5.5250 21 1 1 1 0 5.4188 22 1 1 0 0 2.7658 23 1 1 -1 0 4.7631 24 1 1 1 -1 4.8041 25 1 1 0 -1 4.6176 26 1 1 -1 -1 5.3782 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4131 atoms have been selected out of 4205 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1877 624 624 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13795 atoms and 4590 groups and 4585 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4205 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.782" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1390" Evaluating: 1390-7 Parameter: NUMWAT <- "1383" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1383" Comparing "1081" and "1383". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.782" Parameter: BOX -> "34.782" Parameter: BOX -> "34.782" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.78200 B = 34.78200 C = 34.78200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7263 2 1 -1 0 -1 6.2166 3 1 -1 1 -1 5.5216 4 1 0 -1 -1 3.2274 5 1 0 0 -1 2.2624 6 1 0 1 -1 2.9196 7 1 -1 -1 0 5.4168 8 1 -1 0 0 2.7650 9 1 -1 1 0 4.7624 10 1 0 -1 0 0.7760 11 1 0 1 0 0.7760 12 1 -1 -1 1 4.8006 13 1 -1 0 1 4.6148 14 1 -1 1 1 5.3751 15 1 0 -1 1 2.9196 16 1 0 0 1 2.2624 17 1 0 1 1 3.2274 18 1 1 1 1 4.7263 19 1 1 0 1 6.2166 20 1 1 -1 1 5.5216 21 1 1 1 0 5.4168 22 1 1 0 0 2.7650 23 1 1 -1 0 4.7624 24 1 1 1 -1 4.8006 25 1 1 0 -1 4.6148 26 1 1 -1 -1 5.3751 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4131 atoms have been selected out of 4205 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1877 624 624 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13795 atoms and 4590 groups and 4585 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4205 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.78" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1390" Evaluating: 1390-7 Parameter: NUMWAT <- "1383" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1383" Comparing "1081" and "1383". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.78" Parameter: BOX -> "34.78" Parameter: BOX -> "34.78" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.78000 B = 34.78000 C = 34.78000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7283 2 1 -1 0 -1 6.2177 3 1 -1 1 -1 5.5181 4 1 0 -1 -1 3.2254 5 1 0 0 -1 2.2605 6 1 0 1 -1 2.9173 7 1 -1 -1 0 5.4147 8 1 -1 0 0 2.7642 9 1 -1 1 0 4.7617 10 1 0 -1 0 0.7760 11 1 0 1 0 0.7760 12 1 -1 -1 1 4.7972 13 1 -1 0 1 4.6120 14 1 -1 1 1 5.3720 15 1 0 -1 1 2.9173 16 1 0 0 1 2.2605 17 1 0 1 1 3.2254 18 1 1 1 1 4.7283 19 1 1 0 1 6.2177 20 1 1 -1 1 5.5181 21 1 1 1 0 5.4147 22 1 1 0 0 2.7642 23 1 1 -1 0 4.7617 24 1 1 1 -1 4.7972 25 1 1 0 -1 4.6120 26 1 1 -1 -1 5.3720 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4131 atoms have been selected out of 4205 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1877 624 624 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13801 atoms and 4592 groups and 4587 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4205 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.778" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1390" Evaluating: 1390-7 Parameter: NUMWAT <- "1383" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1383" Comparing "1081" and "1383". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.778" Parameter: BOX -> "34.778" Parameter: BOX -> "34.778" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.77800 B = 34.77800 C = 34.77800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7304 2 1 -1 0 -1 6.2189 3 1 -1 1 -1 5.5147 4 1 0 -1 -1 3.2234 5 1 0 0 -1 2.2585 6 1 0 1 -1 2.9150 7 1 -1 -1 0 5.4127 8 1 -1 0 0 2.7634 9 1 -1 1 0 4.7610 10 1 0 -1 0 0.7759 11 1 0 1 0 0.7759 12 1 -1 -1 1 4.7937 13 1 -1 0 1 4.6092 14 1 -1 1 1 5.3689 15 1 0 -1 1 2.9150 16 1 0 0 1 2.2585 17 1 0 1 1 3.2234 18 1 1 1 1 4.7304 19 1 1 0 1 6.2189 20 1 1 -1 1 5.5147 21 1 1 1 0 5.4127 22 1 1 0 0 2.7634 23 1 1 -1 0 4.7610 24 1 1 1 -1 4.7937 25 1 1 0 -1 4.6092 26 1 1 -1 -1 5.3689 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4131 atoms have been selected out of 4205 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1877 624 624 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13801 atoms and 4592 groups and 4587 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4205 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.776" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1390" Evaluating: 1390-7 Parameter: NUMWAT <- "1383" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1383" Comparing "1081" and "1383". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.776" Parameter: BOX -> "34.776" Parameter: BOX -> "34.776" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.77600 B = 34.77600 C = 34.77600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7325 2 1 -1 0 -1 6.2200 3 1 -1 1 -1 5.5112 4 1 0 -1 -1 3.2214 5 1 0 0 -1 2.2566 6 1 0 1 -1 2.9127 7 1 -1 -1 0 5.4107 8 1 -1 0 0 2.7627 9 1 -1 1 0 4.7603 10 1 0 -1 0 0.7759 11 1 0 1 0 0.7759 12 1 -1 -1 1 4.7903 13 1 -1 0 1 4.6064 14 1 -1 1 1 5.3658 15 1 0 -1 1 2.9127 16 1 0 0 1 2.2566 17 1 0 1 1 3.2214 18 1 1 1 1 4.7325 19 1 1 0 1 6.2200 20 1 1 -1 1 5.5112 21 1 1 1 0 5.4107 22 1 1 0 0 2.7627 23 1 1 -1 0 4.7603 24 1 1 1 -1 4.7903 25 1 1 0 -1 4.6064 26 1 1 -1 -1 5.3658 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4131 atoms have been selected out of 4205 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1877 624 624 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13801 atoms and 4592 groups and 4587 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4205 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.774" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1390" Evaluating: 1390-7 Parameter: NUMWAT <- "1383" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1383" Comparing "1081" and "1383". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.774" Parameter: BOX -> "34.774" Parameter: BOX -> "34.774" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.77400 B = 34.77400 C = 34.77400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7346 2 1 -1 0 -1 6.2211 3 1 -1 1 -1 5.5078 4 1 0 -1 -1 3.2194 5 1 0 0 -1 2.2546 6 1 0 1 -1 2.9104 7 1 -1 -1 0 5.4086 8 1 -1 0 0 2.7619 9 1 -1 1 0 4.7596 10 1 0 -1 0 0.7758 11 1 0 1 0 0.7758 12 1 -1 -1 1 4.7868 13 1 -1 0 1 4.6036 14 1 -1 1 1 5.3627 15 1 0 -1 1 2.9104 16 1 0 0 1 2.2546 17 1 0 1 1 3.2194 18 1 1 1 1 4.7346 19 1 1 0 1 6.2211 20 1 1 -1 1 5.5078 21 1 1 1 0 5.4086 22 1 1 0 0 2.7619 23 1 1 -1 0 4.7596 24 1 1 1 -1 4.7868 25 1 1 0 -1 4.6036 26 1 1 -1 -1 5.3627 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4131 atoms have been selected out of 4205 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1877 624 624 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13801 atoms and 4592 groups and 4587 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4205 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1390 Number of atoms = 4205 Number of groups = 1395 Number of bonds = 4198 Number of angles = 1494 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1392 Number of HB donors = 2762 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.772" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1390" Evaluating: 1390-7 Parameter: NUMWAT <- "1383" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1383" Comparing "1081" and "1383". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.772" Parameter: BOX -> "34.772" Parameter: BOX -> "34.772" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.77200 B = 34.77200 C = 34.77200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7367 2 1 -1 0 -1 6.2223 3 1 -1 1 -1 5.5043 4 1 0 -1 -1 3.2174 5 1 0 0 -1 2.2527 6 1 0 1 -1 2.9080 7 1 -1 -1 0 5.4066 8 1 -1 0 0 2.7611 9 1 -1 1 0 4.7589 10 1 0 -1 0 0.7758 11 1 0 1 0 0.7758 12 1 -1 -1 1 4.7833 13 1 -1 0 1 4.6009 14 1 -1 1 1 5.3596 15 1 0 -1 1 2.9080 16 1 0 0 1 2.2527 17 1 0 1 1 3.2174 18 1 1 1 1 4.7367 19 1 1 0 1 6.2223 20 1 1 -1 1 5.5043 21 1 1 1 0 5.4066 22 1 1 0 0 2.7611 23 1 1 -1 0 4.7589 24 1 1 1 -1 4.7833 25 1 1 0 -1 4.6009 26 1 1 -1 -1 5.3596 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4131 atoms have been selected out of 4205 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 444 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1701 567 567 0.00 6 C006 has 501 167 167 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1877 624 624 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13807 atoms and 4594 groups and 4589 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4205 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1389 Number of atoms = 4202 Number of groups = 1394 Number of bonds = 4195 Number of angles = 1493 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1391 Number of HB donors = 2760 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1389 Number of atoms = 4202 Number of groups = 1394 Number of bonds = 4195 Number of angles = 1493 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1391 Number of HB donors = 2760 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.77" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1389" Evaluating: 1389-7 Parameter: NUMWAT <- "1382" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1382" Comparing "1081" and "1382". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.77" Parameter: BOX -> "34.77" Parameter: BOX -> "34.77" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.77000 B = 34.77000 C = 34.77000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7388 2 1 -1 0 -1 6.2234 3 1 -1 1 -1 5.5009 4 1 0 -1 -1 3.2154 5 1 0 0 -1 2.2507 6 1 0 1 -1 2.9057 7 1 -1 -1 0 5.4046 8 1 -1 0 0 2.7603 9 1 -1 1 0 4.7582 10 1 0 -1 0 0.7758 11 1 0 1 0 0.7758 12 1 -1 -1 1 4.7799 13 1 -1 0 1 4.5981 14 1 -1 1 1 5.3565 15 1 0 -1 1 2.9057 16 1 0 0 1 2.2507 17 1 0 1 1 3.2154 18 1 1 1 1 4.7388 19 1 1 0 1 6.2234 20 1 1 -1 1 5.5009 21 1 1 1 0 5.4046 22 1 1 0 0 2.7603 23 1 1 -1 0 4.7582 24 1 1 1 -1 4.7799 25 1 1 0 -1 4.5981 26 1 1 -1 -1 5.3565 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4128 atoms have been selected out of 4202 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1877 624 624 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 111 37 37 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13795 atoms and 4590 groups and 4585 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4202 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1389 Number of atoms = 4202 Number of groups = 1394 Number of bonds = 4195 Number of angles = 1493 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1391 Number of HB donors = 2760 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1389 Number of atoms = 4202 Number of groups = 1394 Number of bonds = 4195 Number of angles = 1493 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1391 Number of HB donors = 2760 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.768" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1389" Evaluating: 1389-7 Parameter: NUMWAT <- "1382" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1382" Comparing "1081" and "1382". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.768" Parameter: BOX -> "34.768" Parameter: BOX -> "34.768" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.76800 B = 34.76800 C = 34.76800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7409 2 1 -1 0 -1 6.2245 3 1 -1 1 -1 5.4974 4 1 0 -1 -1 3.2135 5 1 0 0 -1 2.2488 6 1 0 1 -1 2.9034 7 1 -1 -1 0 5.4025 8 1 -1 0 0 2.7596 9 1 -1 1 0 4.7575 10 1 0 -1 0 0.7757 11 1 0 1 0 0.7757 12 1 -1 -1 1 4.7764 13 1 -1 0 1 4.5953 14 1 -1 1 1 5.3534 15 1 0 -1 1 2.9034 16 1 0 0 1 2.2488 17 1 0 1 1 3.2135 18 1 1 1 1 4.7409 19 1 1 0 1 6.2245 20 1 1 -1 1 5.4974 21 1 1 1 0 5.4025 22 1 1 0 0 2.7596 23 1 1 -1 0 4.7575 24 1 1 1 -1 4.7764 25 1 1 0 -1 4.5953 26 1 1 -1 -1 5.3534 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4128 atoms have been selected out of 4202 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1877 624 624 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 111 37 37 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13795 atoms and 4590 groups and 4585 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4202 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1389 Number of atoms = 4202 Number of groups = 1394 Number of bonds = 4195 Number of angles = 1493 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1391 Number of HB donors = 2760 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1389 Number of atoms = 4202 Number of groups = 1394 Number of bonds = 4195 Number of angles = 1493 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1391 Number of HB donors = 2760 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.766" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1389" Evaluating: 1389-7 Parameter: NUMWAT <- "1382" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1382" Comparing "1081" and "1382". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.766" Parameter: BOX -> "34.766" Parameter: BOX -> "34.766" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.76600 B = 34.76600 C = 34.76600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7430 2 1 -1 0 -1 6.2257 3 1 -1 1 -1 5.4940 4 1 0 -1 -1 3.2115 5 1 0 0 -1 2.2468 6 1 0 1 -1 2.9011 7 1 -1 -1 0 5.4005 8 1 -1 0 0 2.7588 9 1 -1 1 0 4.7568 10 1 0 -1 0 0.7757 11 1 0 1 0 0.7757 12 1 -1 -1 1 4.7730 13 1 -1 0 1 4.5925 14 1 -1 1 1 5.3504 15 1 0 -1 1 2.9011 16 1 0 0 1 2.2468 17 1 0 1 1 3.2115 18 1 1 1 1 4.7430 19 1 1 0 1 6.2257 20 1 1 -1 1 5.4940 21 1 1 1 0 5.4005 22 1 1 0 0 2.7588 23 1 1 -1 0 4.7568 24 1 1 1 -1 4.7730 25 1 1 0 -1 4.5925 26 1 1 -1 -1 5.3504 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4128 atoms have been selected out of 4202 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1877 624 624 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 111 37 37 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13795 atoms and 4590 groups and 4585 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4202 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1389 Number of atoms = 4202 Number of groups = 1394 Number of bonds = 4195 Number of angles = 1493 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1391 Number of HB donors = 2760 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1389 Number of atoms = 4202 Number of groups = 1394 Number of bonds = 4195 Number of angles = 1493 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1391 Number of HB donors = 2760 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.764" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1389" Evaluating: 1389-7 Parameter: NUMWAT <- "1382" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1382" Comparing "1081" and "1382". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.764" Parameter: BOX -> "34.764" Parameter: BOX -> "34.764" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.76400 B = 34.76400 C = 34.76400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7451 2 1 -1 0 -1 6.2268 3 1 -1 1 -1 5.4905 4 1 0 -1 -1 3.2095 5 1 0 0 -1 2.2449 6 1 0 1 -1 2.8988 7 1 -1 -1 0 5.3985 8 1 -1 0 0 2.7580 9 1 -1 1 0 4.7561 10 1 0 -1 0 0.7757 11 1 0 1 0 0.7757 12 1 -1 -1 1 4.7695 13 1 -1 0 1 4.5897 14 1 -1 1 1 5.3473 15 1 0 -1 1 2.8988 16 1 0 0 1 2.2449 17 1 0 1 1 3.2095 18 1 1 1 1 4.7451 19 1 1 0 1 6.2268 20 1 1 -1 1 5.4905 21 1 1 1 0 5.3985 22 1 1 0 0 2.7580 23 1 1 -1 0 4.7561 24 1 1 1 -1 4.7695 25 1 1 0 -1 4.5897 26 1 1 -1 -1 5.3473 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4128 atoms have been selected out of 4202 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 534 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 726 242 242 0.00 3 C003 has 87 29 29 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1701 567 567 0.00 6 C006 has 501 167 167 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1877 624 624 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13807 atoms and 4594 groups and 4589 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4202 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1388 Number of atoms = 4199 Number of groups = 1393 Number of bonds = 4192 Number of angles = 1492 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1390 Number of HB donors = 2758 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1388 Number of atoms = 4199 Number of groups = 1393 Number of bonds = 4192 Number of angles = 1492 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1390 Number of HB donors = 2758 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.762" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1388" Evaluating: 1388-7 Parameter: NUMWAT <- "1381" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1381" Comparing "1081" and "1381". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.762" Parameter: BOX -> "34.762" Parameter: BOX -> "34.762" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.76200 B = 34.76200 C = 34.76200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7472 2 1 -1 0 -1 6.2279 3 1 -1 1 -1 5.4871 4 1 0 -1 -1 3.2075 5 1 0 0 -1 2.2430 6 1 0 1 -1 2.8965 7 1 -1 -1 0 5.3964 8 1 -1 0 0 2.7572 9 1 -1 1 0 4.7554 10 1 0 -1 0 0.7757 11 1 0 1 0 0.7757 12 1 -1 -1 1 4.7661 13 1 -1 0 1 4.5869 14 1 -1 1 1 5.3442 15 1 0 -1 1 2.8965 16 1 0 0 1 2.2430 17 1 0 1 1 3.2075 18 1 1 1 1 4.7472 19 1 1 0 1 6.2279 20 1 1 -1 1 5.4871 21 1 1 1 0 5.3964 22 1 1 0 0 2.7572 23 1 1 -1 0 4.7554 24 1 1 1 -1 4.7661 25 1 1 0 -1 4.5869 26 1 1 -1 -1 5.3442 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4125 atoms have been selected out of 4199 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1874 623 623 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1770 590 590 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13786 atoms and 4587 groups and 4582 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4199 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1388 Number of atoms = 4199 Number of groups = 1393 Number of bonds = 4192 Number of angles = 1492 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1390 Number of HB donors = 2758 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1388 Number of atoms = 4199 Number of groups = 1393 Number of bonds = 4192 Number of angles = 1492 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1390 Number of HB donors = 2758 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.76" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1388" Evaluating: 1388-7 Parameter: NUMWAT <- "1381" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1381" Comparing "1081" and "1381". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.76" Parameter: BOX -> "34.76" Parameter: BOX -> "34.76" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.76000 B = 34.76000 C = 34.76000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7493 2 1 -1 0 -1 6.2291 3 1 -1 1 -1 5.4837 4 1 0 -1 -1 3.2055 5 1 0 0 -1 2.2410 6 1 0 1 -1 2.8942 7 1 -1 -1 0 5.3944 8 1 -1 0 0 2.7565 9 1 -1 1 0 4.7547 10 1 0 -1 0 0.7757 11 1 0 1 0 0.7757 12 1 -1 -1 1 4.7626 13 1 -1 0 1 4.5841 14 1 -1 1 1 5.3411 15 1 0 -1 1 2.8942 16 1 0 0 1 2.2410 17 1 0 1 1 3.2055 18 1 1 1 1 4.7493 19 1 1 0 1 6.2291 20 1 1 -1 1 5.4837 21 1 1 1 0 5.3944 22 1 1 0 0 2.7565 23 1 1 -1 0 4.7547 24 1 1 1 -1 4.7626 25 1 1 0 -1 4.5841 26 1 1 -1 -1 5.3411 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4125 atoms have been selected out of 4199 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1874 623 623 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1770 590 590 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13786 atoms and 4587 groups and 4582 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4199 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1388 Number of atoms = 4199 Number of groups = 1393 Number of bonds = 4192 Number of angles = 1492 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1390 Number of HB donors = 2758 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1388 Number of atoms = 4199 Number of groups = 1393 Number of bonds = 4192 Number of angles = 1492 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1390 Number of HB donors = 2758 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.758" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1388" Evaluating: 1388-7 Parameter: NUMWAT <- "1381" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1381" Comparing "1081" and "1381". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.758" Parameter: BOX -> "34.758" Parameter: BOX -> "34.758" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.75800 B = 34.75800 C = 34.75800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7514 2 1 -1 0 -1 6.2302 3 1 -1 1 -1 5.4802 4 1 0 -1 -1 3.2035 5 1 0 0 -1 2.2391 6 1 0 1 -1 2.8918 7 1 -1 -1 0 5.3924 8 1 -1 0 0 2.7557 9 1 -1 1 0 4.7538 10 1 0 -1 0 0.7757 11 1 0 1 0 0.7757 12 1 -1 -1 1 4.7592 13 1 -1 0 1 4.5813 14 1 -1 1 1 5.3380 15 1 0 -1 1 2.8918 16 1 0 0 1 2.2391 17 1 0 1 1 3.2035 18 1 1 1 1 4.7514 19 1 1 0 1 6.2302 20 1 1 -1 1 5.4802 21 1 1 1 0 5.3924 22 1 1 0 0 2.7557 23 1 1 -1 0 4.7538 24 1 1 1 -1 4.7592 25 1 1 0 -1 4.5813 26 1 1 -1 -1 5.3380 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4125 atoms have been selected out of 4199 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1877 624 624 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1770 590 590 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13789 atoms and 4588 groups and 4583 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4199 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1388 Number of atoms = 4199 Number of groups = 1393 Number of bonds = 4192 Number of angles = 1492 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1390 Number of HB donors = 2758 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1388 Number of atoms = 4199 Number of groups = 1393 Number of bonds = 4192 Number of angles = 1492 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1390 Number of HB donors = 2758 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.756" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1388" Evaluating: 1388-7 Parameter: NUMWAT <- "1381" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1381" Comparing "1081" and "1381". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.756" Parameter: BOX -> "34.756" Parameter: BOX -> "34.756" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.75600 B = 34.75600 C = 34.75600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7535 2 1 -1 0 -1 6.2314 3 1 -1 1 -1 5.4768 4 1 0 -1 -1 3.2015 5 1 0 0 -1 2.2371 6 1 0 1 -1 2.8895 7 1 -1 -1 0 5.3904 8 1 -1 0 0 2.7549 9 1 -1 1 0 4.7514 10 1 0 -1 0 0.7757 11 1 0 1 0 0.7757 12 1 -1 -1 1 4.7557 13 1 -1 0 1 4.5786 14 1 -1 1 1 5.3349 15 1 0 -1 1 2.8895 16 1 0 0 1 2.2371 17 1 0 1 1 3.2015 18 1 1 1 1 4.7535 19 1 1 0 1 6.2314 20 1 1 -1 1 5.4768 21 1 1 1 0 5.3904 22 1 1 0 0 2.7549 23 1 1 -1 0 4.7514 24 1 1 1 -1 4.7557 25 1 1 0 -1 4.5786 26 1 1 -1 -1 5.3349 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4125 atoms have been selected out of 4199 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1880 625 625 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1770 590 590 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13792 atoms and 4589 groups and 4584 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4199 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1388 Number of atoms = 4199 Number of groups = 1393 Number of bonds = 4192 Number of angles = 1492 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1390 Number of HB donors = 2758 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1388 Number of atoms = 4199 Number of groups = 1393 Number of bonds = 4192 Number of angles = 1492 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1390 Number of HB donors = 2758 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.754" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1388" Evaluating: 1388-7 Parameter: NUMWAT <- "1381" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1381" Comparing "1081" and "1381". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.754" Parameter: BOX -> "34.754" Parameter: BOX -> "34.754" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.75400 B = 34.75400 C = 34.75400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7557 2 1 -1 0 -1 6.2325 3 1 -1 1 -1 5.4733 4 1 0 -1 -1 3.1995 5 1 0 0 -1 2.2352 6 1 0 1 -1 2.8872 7 1 -1 -1 0 5.3883 8 1 -1 0 0 2.7542 9 1 -1 1 0 4.7491 10 1 0 -1 0 0.7757 11 1 0 1 0 0.7757 12 1 -1 -1 1 4.7522 13 1 -1 0 1 4.5758 14 1 -1 1 1 5.3318 15 1 0 -1 1 2.8872 16 1 0 0 1 2.2352 17 1 0 1 1 3.1995 18 1 1 1 1 4.7557 19 1 1 0 1 6.2325 20 1 1 -1 1 5.4733 21 1 1 1 0 5.3883 22 1 1 0 0 2.7542 23 1 1 -1 0 4.7491 24 1 1 1 -1 4.7522 25 1 1 0 -1 4.5758 26 1 1 -1 -1 5.3318 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4125 atoms have been selected out of 4199 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1880 625 625 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1770 590 590 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13792 atoms and 4589 groups and 4584 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4199 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1388 Number of atoms = 4199 Number of groups = 1393 Number of bonds = 4192 Number of angles = 1492 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1390 Number of HB donors = 2758 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1388 Number of atoms = 4199 Number of groups = 1393 Number of bonds = 4192 Number of angles = 1492 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1390 Number of HB donors = 2758 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.752" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1388" Evaluating: 1388-7 Parameter: NUMWAT <- "1381" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1381" Comparing "1081" and "1381". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.752" Parameter: BOX -> "34.752" Parameter: BOX -> "34.752" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.75200 B = 34.75200 C = 34.75200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7578 2 1 -1 0 -1 6.2336 3 1 -1 1 -1 5.4699 4 1 0 -1 -1 3.1976 5 1 0 0 -1 2.2332 6 1 0 1 -1 2.8849 7 1 -1 -1 0 5.3863 8 1 -1 0 0 2.7534 9 1 -1 1 0 4.7468 10 1 0 -1 0 0.7757 11 1 0 1 0 0.7757 12 1 -1 -1 1 4.7488 13 1 -1 0 1 4.5730 14 1 -1 1 1 5.3287 15 1 0 -1 1 2.8849 16 1 0 0 1 2.2332 17 1 0 1 1 3.1976 18 1 1 1 1 4.7578 19 1 1 0 1 6.2336 20 1 1 -1 1 5.4699 21 1 1 1 0 5.3863 22 1 1 0 0 2.7534 23 1 1 -1 0 4.7468 24 1 1 1 -1 4.7488 25 1 1 0 -1 4.5730 26 1 1 -1 -1 5.3287 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4125 atoms have been selected out of 4199 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1880 625 625 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1770 590 590 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13792 atoms and 4589 groups and 4584 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4199 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1388 Number of atoms = 4199 Number of groups = 1393 Number of bonds = 4192 Number of angles = 1492 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1390 Number of HB donors = 2758 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1388 Number of atoms = 4199 Number of groups = 1393 Number of bonds = 4192 Number of angles = 1492 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1390 Number of HB donors = 2758 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.75" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1388" Evaluating: 1388-7 Parameter: NUMWAT <- "1381" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1381" Comparing "1081" and "1381". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.75" Parameter: BOX -> "34.75" Parameter: BOX -> "34.75" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.75000 B = 34.75000 C = 34.75000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7599 2 1 -1 0 -1 6.2348 3 1 -1 1 -1 5.4664 4 1 0 -1 -1 3.1956 5 1 0 0 -1 2.2313 6 1 0 1 -1 2.8826 7 1 -1 -1 0 5.3843 8 1 -1 0 0 2.7526 9 1 -1 1 0 4.7445 10 1 0 -1 0 0.7757 11 1 0 1 0 0.7757 12 1 -1 -1 1 4.7453 13 1 -1 0 1 4.5702 14 1 -1 1 1 5.3256 15 1 0 -1 1 2.8826 16 1 0 0 1 2.2313 17 1 0 1 1 3.1956 18 1 1 1 1 4.7599 19 1 1 0 1 6.2348 20 1 1 -1 1 5.4664 21 1 1 1 0 5.3843 22 1 1 0 0 2.7526 23 1 1 -1 0 4.7445 24 1 1 1 -1 4.7453 25 1 1 0 -1 4.5702 26 1 1 -1 -1 5.3256 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4125 atoms have been selected out of 4199 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1701 567 567 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1880 625 625 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1770 590 590 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13798 atoms and 4591 groups and 4586 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4199 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1388 Number of atoms = 4199 Number of groups = 1393 Number of bonds = 4192 Number of angles = 1492 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1390 Number of HB donors = 2758 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1388 Number of atoms = 4199 Number of groups = 1393 Number of bonds = 4192 Number of angles = 1492 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1390 Number of HB donors = 2758 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.748" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1388" Evaluating: 1388-7 Parameter: NUMWAT <- "1381" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1381" Comparing "1081" and "1381". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.748" Parameter: BOX -> "34.748" Parameter: BOX -> "34.748" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.74800 B = 34.74800 C = 34.74800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7620 2 1 -1 0 -1 6.2359 3 1 -1 1 -1 5.4630 4 1 0 -1 -1 3.1936 5 1 0 0 -1 2.2294 6 1 0 1 -1 2.8803 7 1 -1 -1 0 5.3823 8 1 -1 0 0 2.7519 9 1 -1 1 0 4.7422 10 1 0 -1 0 0.7758 11 1 0 1 0 0.7758 12 1 -1 -1 1 4.7419 13 1 -1 0 1 4.5674 14 1 -1 1 1 5.3226 15 1 0 -1 1 2.8803 16 1 0 0 1 2.2294 17 1 0 1 1 3.1936 18 1 1 1 1 4.7620 19 1 1 0 1 6.2359 20 1 1 -1 1 5.4630 21 1 1 1 0 5.3823 22 1 1 0 0 2.7519 23 1 1 -1 0 4.7422 24 1 1 1 -1 4.7419 25 1 1 0 -1 4.5674 26 1 1 -1 -1 5.3226 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4125 atoms have been selected out of 4199 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1701 567 567 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1880 625 625 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1770 590 590 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13798 atoms and 4591 groups and 4586 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4199 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1388 Number of atoms = 4199 Number of groups = 1393 Number of bonds = 4192 Number of angles = 1492 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1390 Number of HB donors = 2758 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1388 Number of atoms = 4199 Number of groups = 1393 Number of bonds = 4192 Number of angles = 1492 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1390 Number of HB donors = 2758 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.746" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1388" Evaluating: 1388-7 Parameter: NUMWAT <- "1381" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1381" Comparing "1081" and "1381". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.746" Parameter: BOX -> "34.746" Parameter: BOX -> "34.746" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.74600 B = 34.74600 C = 34.74600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7641 2 1 -1 0 -1 6.2371 3 1 -1 1 -1 5.4595 4 1 0 -1 -1 3.1916 5 1 0 0 -1 2.2274 6 1 0 1 -1 2.8780 7 1 -1 -1 0 5.3802 8 1 -1 0 0 2.7511 9 1 -1 1 0 4.7399 10 1 0 -1 0 0.7758 11 1 0 1 0 0.7758 12 1 -1 -1 1 4.7384 13 1 -1 0 1 4.5646 14 1 -1 1 1 5.3195 15 1 0 -1 1 2.8780 16 1 0 0 1 2.2274 17 1 0 1 1 3.1916 18 1 1 1 1 4.7641 19 1 1 0 1 6.2371 20 1 1 -1 1 5.4595 21 1 1 1 0 5.3802 22 1 1 0 0 2.7511 23 1 1 -1 0 4.7399 24 1 1 1 -1 4.7384 25 1 1 0 -1 4.5646 26 1 1 -1 -1 5.3195 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4125 atoms have been selected out of 4199 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1701 567 567 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1880 625 625 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1770 590 590 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13798 atoms and 4591 groups and 4586 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4199 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1388 Number of atoms = 4199 Number of groups = 1393 Number of bonds = 4192 Number of angles = 1492 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1390 Number of HB donors = 2758 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1388 Number of atoms = 4199 Number of groups = 1393 Number of bonds = 4192 Number of angles = 1492 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1390 Number of HB donors = 2758 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.744" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1388" Evaluating: 1388-7 Parameter: NUMWAT <- "1381" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1381" Comparing "1081" and "1381". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.744" Parameter: BOX -> "34.744" Parameter: BOX -> "34.744" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.74400 B = 34.74400 C = 34.74400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7662 2 1 -1 0 -1 6.2382 3 1 -1 1 -1 5.4561 4 1 0 -1 -1 3.1897 5 1 0 0 -1 2.2255 6 1 0 1 -1 2.8757 7 1 -1 -1 0 5.3782 8 1 -1 0 0 2.7503 9 1 -1 1 0 4.7376 10 1 0 -1 0 0.7758 11 1 0 1 0 0.7758 12 1 -1 -1 1 4.7350 13 1 -1 0 1 4.5618 14 1 -1 1 1 5.3164 15 1 0 -1 1 2.8757 16 1 0 0 1 2.2255 17 1 0 1 1 3.1897 18 1 1 1 1 4.7662 19 1 1 0 1 6.2382 20 1 1 -1 1 5.4561 21 1 1 1 0 5.3782 22 1 1 0 0 2.7503 23 1 1 -1 0 4.7376 24 1 1 1 -1 4.7350 25 1 1 0 -1 4.5618 26 1 1 -1 -1 5.3164 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4125 atoms have been selected out of 4199 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1701 567 567 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1880 625 625 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1770 590 590 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13798 atoms and 4591 groups and 4586 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4199 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1388 Number of atoms = 4199 Number of groups = 1393 Number of bonds = 4192 Number of angles = 1492 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1390 Number of HB donors = 2758 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1388 Number of atoms = 4199 Number of groups = 1393 Number of bonds = 4192 Number of angles = 1492 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1390 Number of HB donors = 2758 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.742" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1388" Evaluating: 1388-7 Parameter: NUMWAT <- "1381" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1381" Comparing "1081" and "1381". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.742" Parameter: BOX -> "34.742" Parameter: BOX -> "34.742" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.74200 B = 34.74200 C = 34.74200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7684 2 1 -1 0 -1 6.2394 3 1 -1 1 -1 5.4526 4 1 0 -1 -1 3.1877 5 1 0 0 -1 2.2235 6 1 0 1 -1 2.8734 7 1 -1 -1 0 5.3762 8 1 -1 0 0 2.7496 9 1 -1 1 0 4.7353 10 1 0 -1 0 0.7759 11 1 0 1 0 0.7759 12 1 -1 -1 1 4.7315 13 1 -1 0 1 4.5590 14 1 -1 1 1 5.3133 15 1 0 -1 1 2.8734 16 1 0 0 1 2.2235 17 1 0 1 1 3.1877 18 1 1 1 1 4.7684 19 1 1 0 1 6.2394 20 1 1 -1 1 5.4526 21 1 1 1 0 5.3762 22 1 1 0 0 2.7496 23 1 1 -1 0 4.7353 24 1 1 1 -1 4.7315 25 1 1 0 -1 4.5590 26 1 1 -1 -1 5.3133 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4125 atoms have been selected out of 4199 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1701 567 567 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1880 625 625 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1770 590 590 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13798 atoms and 4591 groups and 4586 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4199 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1388 Number of atoms = 4199 Number of groups = 1393 Number of bonds = 4192 Number of angles = 1492 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1390 Number of HB donors = 2758 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1388 Number of atoms = 4199 Number of groups = 1393 Number of bonds = 4192 Number of angles = 1492 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1390 Number of HB donors = 2758 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.74" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1388" Evaluating: 1388-7 Parameter: NUMWAT <- "1381" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1381" Comparing "1081" and "1381". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.74" Parameter: BOX -> "34.74" Parameter: BOX -> "34.74" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.74000 B = 34.74000 C = 34.74000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7705 2 1 -1 0 -1 6.2405 3 1 -1 1 -1 5.4492 4 1 0 -1 -1 3.1857 5 1 0 0 -1 2.2216 6 1 0 1 -1 2.8711 7 1 -1 -1 0 5.3742 8 1 -1 0 0 2.7488 9 1 -1 1 0 4.7330 10 1 0 -1 0 0.7759 11 1 0 1 0 0.7759 12 1 -1 -1 1 4.7281 13 1 -1 0 1 4.5563 14 1 -1 1 1 5.3102 15 1 0 -1 1 2.8711 16 1 0 0 1 2.2216 17 1 0 1 1 3.1857 18 1 1 1 1 4.7705 19 1 1 0 1 6.2405 20 1 1 -1 1 5.4492 21 1 1 1 0 5.3742 22 1 1 0 0 2.7488 23 1 1 -1 0 4.7330 24 1 1 1 -1 4.7281 25 1 1 0 -1 4.5563 26 1 1 -1 -1 5.3102 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4125 atoms have been selected out of 4199 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 740 OPERATED ON BY TRANSFORMATION C005 RESIDUE 921 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 369 123 123 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 501 167 167 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1880 625 625 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13786 atoms and 4587 groups and 4582 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 4199 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1386 Number of atoms = 4193 Number of groups = 1391 Number of bonds = 4186 Number of angles = 1490 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1388 Number of HB donors = 2754 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1386 Number of atoms = 4193 Number of groups = 1391 Number of bonds = 4186 Number of angles = 1490 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1388 Number of HB donors = 2754 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.738" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1386" Evaluating: 1386-7 Parameter: NUMWAT <- "1379" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1379" Comparing "1081" and "1379". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.738" Parameter: BOX -> "34.738" Parameter: BOX -> "34.738" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.73800 B = 34.73800 C = 34.73800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7726 2 1 -1 0 -1 6.2417 3 1 -1 1 -1 5.4458 4 1 0 -1 -1 3.1837 5 1 0 0 -1 2.2197 6 1 0 1 -1 2.8688 7 1 -1 -1 0 5.3722 8 1 -1 0 0 2.5933 9 1 -1 1 0 4.7306 10 1 0 -1 0 0.7760 11 1 0 1 0 0.7760 12 1 -1 -1 1 4.7246 13 1 -1 0 1 4.5535 14 1 -1 1 1 5.3071 15 1 0 -1 1 2.8688 16 1 0 0 1 2.2197 17 1 0 1 1 3.1837 18 1 1 1 1 4.7726 19 1 1 0 1 6.2417 20 1 1 -1 1 5.4458 21 1 1 1 0 5.3722 22 1 1 0 0 2.5933 23 1 1 -1 0 4.7306 24 1 1 1 -1 4.7246 25 1 1 0 -1 4.5535 26 1 1 -1 -1 5.3071 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4119 atoms have been selected out of 4193 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 369 123 123 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1877 624 624 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1770 590 590 0.00 12 C012 has 111 37 37 0.00 13 C013 has 474 158 158 0.00 14 C014 has 102 34 34 0.00 Total of13768 atoms and 4581 groups and 4576 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4193 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1386 Number of atoms = 4193 Number of groups = 1391 Number of bonds = 4186 Number of angles = 1490 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1388 Number of HB donors = 2754 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1386 Number of atoms = 4193 Number of groups = 1391 Number of bonds = 4186 Number of angles = 1490 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1388 Number of HB donors = 2754 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.736" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1386" Evaluating: 1386-7 Parameter: NUMWAT <- "1379" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1379" Comparing "1081" and "1379". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.736" Parameter: BOX -> "34.736" Parameter: BOX -> "34.736" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.73600 B = 34.73600 C = 34.73600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7747 2 1 -1 0 -1 6.2428 3 1 -1 1 -1 5.4423 4 1 0 -1 -1 3.1818 5 1 0 0 -1 2.2177 6 1 0 1 -1 2.8665 7 1 -1 -1 0 5.3701 8 1 -1 0 0 2.5925 9 1 -1 1 0 4.7283 10 1 0 -1 0 0.7760 11 1 0 1 0 0.7760 12 1 -1 -1 1 4.7212 13 1 -1 0 1 4.5507 14 1 -1 1 1 5.3041 15 1 0 -1 1 2.8665 16 1 0 0 1 2.2177 17 1 0 1 1 3.1818 18 1 1 1 1 4.7747 19 1 1 0 1 6.2428 20 1 1 -1 1 5.4423 21 1 1 1 0 5.3701 22 1 1 0 0 2.5925 23 1 1 -1 0 4.7283 24 1 1 1 -1 4.7212 25 1 1 0 -1 4.5507 26 1 1 -1 -1 5.3041 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4119 atoms have been selected out of 4193 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 369 123 123 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 504 168 168 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1877 624 624 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1770 590 590 0.00 12 C012 has 111 37 37 0.00 13 C013 has 474 158 158 0.00 14 C014 has 102 34 34 0.00 Total of13771 atoms and 4582 groups and 4577 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4193 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1386 Number of atoms = 4193 Number of groups = 1391 Number of bonds = 4186 Number of angles = 1490 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1388 Number of HB donors = 2754 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1386 Number of atoms = 4193 Number of groups = 1391 Number of bonds = 4186 Number of angles = 1490 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1388 Number of HB donors = 2754 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.734" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1386" Evaluating: 1386-7 Parameter: NUMWAT <- "1379" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1379" Comparing "1081" and "1379". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.734" Parameter: BOX -> "34.734" Parameter: BOX -> "34.734" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.73400 B = 34.73400 C = 34.73400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7768 2 1 -1 0 -1 6.2440 3 1 -1 1 -1 5.4389 4 1 0 -1 -1 3.1798 5 1 0 0 -1 2.2158 6 1 0 1 -1 2.8642 7 1 -1 -1 0 5.3681 8 1 -1 0 0 2.5917 9 1 -1 1 0 4.7260 10 1 0 -1 0 0.7761 11 1 0 1 0 0.7761 12 1 -1 -1 1 4.7177 13 1 -1 0 1 4.5479 14 1 -1 1 1 5.3010 15 1 0 -1 1 2.8642 16 1 0 0 1 2.2158 17 1 0 1 1 3.1798 18 1 1 1 1 4.7768 19 1 1 0 1 6.2440 20 1 1 -1 1 5.4389 21 1 1 1 0 5.3681 22 1 1 0 0 2.5917 23 1 1 -1 0 4.7260 24 1 1 1 -1 4.7177 25 1 1 0 -1 4.5479 26 1 1 -1 -1 5.3010 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4119 atoms have been selected out of 4193 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 194 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1287 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 723 241 241 0.00 3 C003 has 87 29 29 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 507 169 169 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1874 623 623 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1770 590 590 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13783 atoms and 4586 groups and 4581 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 4193 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1384 Number of atoms = 4187 Number of groups = 1389 Number of bonds = 4180 Number of angles = 1488 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1386 Number of HB donors = 2750 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1384 Number of atoms = 4187 Number of groups = 1389 Number of bonds = 4180 Number of angles = 1488 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1386 Number of HB donors = 2750 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.732" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1384" Evaluating: 1384-7 Parameter: NUMWAT <- "1377" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1377" Comparing "1081" and "1377". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.732" Parameter: BOX -> "34.732" Parameter: BOX -> "34.732" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.73200 B = 34.73200 C = 34.73200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7790 2 1 -1 0 -1 6.2451 3 1 -1 1 -1 5.4354 4 1 0 -1 -1 3.1778 5 1 0 0 -1 2.2138 6 1 0 1 -1 2.8619 7 1 -1 -1 0 5.3661 8 1 -1 0 0 2.5910 9 1 -1 1 0 4.7237 10 1 0 -1 0 0.7762 11 1 0 1 0 0.7762 12 1 -1 -1 1 4.7142 13 1 -1 0 1 4.5451 14 1 -1 1 1 5.2979 15 1 0 -1 1 2.8619 16 1 0 0 1 2.2138 17 1 0 1 1 3.1778 18 1 1 1 1 4.7790 19 1 1 0 1 6.2451 20 1 1 -1 1 5.4354 21 1 1 1 0 5.3661 22 1 1 0 0 2.5910 23 1 1 -1 0 4.7237 24 1 1 1 -1 4.7142 25 1 1 0 -1 4.5451 26 1 1 -1 -1 5.2979 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4113 atoms have been selected out of 4187 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 720 240 240 0.00 3 C003 has 87 29 29 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 504 168 168 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1871 622 622 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1770 590 590 0.00 12 C012 has 114 38 38 0.00 13 C013 has 474 158 158 0.00 14 C014 has 102 34 34 0.00 Total of13759 atoms and 4578 groups and 4573 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4187 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1384 Number of atoms = 4187 Number of groups = 1389 Number of bonds = 4180 Number of angles = 1488 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1386 Number of HB donors = 2750 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1384 Number of atoms = 4187 Number of groups = 1389 Number of bonds = 4180 Number of angles = 1488 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1386 Number of HB donors = 2750 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.73" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1384" Evaluating: 1384-7 Parameter: NUMWAT <- "1377" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1377" Comparing "1081" and "1377". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.73" Parameter: BOX -> "34.73" Parameter: BOX -> "34.73" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.73000 B = 34.73000 C = 34.73000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7811 2 1 -1 0 -1 6.2463 3 1 -1 1 -1 5.4320 4 1 0 -1 -1 3.1759 5 1 0 0 -1 2.2119 6 1 0 1 -1 2.8596 7 1 -1 -1 0 5.3641 8 1 -1 0 0 2.5902 9 1 -1 1 0 4.7214 10 1 0 -1 0 0.7762 11 1 0 1 0 0.7762 12 1 -1 -1 1 4.7108 13 1 -1 0 1 4.5423 14 1 -1 1 1 5.2948 15 1 0 -1 1 2.8596 16 1 0 0 1 2.2119 17 1 0 1 1 3.1759 18 1 1 1 1 4.7811 19 1 1 0 1 6.2463 20 1 1 -1 1 5.4320 21 1 1 1 0 5.3641 22 1 1 0 0 2.5902 23 1 1 -1 0 4.7214 24 1 1 1 -1 4.7108 25 1 1 0 -1 4.5423 26 1 1 -1 -1 5.2948 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4113 atoms have been selected out of 4187 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 81 OPERATED ON BY TRANSFORMATION C011 RESIDUE 752 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 369 123 123 0.00 2 C002 has 717 239 239 0.00 3 C003 has 87 29 29 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 510 170 170 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1868 621 621 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1767 589 589 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13753 atoms and 4576 groups and 4571 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 4187 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1382 Number of atoms = 4181 Number of groups = 1387 Number of bonds = 4174 Number of angles = 1486 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1384 Number of HB donors = 2746 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1382 Number of atoms = 4181 Number of groups = 1387 Number of bonds = 4174 Number of angles = 1486 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1384 Number of HB donors = 2746 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.728" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1382" Evaluating: 1382-7 Parameter: NUMWAT <- "1375" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1375" Comparing "1081" and "1375". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.728" Parameter: BOX -> "34.728" Parameter: BOX -> "34.728" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.72800 B = 34.72800 C = 34.72800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7832 2 1 -1 0 -1 6.2474 3 1 -1 1 -1 5.4285 4 1 0 -1 -1 3.1739 5 1 0 0 -1 2.2099 6 1 0 1 -1 3.8043 7 1 -1 -1 0 5.3621 8 1 -1 0 0 2.5894 9 1 -1 1 0 4.7191 10 1 0 -1 0 1.4477 11 1 0 1 0 1.4477 12 1 -1 -1 1 4.7073 13 1 -1 0 1 4.5395 14 1 -1 1 1 5.2917 15 1 0 -1 1 3.8043 16 1 0 0 1 2.2099 17 1 0 1 1 3.1739 18 1 1 1 1 4.7832 19 1 1 0 1 6.2474 20 1 1 -1 1 5.4285 21 1 1 1 0 5.3621 22 1 1 0 0 2.5894 23 1 1 -1 0 4.7191 24 1 1 1 -1 4.7073 25 1 1 0 -1 4.5395 26 1 1 -1 -1 5.2917 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4107 atoms have been selected out of 4181 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 717 239 239 0.00 3 C003 has 87 29 29 0.00 4 C004 has 606 202 202 0.00 5 C005 has 1692 564 564 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1871 622 622 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1761 587 587 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 105 35 35 0.00 Total of13726 atoms and 4567 groups and 4562 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4181 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1382 Number of atoms = 4181 Number of groups = 1387 Number of bonds = 4174 Number of angles = 1486 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1384 Number of HB donors = 2746 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1382 Number of atoms = 4181 Number of groups = 1387 Number of bonds = 4174 Number of angles = 1486 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1384 Number of HB donors = 2746 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.726" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1382" Evaluating: 1382-7 Parameter: NUMWAT <- "1375" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1375" Comparing "1081" and "1375". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.726" Parameter: BOX -> "34.726" Parameter: BOX -> "34.726" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.72600 B = 34.72600 C = 34.72600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7854 2 1 -1 0 -1 6.2486 3 1 -1 1 -1 5.4251 4 1 0 -1 -1 3.1719 5 1 0 0 -1 2.2080 6 1 0 1 -1 3.8015 7 1 -1 -1 0 5.3601 8 1 -1 0 0 2.5886 9 1 -1 1 0 4.7168 10 1 0 -1 0 1.4466 11 1 0 1 0 1.4466 12 1 -1 -1 1 4.7039 13 1 -1 0 1 4.5367 14 1 -1 1 1 5.2886 15 1 0 -1 1 3.8015 16 1 0 0 1 2.2080 17 1 0 1 1 3.1719 18 1 1 1 1 4.7854 19 1 1 0 1 6.2486 20 1 1 -1 1 5.4251 21 1 1 1 0 5.3601 22 1 1 0 0 2.5886 23 1 1 -1 0 4.7168 24 1 1 1 -1 4.7039 25 1 1 0 -1 4.5367 26 1 1 -1 -1 5.2886 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4107 atoms have been selected out of 4181 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 717 239 239 0.00 3 C003 has 87 29 29 0.00 4 C004 has 606 202 202 0.00 5 C005 has 1692 564 564 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1871 622 622 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1761 587 587 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 105 35 35 0.00 Total of13729 atoms and 4568 groups and 4563 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4181 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1382 Number of atoms = 4181 Number of groups = 1387 Number of bonds = 4174 Number of angles = 1486 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1384 Number of HB donors = 2746 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1382 Number of atoms = 4181 Number of groups = 1387 Number of bonds = 4174 Number of angles = 1486 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1384 Number of HB donors = 2746 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.724" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1382" Evaluating: 1382-7 Parameter: NUMWAT <- "1375" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1375" Comparing "1081" and "1375". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.724" Parameter: BOX -> "34.724" Parameter: BOX -> "34.724" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.72400 B = 34.72400 C = 34.72400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7875 2 1 -1 0 -1 6.2498 3 1 -1 1 -1 5.4216 4 1 0 -1 -1 3.1700 5 1 0 0 -1 2.2061 6 1 0 1 -1 3.7988 7 1 -1 -1 0 5.3580 8 1 -1 0 0 2.5878 9 1 -1 1 0 4.7145 10 1 0 -1 0 1.4454 11 1 0 1 0 1.4454 12 1 -1 -1 1 4.7004 13 1 -1 0 1 4.5340 14 1 -1 1 1 5.2856 15 1 0 -1 1 3.7988 16 1 0 0 1 2.2061 17 1 0 1 1 3.1700 18 1 1 1 1 4.7875 19 1 1 0 1 6.2498 20 1 1 -1 1 5.4216 21 1 1 1 0 5.3580 22 1 1 0 0 2.5878 23 1 1 -1 0 4.7145 24 1 1 1 -1 4.7004 25 1 1 0 -1 4.5340 26 1 1 -1 -1 5.2856 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4107 atoms have been selected out of 4181 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 720 240 240 0.00 3 C003 has 87 29 29 0.00 4 C004 has 606 202 202 0.00 5 C005 has 1692 564 564 0.00 6 C006 has 501 167 167 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1871 622 622 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1761 587 587 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 105 35 35 0.00 Total of13735 atoms and 4570 groups and 4565 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4181 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1382 Number of atoms = 4181 Number of groups = 1387 Number of bonds = 4174 Number of angles = 1486 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1384 Number of HB donors = 2746 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1382 Number of atoms = 4181 Number of groups = 1387 Number of bonds = 4174 Number of angles = 1486 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1384 Number of HB donors = 2746 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.722" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1382" Evaluating: 1382-7 Parameter: NUMWAT <- "1375" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1375" Comparing "1081" and "1375". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.722" Parameter: BOX -> "34.722" Parameter: BOX -> "34.722" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.72200 B = 34.72200 C = 34.72200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7896 2 1 -1 0 -1 6.2509 3 1 -1 1 -1 5.4182 4 1 0 -1 -1 3.1680 5 1 0 0 -1 2.2041 6 1 0 1 -1 3.7960 7 1 -1 -1 0 5.3560 8 1 -1 0 0 2.5870 9 1 -1 1 0 4.7122 10 1 0 -1 0 1.4443 11 1 0 1 0 1.4443 12 1 -1 -1 1 4.6970 13 1 -1 0 1 4.5312 14 1 -1 1 1 5.2825 15 1 0 -1 1 3.7960 16 1 0 0 1 2.2041 17 1 0 1 1 3.1680 18 1 1 1 1 4.7896 19 1 1 0 1 6.2509 20 1 1 -1 1 5.4182 21 1 1 1 0 5.3560 22 1 1 0 0 2.5870 23 1 1 -1 0 4.7122 24 1 1 1 -1 4.6970 25 1 1 0 -1 4.5312 26 1 1 -1 -1 5.2825 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4107 atoms have been selected out of 4181 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 720 240 240 0.00 3 C003 has 87 29 29 0.00 4 C004 has 606 202 202 0.00 5 C005 has 1692 564 564 0.00 6 C006 has 501 167 167 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1871 622 622 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1761 587 587 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 105 35 35 0.00 Total of13735 atoms and 4570 groups and 4565 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4181 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1382 Number of atoms = 4181 Number of groups = 1387 Number of bonds = 4174 Number of angles = 1486 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1384 Number of HB donors = 2746 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1382 Number of atoms = 4181 Number of groups = 1387 Number of bonds = 4174 Number of angles = 1486 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1384 Number of HB donors = 2746 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.72" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1382" Evaluating: 1382-7 Parameter: NUMWAT <- "1375" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1375" Comparing "1081" and "1375". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.72" Parameter: BOX -> "34.72" Parameter: BOX -> "34.72" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.72000 B = 34.72000 C = 34.72000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7918 2 1 -1 0 -1 6.2521 3 1 -1 1 -1 5.4148 4 1 0 -1 -1 3.1660 5 1 0 0 -1 2.2022 6 1 0 1 -1 3.7932 7 1 -1 -1 0 5.3540 8 1 -1 0 0 2.5862 9 1 -1 1 0 4.7099 10 1 0 -1 0 1.4432 11 1 0 1 0 1.4432 12 1 -1 -1 1 4.6935 13 1 -1 0 1 4.5284 14 1 -1 1 1 5.2794 15 1 0 -1 1 3.7932 16 1 0 0 1 2.2022 17 1 0 1 1 3.1660 18 1 1 1 1 4.7918 19 1 1 0 1 6.2521 20 1 1 -1 1 5.4148 21 1 1 1 0 5.3540 22 1 1 0 0 2.5862 23 1 1 -1 0 4.7099 24 1 1 1 -1 4.6935 25 1 1 0 -1 4.5284 26 1 1 -1 -1 5.2794 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4107 atoms have been selected out of 4181 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 454 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 720 240 240 0.00 3 C003 has 87 29 29 0.00 4 C004 has 606 202 202 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 501 167 167 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1871 622 622 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1761 587 587 0.00 12 C012 has 117 39 39 0.00 13 C013 has 480 160 160 0.00 14 C014 has 105 35 35 0.00 Total of13750 atoms and 4575 groups and 4570 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4181 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1381 Number of atoms = 4178 Number of groups = 1386 Number of bonds = 4171 Number of angles = 1485 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1383 Number of HB donors = 2744 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1381 Number of atoms = 4178 Number of groups = 1386 Number of bonds = 4171 Number of angles = 1485 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1383 Number of HB donors = 2744 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.718" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1381" Evaluating: 1381-7 Parameter: NUMWAT <- "1374" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1374" Comparing "1081" and "1374". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.718" Parameter: BOX -> "34.718" Parameter: BOX -> "34.718" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.71800 B = 34.71800 C = 34.71800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7939 2 1 -1 0 -1 6.2532 3 1 -1 1 -1 5.4113 4 1 0 -1 -1 3.1641 5 1 0 0 -1 2.2002 6 1 0 1 -1 3.7905 7 1 -1 -1 0 5.3520 8 1 -1 0 0 2.5854 9 1 -1 1 0 4.7076 10 1 0 -1 0 1.4420 11 1 0 1 0 1.4420 12 1 -1 -1 1 4.6901 13 1 -1 0 1 4.5256 14 1 -1 1 1 5.2763 15 1 0 -1 1 3.7905 16 1 0 0 1 2.2002 17 1 0 1 1 3.1641 18 1 1 1 1 4.7939 19 1 1 0 1 6.2532 20 1 1 -1 1 5.4113 21 1 1 1 0 5.3520 22 1 1 0 0 2.5854 23 1 1 -1 0 4.7076 24 1 1 1 -1 4.6901 25 1 1 0 -1 4.5256 26 1 1 -1 -1 5.2763 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4104 atoms have been selected out of 4178 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 463 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 720 240 240 0.00 3 C003 has 87 29 29 0.00 4 C004 has 606 202 202 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 501 167 167 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1862 619 619 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 117 39 39 0.00 13 C013 has 477 159 159 0.00 14 C014 has 105 35 35 0.00 Total of13732 atoms and 4569 groups and 4564 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4178 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1380 Number of atoms = 4175 Number of groups = 1385 Number of bonds = 4168 Number of angles = 1484 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1382 Number of HB donors = 2742 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1380 Number of atoms = 4175 Number of groups = 1385 Number of bonds = 4168 Number of angles = 1484 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1382 Number of HB donors = 2742 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.716" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1380" Evaluating: 1380-7 Parameter: NUMWAT <- "1373" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1373" Comparing "1081" and "1373". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.716" Parameter: BOX -> "34.716" Parameter: BOX -> "34.716" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.71600 B = 34.71600 C = 34.71600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7961 2 1 -1 0 -1 6.2544 3 1 -1 1 -1 5.4079 4 1 0 -1 -1 3.1621 5 1 0 0 -1 2.1983 6 1 0 1 -1 3.7877 7 1 -1 -1 0 5.3500 8 1 -1 0 0 2.5847 9 1 -1 1 0 4.7053 10 1 0 -1 0 1.4409 11 1 0 1 0 1.4409 12 1 -1 -1 1 4.6866 13 1 -1 0 1 4.5228 14 1 -1 1 1 5.2733 15 1 0 -1 1 3.7877 16 1 0 0 1 2.1983 17 1 0 1 1 3.1621 18 1 1 1 1 4.7961 19 1 1 0 1 6.2544 20 1 1 -1 1 5.4079 21 1 1 1 0 5.3500 22 1 1 0 0 2.5847 23 1 1 -1 0 4.7053 24 1 1 1 -1 4.6866 25 1 1 0 -1 4.5228 26 1 1 -1 -1 5.2733 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4101 atoms have been selected out of 4175 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 720 240 240 0.00 3 C003 has 87 29 29 0.00 4 C004 has 606 202 202 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1859 618 618 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 117 39 39 0.00 13 C013 has 477 159 159 0.00 14 C014 has 105 35 35 0.00 Total of13723 atoms and 4566 groups and 4561 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4175 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1380 Number of atoms = 4175 Number of groups = 1385 Number of bonds = 4168 Number of angles = 1484 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1382 Number of HB donors = 2742 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1380 Number of atoms = 4175 Number of groups = 1385 Number of bonds = 4168 Number of angles = 1484 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1382 Number of HB donors = 2742 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.714" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1380" Evaluating: 1380-7 Parameter: NUMWAT <- "1373" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1373" Comparing "1081" and "1373". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.714" Parameter: BOX -> "34.714" Parameter: BOX -> "34.714" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.71400 B = 34.71400 C = 34.71400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.7982 2 1 -1 0 -1 6.2556 3 1 -1 1 -1 5.4044 4 1 0 -1 -1 3.1602 5 1 0 0 -1 2.1964 6 1 0 1 -1 3.7849 7 1 -1 -1 0 5.3480 8 1 -1 0 0 2.5839 9 1 -1 1 0 4.7030 10 1 0 -1 0 1.4398 11 1 0 1 0 1.4398 12 1 -1 -1 1 4.6831 13 1 -1 0 1 4.5200 14 1 -1 1 1 5.2702 15 1 0 -1 1 3.7849 16 1 0 0 1 2.1964 17 1 0 1 1 3.1602 18 1 1 1 1 4.7982 19 1 1 0 1 6.2556 20 1 1 -1 1 5.4044 21 1 1 1 0 5.3480 22 1 1 0 0 2.5839 23 1 1 -1 0 4.7030 24 1 1 1 -1 4.6831 25 1 1 0 -1 4.5200 26 1 1 -1 -1 5.2702 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4101 atoms have been selected out of 4175 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 720 240 240 0.00 3 C003 has 87 29 29 0.00 4 C004 has 606 202 202 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1859 618 618 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 117 39 39 0.00 13 C013 has 477 159 159 0.00 14 C014 has 105 35 35 0.00 Total of13726 atoms and 4567 groups and 4562 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4175 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1380 Number of atoms = 4175 Number of groups = 1385 Number of bonds = 4168 Number of angles = 1484 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1382 Number of HB donors = 2742 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1380 Number of atoms = 4175 Number of groups = 1385 Number of bonds = 4168 Number of angles = 1484 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1382 Number of HB donors = 2742 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.712" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1380" Evaluating: 1380-7 Parameter: NUMWAT <- "1373" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1373" Comparing "1081" and "1373". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.712" Parameter: BOX -> "34.712" Parameter: BOX -> "34.712" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.71200 B = 34.71200 C = 34.71200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8003 2 1 -1 0 -1 6.2567 3 1 -1 1 -1 5.4010 4 1 0 -1 -1 3.1582 5 1 0 0 -1 2.1944 6 1 0 1 -1 3.7821 7 1 -1 -1 0 5.3460 8 1 -1 0 0 2.5831 9 1 -1 1 0 4.7007 10 1 0 -1 0 1.4386 11 1 0 1 0 1.4386 12 1 -1 -1 1 4.6797 13 1 -1 0 1 4.5172 14 1 -1 1 1 5.2671 15 1 0 -1 1 3.7821 16 1 0 0 1 2.1944 17 1 0 1 1 3.1582 18 1 1 1 1 4.8003 19 1 1 0 1 6.2567 20 1 1 -1 1 5.4010 21 1 1 1 0 5.3460 22 1 1 0 0 2.5831 23 1 1 -1 0 4.7007 24 1 1 1 -1 4.6797 25 1 1 0 -1 4.5172 26 1 1 -1 -1 5.2671 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4101 atoms have been selected out of 4175 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 720 240 240 0.00 3 C003 has 87 29 29 0.00 4 C004 has 606 202 202 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1859 618 618 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 117 39 39 0.00 13 C013 has 477 159 159 0.00 14 C014 has 105 35 35 0.00 Total of13726 atoms and 4567 groups and 4562 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4175 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1380 Number of atoms = 4175 Number of groups = 1385 Number of bonds = 4168 Number of angles = 1484 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1382 Number of HB donors = 2742 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1380 Number of atoms = 4175 Number of groups = 1385 Number of bonds = 4168 Number of angles = 1484 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1382 Number of HB donors = 2742 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.71" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1380" Evaluating: 1380-7 Parameter: NUMWAT <- "1373" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1373" Comparing "1081" and "1373". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.71" Parameter: BOX -> "34.71" Parameter: BOX -> "34.71" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.71000 B = 34.71000 C = 34.71000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8025 2 1 -1 0 -1 6.2579 3 1 -1 1 -1 5.3975 4 1 0 -1 -1 3.1563 5 1 0 0 -1 2.1925 6 1 0 1 -1 3.7794 7 1 -1 -1 0 5.3440 8 1 -1 0 0 2.5823 9 1 -1 1 0 4.6984 10 1 0 -1 0 1.4375 11 1 0 1 0 1.4375 12 1 -1 -1 1 4.6762 13 1 -1 0 1 4.5144 14 1 -1 1 1 5.2640 15 1 0 -1 1 3.7794 16 1 0 0 1 2.1925 17 1 0 1 1 3.1563 18 1 1 1 1 4.8025 19 1 1 0 1 6.2579 20 1 1 -1 1 5.3975 21 1 1 1 0 5.3440 22 1 1 0 0 2.5823 23 1 1 -1 0 4.6984 24 1 1 1 -1 4.6762 25 1 1 0 -1 4.5144 26 1 1 -1 -1 5.2640 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4101 atoms have been selected out of 4175 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 720 240 240 0.00 3 C003 has 87 29 29 0.00 4 C004 has 606 202 202 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1859 618 618 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 117 39 39 0.00 13 C013 has 477 159 159 0.00 14 C014 has 105 35 35 0.00 Total of13726 atoms and 4567 groups and 4562 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4175 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1380 Number of atoms = 4175 Number of groups = 1385 Number of bonds = 4168 Number of angles = 1484 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1382 Number of HB donors = 2742 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1380 Number of atoms = 4175 Number of groups = 1385 Number of bonds = 4168 Number of angles = 1484 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1382 Number of HB donors = 2742 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.708" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1380" Evaluating: 1380-7 Parameter: NUMWAT <- "1373" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1373" Comparing "1081" and "1373". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.708" Parameter: BOX -> "34.708" Parameter: BOX -> "34.708" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.70800 B = 34.70800 C = 34.70800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8046 2 1 -1 0 -1 6.2591 3 1 -1 1 -1 5.3941 4 1 0 -1 -1 3.1543 5 1 0 0 -1 2.1905 6 1 0 1 -1 3.7766 7 1 -1 -1 0 5.3420 8 1 -1 0 0 2.5815 9 1 -1 1 0 4.6961 10 1 0 -1 0 1.4364 11 1 0 1 0 1.4364 12 1 -1 -1 1 4.6728 13 1 -1 0 1 4.5117 14 1 -1 1 1 5.2609 15 1 0 -1 1 3.7766 16 1 0 0 1 2.1905 17 1 0 1 1 3.1543 18 1 1 1 1 4.8046 19 1 1 0 1 6.2591 20 1 1 -1 1 5.3941 21 1 1 1 0 5.3420 22 1 1 0 0 2.5815 23 1 1 -1 0 4.6961 24 1 1 1 -1 4.6728 25 1 1 0 -1 4.5117 26 1 1 -1 -1 5.2609 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4101 atoms have been selected out of 4175 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 720 240 240 0.00 3 C003 has 87 29 29 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1859 618 618 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 117 39 39 0.00 13 C013 has 477 159 159 0.00 14 C014 has 105 35 35 0.00 Total of13729 atoms and 4568 groups and 4563 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4175 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1380 Number of atoms = 4175 Number of groups = 1385 Number of bonds = 4168 Number of angles = 1484 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1382 Number of HB donors = 2742 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1380 Number of atoms = 4175 Number of groups = 1385 Number of bonds = 4168 Number of angles = 1484 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1382 Number of HB donors = 2742 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.706" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1380" Evaluating: 1380-7 Parameter: NUMWAT <- "1373" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1373" Comparing "1081" and "1373". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.706" Parameter: BOX -> "34.706" Parameter: BOX -> "34.706" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.70600 B = 34.70600 C = 34.70600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8068 2 1 -1 0 -1 6.2602 3 1 -1 1 -1 5.3906 4 1 0 -1 -1 3.1524 5 1 0 0 -1 2.1886 6 1 0 1 -1 3.7738 7 1 -1 -1 0 5.3399 8 1 -1 0 0 2.5808 9 1 -1 1 0 4.6938 10 1 0 -1 0 1.4353 11 1 0 1 0 1.4353 12 1 -1 -1 1 4.6693 13 1 -1 0 1 4.5089 14 1 -1 1 1 5.2579 15 1 0 -1 1 3.7738 16 1 0 0 1 2.1886 17 1 0 1 1 3.1524 18 1 1 1 1 4.8068 19 1 1 0 1 6.2602 20 1 1 -1 1 5.3906 21 1 1 1 0 5.3399 22 1 1 0 0 2.5808 23 1 1 -1 0 4.6938 24 1 1 1 -1 4.6693 25 1 1 0 -1 4.5089 26 1 1 -1 -1 5.2579 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4101 atoms have been selected out of 4175 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1329 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 717 239 239 0.00 3 C003 has 87 29 29 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 501 167 167 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1859 618 618 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 117 39 39 0.00 13 C013 has 477 159 159 0.00 14 C014 has 105 35 35 0.00 Total of13723 atoms and 4566 groups and 4561 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4175 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1379 Number of atoms = 4172 Number of groups = 1384 Number of bonds = 4165 Number of angles = 1483 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1381 Number of HB donors = 2740 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1379 Number of atoms = 4172 Number of groups = 1384 Number of bonds = 4165 Number of angles = 1483 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1381 Number of HB donors = 2740 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.704" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1379" Evaluating: 1379-7 Parameter: NUMWAT <- "1372" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1372" Comparing "1081" and "1372". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.704" Parameter: BOX -> "34.704" Parameter: BOX -> "34.704" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.70400 B = 34.70400 C = 34.70400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8089 2 1 -1 0 -1 6.2614 3 1 -1 1 -1 5.3872 4 1 0 -1 -1 3.1504 5 1 0 0 -1 2.1867 6 1 0 1 -1 3.7711 7 1 -1 -1 0 5.3379 8 1 -1 0 0 2.5800 9 1 -1 1 0 4.6915 10 1 0 -1 0 1.4341 11 1 0 1 0 1.4341 12 1 -1 -1 1 4.6659 13 1 -1 0 1 4.5061 14 1 -1 1 1 5.2548 15 1 0 -1 1 3.7711 16 1 0 0 1 2.1867 17 1 0 1 1 3.1504 18 1 1 1 1 4.8089 19 1 1 0 1 6.2614 20 1 1 -1 1 5.3872 21 1 1 1 0 5.3379 22 1 1 0 0 2.5800 23 1 1 -1 0 4.6915 24 1 1 1 -1 4.6659 25 1 1 0 -1 4.5061 26 1 1 -1 -1 5.2548 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4098 atoms have been selected out of 4172 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 678 OPERATED ON BY TRANSFORMATION C010 RESIDUE 933 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 717 239 239 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1695 565 565 0.00 6 C006 has 498 166 166 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1856 617 617 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1767 589 589 0.00 12 C012 has 117 39 39 0.00 13 C013 has 477 159 159 0.00 14 C014 has 105 35 35 0.00 Total of13726 atoms and 4567 groups and 4562 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 4172 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1377 Number of atoms = 4166 Number of groups = 1382 Number of bonds = 4159 Number of angles = 1481 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1379 Number of HB donors = 2736 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1377 Number of atoms = 4166 Number of groups = 1382 Number of bonds = 4159 Number of angles = 1481 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1379 Number of HB donors = 2736 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.702" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1377" Evaluating: 1377-7 Parameter: NUMWAT <- "1370" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1370" Comparing "1081" and "1370". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.702" Parameter: BOX -> "34.702" Parameter: BOX -> "34.702" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.70200 B = 34.70200 C = 34.70200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8111 2 1 -1 0 -1 6.2626 3 1 -1 1 -1 5.3837 4 1 0 -1 -1 3.1485 5 1 0 0 -1 2.1847 6 1 0 1 -1 3.7683 7 1 -1 -1 0 5.3359 8 1 -1 0 0 2.5792 9 1 -1 1 0 4.6892 10 1 0 -1 0 1.4330 11 1 0 1 0 1.4330 12 1 -1 -1 1 4.6624 13 1 -1 0 1 4.5033 14 1 -1 1 1 5.2517 15 1 0 -1 1 3.7683 16 1 0 0 1 2.1847 17 1 0 1 1 3.1485 18 1 1 1 1 4.8111 19 1 1 0 1 6.2626 20 1 1 -1 1 5.3837 21 1 1 1 0 5.3359 22 1 1 0 0 2.5792 23 1 1 -1 0 4.6892 24 1 1 1 -1 4.6624 25 1 1 0 -1 4.5033 26 1 1 -1 -1 5.2517 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4092 atoms have been selected out of 4166 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 542 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 714 238 238 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1692 564 564 0.00 6 C006 has 498 166 166 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1850 615 615 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 117 39 39 0.00 13 C013 has 477 159 159 0.00 14 C014 has 105 35 35 0.00 Total of13684 atoms and 4553 groups and 4548 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4166 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1376 Number of atoms = 4163 Number of groups = 1381 Number of bonds = 4156 Number of angles = 1480 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1378 Number of HB donors = 2734 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1376 Number of atoms = 4163 Number of groups = 1381 Number of bonds = 4156 Number of angles = 1480 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1378 Number of HB donors = 2734 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.7" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1376" Evaluating: 1376-7 Parameter: NUMWAT <- "1369" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1369" Comparing "1081" and "1369". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.7" Parameter: BOX -> "34.7" Parameter: BOX -> "34.7" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.70000 B = 34.70000 C = 34.70000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8132 2 1 -1 0 -1 6.2638 3 1 -1 1 -1 5.3803 4 1 0 -1 -1 3.1465 5 1 0 0 -1 2.1828 6 1 0 1 -1 3.7655 7 1 -1 -1 0 5.3339 8 1 -1 0 0 2.5784 9 1 -1 1 0 4.6869 10 1 0 -1 0 1.4319 11 1 0 1 0 1.4319 12 1 -1 -1 1 4.6590 13 1 -1 0 1 4.5005 14 1 -1 1 1 5.2486 15 1 0 -1 1 3.7655 16 1 0 0 1 2.1828 17 1 0 1 1 3.1465 18 1 1 1 1 4.8132 19 1 1 0 1 6.2638 20 1 1 -1 1 5.3803 21 1 1 1 0 5.3339 22 1 1 0 0 2.5784 23 1 1 -1 0 4.6869 24 1 1 1 -1 4.6590 25 1 1 0 -1 4.5005 26 1 1 -1 -1 5.2486 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4089 atoms have been selected out of 4163 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 714 238 238 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1692 564 564 0.00 6 C006 has 501 167 167 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1752 584 584 0.00 12 C012 has 117 39 39 0.00 13 C013 has 477 159 159 0.00 14 C014 has 105 35 35 0.00 Total of13684 atoms and 4553 groups and 4548 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4163 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1376 Number of atoms = 4163 Number of groups = 1381 Number of bonds = 4156 Number of angles = 1480 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1378 Number of HB donors = 2734 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1376 Number of atoms = 4163 Number of groups = 1381 Number of bonds = 4156 Number of angles = 1480 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1378 Number of HB donors = 2734 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.698" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1376" Evaluating: 1376-7 Parameter: NUMWAT <- "1369" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1369" Comparing "1081" and "1369". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.698" Parameter: BOX -> "34.698" Parameter: BOX -> "34.698" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.69800 B = 34.69800 C = 34.69800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8154 2 1 -1 0 -1 6.2649 3 1 -1 1 -1 5.3769 4 1 0 -1 -1 3.1446 5 1 0 0 -1 2.1808 6 1 0 1 -1 3.7627 7 1 -1 -1 0 5.3319 8 1 -1 0 0 2.5777 9 1 -1 1 0 4.6846 10 1 0 -1 0 1.4308 11 1 0 1 0 1.4308 12 1 -1 -1 1 4.6555 13 1 -1 0 1 4.4977 14 1 -1 1 1 5.2456 15 1 0 -1 1 3.7627 16 1 0 0 1 2.1808 17 1 0 1 1 3.1446 18 1 1 1 1 4.8154 19 1 1 0 1 6.2649 20 1 1 -1 1 5.3769 21 1 1 1 0 5.3319 22 1 1 0 0 2.5777 23 1 1 -1 0 4.6846 24 1 1 1 -1 4.6555 25 1 1 0 -1 4.4977 26 1 1 -1 -1 5.2456 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4089 atoms have been selected out of 4163 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 714 238 238 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1692 564 564 0.00 6 C006 has 504 168 168 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1752 584 584 0.00 12 C012 has 117 39 39 0.00 13 C013 has 477 159 159 0.00 14 C014 has 105 35 35 0.00 Total of13687 atoms and 4554 groups and 4549 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4163 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1376 Number of atoms = 4163 Number of groups = 1381 Number of bonds = 4156 Number of angles = 1480 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1378 Number of HB donors = 2734 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1376 Number of atoms = 4163 Number of groups = 1381 Number of bonds = 4156 Number of angles = 1480 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1378 Number of HB donors = 2734 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.696" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1376" Evaluating: 1376-7 Parameter: NUMWAT <- "1369" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1369" Comparing "1081" and "1369". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.696" Parameter: BOX -> "34.696" Parameter: BOX -> "34.696" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.69600 B = 34.69600 C = 34.69600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8175 2 1 -1 0 -1 6.2661 3 1 -1 1 -1 5.3734 4 1 0 -1 -1 3.1426 5 1 0 0 -1 2.1789 6 1 0 1 -1 3.7600 7 1 -1 -1 0 5.3299 8 1 -1 0 0 2.5769 9 1 -1 1 0 4.6823 10 1 0 -1 0 1.4297 11 1 0 1 0 1.4297 12 1 -1 -1 1 4.6521 13 1 -1 0 1 4.4949 14 1 -1 1 1 5.2425 15 1 0 -1 1 3.7600 16 1 0 0 1 2.1789 17 1 0 1 1 3.1426 18 1 1 1 1 4.8175 19 1 1 0 1 6.2661 20 1 1 -1 1 5.3734 21 1 1 1 0 5.3299 22 1 1 0 0 2.5769 23 1 1 -1 0 4.6823 24 1 1 1 -1 4.6521 25 1 1 0 -1 4.4949 26 1 1 -1 -1 5.2425 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4089 atoms have been selected out of 4163 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 714 238 238 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1692 564 564 0.00 6 C006 has 504 168 168 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 117 39 39 0.00 13 C013 has 477 159 159 0.00 14 C014 has 105 35 35 0.00 Total of13693 atoms and 4556 groups and 4551 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4163 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1376 Number of atoms = 4163 Number of groups = 1381 Number of bonds = 4156 Number of angles = 1480 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1378 Number of HB donors = 2734 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1376 Number of atoms = 4163 Number of groups = 1381 Number of bonds = 4156 Number of angles = 1480 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1378 Number of HB donors = 2734 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.694" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1376" Evaluating: 1376-7 Parameter: NUMWAT <- "1369" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1369" Comparing "1081" and "1369". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.694" Parameter: BOX -> "34.694" Parameter: BOX -> "34.694" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.69400 B = 34.69400 C = 34.69400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8197 2 1 -1 0 -1 6.2673 3 1 -1 1 -1 5.3700 4 1 0 -1 -1 3.1407 5 1 0 0 -1 2.1770 6 1 0 1 -1 3.7572 7 1 -1 -1 0 5.3279 8 1 -1 0 0 2.5761 9 1 -1 1 0 4.6800 10 1 0 -1 0 1.4286 11 1 0 1 0 1.4286 12 1 -1 -1 1 4.6486 13 1 -1 0 1 4.4922 14 1 -1 1 1 5.2394 15 1 0 -1 1 3.7572 16 1 0 0 1 2.1770 17 1 0 1 1 3.1407 18 1 1 1 1 4.8197 19 1 1 0 1 6.2673 20 1 1 -1 1 5.3700 21 1 1 1 0 5.3279 22 1 1 0 0 2.5761 23 1 1 -1 0 4.6800 24 1 1 1 -1 4.6486 25 1 1 0 -1 4.4922 26 1 1 -1 -1 5.2394 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4089 atoms have been selected out of 4163 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 714 238 238 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1692 564 564 0.00 6 C006 has 504 168 168 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 117 39 39 0.00 13 C013 has 477 159 159 0.00 14 C014 has 105 35 35 0.00 Total of13696 atoms and 4557 groups and 4552 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4163 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1376 Number of atoms = 4163 Number of groups = 1381 Number of bonds = 4156 Number of angles = 1480 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1378 Number of HB donors = 2734 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1376 Number of atoms = 4163 Number of groups = 1381 Number of bonds = 4156 Number of angles = 1480 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1378 Number of HB donors = 2734 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.692" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1376" Evaluating: 1376-7 Parameter: NUMWAT <- "1369" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1369" Comparing "1081" and "1369". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.692" Parameter: BOX -> "34.692" Parameter: BOX -> "34.692" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.69200 B = 34.69200 C = 34.69200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8219 2 1 -1 0 -1 6.2684 3 1 -1 1 -1 5.3665 4 1 0 -1 -1 3.1387 5 1 0 0 -1 2.1750 6 1 0 1 -1 3.7544 7 1 -1 -1 0 5.3259 8 1 -1 0 0 2.5754 9 1 -1 1 0 4.6777 10 1 0 -1 0 1.4275 11 1 0 1 0 1.4275 12 1 -1 -1 1 4.6451 13 1 -1 0 1 4.4894 14 1 -1 1 1 5.2363 15 1 0 -1 1 3.7544 16 1 0 0 1 2.1750 17 1 0 1 1 3.1387 18 1 1 1 1 4.8219 19 1 1 0 1 6.2684 20 1 1 -1 1 5.3665 21 1 1 1 0 5.3259 22 1 1 0 0 2.5754 23 1 1 -1 0 4.6777 24 1 1 1 -1 4.6451 25 1 1 0 -1 4.4894 26 1 1 -1 -1 5.2363 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4089 atoms have been selected out of 4163 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 714 238 238 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1692 564 564 0.00 6 C006 has 504 168 168 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 117 39 39 0.00 13 C013 has 477 159 159 0.00 14 C014 has 105 35 35 0.00 Total of13696 atoms and 4557 groups and 4552 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4163 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1376 Number of atoms = 4163 Number of groups = 1381 Number of bonds = 4156 Number of angles = 1480 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1378 Number of HB donors = 2734 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1376 Number of atoms = 4163 Number of groups = 1381 Number of bonds = 4156 Number of angles = 1480 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1378 Number of HB donors = 2734 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.69" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1376" Evaluating: 1376-7 Parameter: NUMWAT <- "1369" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1369" Comparing "1081" and "1369". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.69" Parameter: BOX -> "34.69" Parameter: BOX -> "34.69" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.69000 B = 34.69000 C = 34.69000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8240 2 1 -1 0 -1 6.2696 3 1 -1 1 -1 5.3631 4 1 0 -1 -1 3.1368 5 1 0 0 -1 2.1731 6 1 0 1 -1 3.7517 7 1 -1 -1 0 5.3239 8 1 -1 0 0 2.5746 9 1 -1 1 0 4.6754 10 1 0 -1 0 1.4264 11 1 0 1 0 1.4264 12 1 -1 -1 1 4.6417 13 1 -1 0 1 4.4866 14 1 -1 1 1 5.2333 15 1 0 -1 1 3.7517 16 1 0 0 1 2.1731 17 1 0 1 1 3.1368 18 1 1 1 1 4.8240 19 1 1 0 1 6.2696 20 1 1 -1 1 5.3631 21 1 1 1 0 5.3239 22 1 1 0 0 2.5746 23 1 1 -1 0 4.6754 24 1 1 1 -1 4.6417 25 1 1 0 -1 4.4866 26 1 1 -1 -1 5.2333 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4089 atoms have been selected out of 4163 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 714 238 238 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1692 564 564 0.00 6 C006 has 504 168 168 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 117 39 39 0.00 13 C013 has 477 159 159 0.00 14 C014 has 105 35 35 0.00 Total of13696 atoms and 4557 groups and 4552 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4163 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1376 Number of atoms = 4163 Number of groups = 1381 Number of bonds = 4156 Number of angles = 1480 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1378 Number of HB donors = 2734 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1376 Number of atoms = 4163 Number of groups = 1381 Number of bonds = 4156 Number of angles = 1480 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1378 Number of HB donors = 2734 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.688" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1376" Evaluating: 1376-7 Parameter: NUMWAT <- "1369" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1369" Comparing "1081" and "1369". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.688" Parameter: BOX -> "34.688" Parameter: BOX -> "34.688" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.68800 B = 34.68800 C = 34.68800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8262 2 1 -1 0 -1 6.2708 3 1 -1 1 -1 5.3596 4 1 0 -1 -1 3.1348 5 1 0 0 -1 2.1711 6 1 0 1 -1 3.7489 7 1 -1 -1 0 5.3219 8 1 -1 0 0 2.5738 9 1 -1 1 0 4.6731 10 1 0 -1 0 1.4253 11 1 0 1 0 1.4253 12 1 -1 -1 1 4.6382 13 1 -1 0 1 4.4838 14 1 -1 1 1 5.2302 15 1 0 -1 1 3.7489 16 1 0 0 1 2.1711 17 1 0 1 1 3.1348 18 1 1 1 1 4.8262 19 1 1 0 1 6.2708 20 1 1 -1 1 5.3596 21 1 1 1 0 5.3219 22 1 1 0 0 2.5738 23 1 1 -1 0 4.6731 24 1 1 1 -1 4.6382 25 1 1 0 -1 4.4838 26 1 1 -1 -1 5.2302 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4089 atoms have been selected out of 4163 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 714 238 238 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1692 564 564 0.00 6 C006 has 504 168 168 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 117 39 39 0.00 13 C013 has 477 159 159 0.00 14 C014 has 105 35 35 0.00 Total of13696 atoms and 4557 groups and 4552 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4163 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1376 Number of atoms = 4163 Number of groups = 1381 Number of bonds = 4156 Number of angles = 1480 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1378 Number of HB donors = 2734 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1376 Number of atoms = 4163 Number of groups = 1381 Number of bonds = 4156 Number of angles = 1480 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1378 Number of HB donors = 2734 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.686" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1376" Evaluating: 1376-7 Parameter: NUMWAT <- "1369" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1369" Comparing "1081" and "1369". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.686" Parameter: BOX -> "34.686" Parameter: BOX -> "34.686" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.68600 B = 34.68600 C = 34.68600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8283 2 1 -1 0 -1 6.2720 3 1 -1 1 -1 5.3562 4 1 0 -1 -1 3.1329 5 1 0 0 -1 2.1692 6 1 0 1 -1 3.7461 7 1 -1 -1 0 5.3199 8 1 -1 0 0 2.5731 9 1 -1 1 0 4.6708 10 1 0 -1 0 1.4242 11 1 0 1 0 1.4242 12 1 -1 -1 1 4.6348 13 1 -1 0 1 4.4810 14 1 -1 1 1 5.2271 15 1 0 -1 1 3.7461 16 1 0 0 1 2.1692 17 1 0 1 1 3.1329 18 1 1 1 1 4.8283 19 1 1 0 1 6.2720 20 1 1 -1 1 5.3562 21 1 1 1 0 5.3199 22 1 1 0 0 2.5731 23 1 1 -1 0 4.6708 24 1 1 1 -1 4.6348 25 1 1 0 -1 4.4810 26 1 1 -1 -1 5.2271 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4089 atoms have been selected out of 4163 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 714 238 238 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1692 564 564 0.00 6 C006 has 504 168 168 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 117 39 39 0.00 13 C013 has 477 159 159 0.00 14 C014 has 105 35 35 0.00 Total of13699 atoms and 4558 groups and 4553 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4163 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1376 Number of atoms = 4163 Number of groups = 1381 Number of bonds = 4156 Number of angles = 1480 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1378 Number of HB donors = 2734 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1376 Number of atoms = 4163 Number of groups = 1381 Number of bonds = 4156 Number of angles = 1480 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1378 Number of HB donors = 2734 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.684" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1376" Evaluating: 1376-7 Parameter: NUMWAT <- "1369" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1369" Comparing "1081" and "1369". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.684" Parameter: BOX -> "34.684" Parameter: BOX -> "34.684" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.68400 B = 34.68400 C = 34.68400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8305 2 1 -1 0 -1 6.2732 3 1 -1 1 -1 5.3527 4 1 0 -1 -1 3.1310 5 1 0 0 -1 2.1673 6 1 0 1 -1 3.7434 7 1 -1 -1 0 5.3179 8 1 -1 0 0 2.5723 9 1 -1 1 0 4.6685 10 1 0 -1 0 1.4231 11 1 0 1 0 1.4231 12 1 -1 -1 1 4.6313 13 1 -1 0 1 4.4782 14 1 -1 1 1 5.2241 15 1 0 -1 1 3.7434 16 1 0 0 1 2.1673 17 1 0 1 1 3.1310 18 1 1 1 1 4.8305 19 1 1 0 1 6.2732 20 1 1 -1 1 5.3527 21 1 1 1 0 5.3179 22 1 1 0 0 2.5723 23 1 1 -1 0 4.6685 24 1 1 1 -1 4.6313 25 1 1 0 -1 4.4782 26 1 1 -1 -1 5.2241 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4089 atoms have been selected out of 4163 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 494 OPERATED ON BY TRANSFORMATION C016 RESIDUE 663 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 369 123 123 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1698 566 566 0.00 6 C006 has 507 169 169 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 114 38 38 0.00 13 C013 has 489 163 163 0.00 14 C014 has 105 35 35 0.00 Total of13699 atoms and 4558 groups and 4553 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 4163 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1374 Number of atoms = 4157 Number of groups = 1379 Number of bonds = 4150 Number of angles = 1478 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1376 Number of HB donors = 2730 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1374 Number of atoms = 4157 Number of groups = 1379 Number of bonds = 4150 Number of angles = 1478 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1376 Number of HB donors = 2730 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.682" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1374" Evaluating: 1374-7 Parameter: NUMWAT <- "1367" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1367" Comparing "1081" and "1367". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.682" Parameter: BOX -> "34.682" Parameter: BOX -> "34.682" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.68200 B = 34.68200 C = 34.68200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8327 2 1 -1 0 -1 6.2743 3 1 -1 1 -1 5.3493 4 1 0 -1 -1 3.1290 5 1 0 0 -1 2.1653 6 1 0 1 -1 3.7406 7 1 -1 -1 0 5.3159 8 1 -1 0 0 2.5716 9 1 -1 1 0 4.6663 10 1 0 -1 0 1.4220 11 1 0 1 0 1.4220 12 1 -1 -1 1 4.6279 13 1 -1 0 1 4.4754 14 1 -1 1 1 5.2210 15 1 0 -1 1 3.7406 16 1 0 0 1 2.1653 17 1 0 1 1 3.1290 18 1 1 1 1 4.8327 19 1 1 0 1 6.2743 20 1 1 -1 1 5.3493 21 1 1 1 0 5.3159 22 1 1 0 0 2.5716 23 1 1 -1 0 4.6663 24 1 1 1 -1 4.6279 25 1 1 0 -1 4.4754 26 1 1 -1 -1 5.2210 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4083 atoms have been selected out of 4157 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 684 228 228 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1692 564 564 0.00 6 C006 has 507 169 169 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1749 583 583 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 105 35 35 0.00 Total of13654 atoms and 4543 groups and 4538 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4157 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1374 Number of atoms = 4157 Number of groups = 1379 Number of bonds = 4150 Number of angles = 1478 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1376 Number of HB donors = 2730 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1374 Number of atoms = 4157 Number of groups = 1379 Number of bonds = 4150 Number of angles = 1478 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1376 Number of HB donors = 2730 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.68" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1374" Evaluating: 1374-7 Parameter: NUMWAT <- "1367" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1367" Comparing "1081" and "1367". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.68" Parameter: BOX -> "34.68" Parameter: BOX -> "34.68" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.68000 B = 34.68000 C = 34.68000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8348 2 1 -1 0 -1 6.2755 3 1 -1 1 -1 5.3459 4 1 0 -1 -1 3.1271 5 1 0 0 -1 2.1634 6 1 0 1 -1 3.7378 7 1 -1 -1 0 5.3139 8 1 -1 0 0 2.5708 9 1 -1 1 0 4.6640 10 1 0 -1 0 1.4209 11 1 0 1 0 1.4209 12 1 -1 -1 1 4.6244 13 1 -1 0 1 4.4727 14 1 -1 1 1 5.2179 15 1 0 -1 1 3.7378 16 1 0 0 1 2.1634 17 1 0 1 1 3.1271 18 1 1 1 1 4.8348 19 1 1 0 1 6.2755 20 1 1 -1 1 5.3459 21 1 1 1 0 5.3139 22 1 1 0 0 2.5708 23 1 1 -1 0 4.6640 24 1 1 1 -1 4.6244 25 1 1 0 -1 4.4727 26 1 1 -1 -1 5.2179 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4083 atoms have been selected out of 4157 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 684 228 228 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1692 564 564 0.00 6 C006 has 507 169 169 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1749 583 583 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 105 35 35 0.00 Total of13654 atoms and 4543 groups and 4538 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4157 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1374 Number of atoms = 4157 Number of groups = 1379 Number of bonds = 4150 Number of angles = 1478 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1376 Number of HB donors = 2730 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1374 Number of atoms = 4157 Number of groups = 1379 Number of bonds = 4150 Number of angles = 1478 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1376 Number of HB donors = 2730 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.678" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1374" Evaluating: 1374-7 Parameter: NUMWAT <- "1367" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1367" Comparing "1081" and "1367". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.678" Parameter: BOX -> "34.678" Parameter: BOX -> "34.678" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.67800 B = 34.67800 C = 34.67800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8370 2 1 -1 0 -1 6.2767 3 1 -1 1 -1 5.3424 4 1 0 -1 -1 3.1252 5 1 0 0 -1 2.1615 6 1 0 1 -1 3.7350 7 1 -1 -1 0 5.3119 8 1 -1 0 0 2.5700 9 1 -1 1 0 4.6617 10 1 0 -1 0 1.4198 11 1 0 1 0 1.4198 12 1 -1 -1 1 4.6210 13 1 -1 0 1 4.4699 14 1 -1 1 1 5.2149 15 1 0 -1 1 3.7350 16 1 0 0 1 2.1615 17 1 0 1 1 3.1252 18 1 1 1 1 4.8370 19 1 1 0 1 6.2767 20 1 1 -1 1 5.3424 21 1 1 1 0 5.3119 22 1 1 0 0 2.5700 23 1 1 -1 0 4.6617 24 1 1 1 -1 4.6210 25 1 1 0 -1 4.4699 26 1 1 -1 -1 5.2149 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4083 atoms have been selected out of 4157 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 684 228 228 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1692 564 564 0.00 6 C006 has 507 169 169 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1749 583 583 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 105 35 35 0.00 Total of13654 atoms and 4543 groups and 4538 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4157 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1374 Number of atoms = 4157 Number of groups = 1379 Number of bonds = 4150 Number of angles = 1478 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1376 Number of HB donors = 2730 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1374 Number of atoms = 4157 Number of groups = 1379 Number of bonds = 4150 Number of angles = 1478 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1376 Number of HB donors = 2730 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.676" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1374" Evaluating: 1374-7 Parameter: NUMWAT <- "1367" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1367" Comparing "1081" and "1367". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.676" Parameter: BOX -> "34.676" Parameter: BOX -> "34.676" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.67600 B = 34.67600 C = 34.67600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8392 2 1 -1 0 -1 6.2779 3 1 -1 1 -1 5.3390 4 1 0 -1 -1 3.1232 5 1 0 0 -1 2.1595 6 1 0 1 -1 3.7323 7 1 -1 -1 0 5.3099 8 1 -1 0 0 2.5693 9 1 -1 1 0 4.6594 10 1 0 -1 0 1.4187 11 1 0 1 0 1.4187 12 1 -1 -1 1 4.6175 13 1 -1 0 1 4.4671 14 1 -1 1 1 5.2118 15 1 0 -1 1 3.7323 16 1 0 0 1 2.1595 17 1 0 1 1 3.1232 18 1 1 1 1 4.8392 19 1 1 0 1 6.2779 20 1 1 -1 1 5.3390 21 1 1 1 0 5.3099 22 1 1 0 0 2.5693 23 1 1 -1 0 4.6594 24 1 1 1 -1 4.6175 25 1 1 0 -1 4.4671 26 1 1 -1 -1 5.2118 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4083 atoms have been selected out of 4157 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1037 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 507 169 169 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1749 583 583 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 0.00 Total of13654 atoms and 4543 groups and 4538 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4157 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1373 Number of atoms = 4154 Number of groups = 1378 Number of bonds = 4147 Number of angles = 1477 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1375 Number of HB donors = 2728 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1373 Number of atoms = 4154 Number of groups = 1378 Number of bonds = 4147 Number of angles = 1477 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1375 Number of HB donors = 2728 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.674" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1373" Evaluating: 1373-7 Parameter: NUMWAT <- "1366" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1366" Comparing "1081" and "1366". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.674" Parameter: BOX -> "34.674" Parameter: BOX -> "34.674" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.67400 B = 34.67400 C = 34.67400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8414 2 1 -1 0 -1 6.2791 3 1 -1 1 -1 5.3355 4 1 0 -1 -1 3.1213 5 1 0 0 -1 2.1576 6 1 0 1 -1 3.7295 7 1 -1 -1 0 5.3079 8 1 -1 0 0 2.5685 9 1 -1 1 0 4.6571 10 1 0 -1 0 1.4176 11 1 0 1 0 1.4176 12 1 -1 -1 1 4.6141 13 1 -1 0 1 4.4643 14 1 -1 1 1 5.2087 15 1 0 -1 1 3.7295 16 1 0 0 1 2.1576 17 1 0 1 1 3.1213 18 1 1 1 1 4.8414 19 1 1 0 1 6.2791 20 1 1 -1 1 5.3355 21 1 1 1 0 5.3079 22 1 1 0 0 2.5685 23 1 1 -1 0 4.6571 24 1 1 1 -1 4.6141 25 1 1 0 -1 4.4643 26 1 1 -1 -1 5.2087 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4080 atoms have been selected out of 4154 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 684 228 228 0.00 3 C003 has 84 28 28 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 507 169 169 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1746 582 582 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 0.00 Total of13645 atoms and 4540 groups and 4535 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4154 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1373 Number of atoms = 4154 Number of groups = 1378 Number of bonds = 4147 Number of angles = 1477 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1375 Number of HB donors = 2728 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1373 Number of atoms = 4154 Number of groups = 1378 Number of bonds = 4147 Number of angles = 1477 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1375 Number of HB donors = 2728 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.672" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1373" Evaluating: 1373-7 Parameter: NUMWAT <- "1366" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1366" Comparing "1081" and "1366". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.672" Parameter: BOX -> "34.672" Parameter: BOX -> "34.672" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.67200 B = 34.67200 C = 34.67200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8435 2 1 -1 0 -1 6.2803 3 1 -1 1 -1 5.3321 4 1 0 -1 -1 3.1194 5 1 0 0 -1 2.1556 6 1 0 1 -1 3.7267 7 1 -1 -1 0 5.3059 8 1 -1 0 0 2.5678 9 1 -1 1 0 4.6548 10 1 0 -1 0 1.4165 11 1 0 1 0 1.4165 12 1 -1 -1 1 4.6106 13 1 -1 0 1 4.4615 14 1 -1 1 1 5.2057 15 1 0 -1 1 3.7267 16 1 0 0 1 2.1556 17 1 0 1 1 3.1194 18 1 1 1 1 4.8435 19 1 1 0 1 6.2803 20 1 1 -1 1 5.3321 21 1 1 1 0 5.3059 22 1 1 0 0 2.5678 23 1 1 -1 0 4.6548 24 1 1 1 -1 4.6106 25 1 1 0 -1 4.4615 26 1 1 -1 -1 5.2057 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4080 atoms have been selected out of 4154 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 684 228 228 0.00 3 C003 has 84 28 28 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1692 564 564 0.00 6 C006 has 507 169 169 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1749 583 583 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 0.00 Total of13651 atoms and 4542 groups and 4537 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4154 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1373 Number of atoms = 4154 Number of groups = 1378 Number of bonds = 4147 Number of angles = 1477 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1375 Number of HB donors = 2728 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1373 Number of atoms = 4154 Number of groups = 1378 Number of bonds = 4147 Number of angles = 1477 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1375 Number of HB donors = 2728 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.67" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1373" Evaluating: 1373-7 Parameter: NUMWAT <- "1366" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1366" Comparing "1081" and "1366". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.67" Parameter: BOX -> "34.67" Parameter: BOX -> "34.67" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.67000 B = 34.67000 C = 34.67000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8457 2 1 -1 0 -1 6.2815 3 1 -1 1 -1 5.3286 4 1 0 -1 -1 3.1175 5 1 0 0 -1 2.1537 6 1 0 1 -1 3.7240 7 1 -1 -1 0 5.3039 8 1 -1 0 0 2.5670 9 1 -1 1 0 4.6525 10 1 0 -1 0 1.4154 11 1 0 1 0 1.4154 12 1 -1 -1 1 4.6071 13 1 -1 0 1 4.4587 14 1 -1 1 1 5.2026 15 1 0 -1 1 3.7240 16 1 0 0 1 2.1537 17 1 0 1 1 3.1175 18 1 1 1 1 4.8457 19 1 1 0 1 6.2815 20 1 1 -1 1 5.3286 21 1 1 1 0 5.3039 22 1 1 0 0 2.5670 23 1 1 -1 0 4.6525 24 1 1 1 -1 4.6071 25 1 1 0 -1 4.4587 26 1 1 -1 -1 5.2026 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4080 atoms have been selected out of 4154 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 472 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 684 228 228 0.00 3 C003 has 84 28 28 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1692 564 564 0.00 6 C006 has 507 169 169 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1752 584 584 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 0.00 Total of13657 atoms and 4544 groups and 4539 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4154 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1372 Number of atoms = 4151 Number of groups = 1377 Number of bonds = 4144 Number of angles = 1476 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1374 Number of HB donors = 2726 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1372 Number of atoms = 4151 Number of groups = 1377 Number of bonds = 4144 Number of angles = 1476 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1374 Number of HB donors = 2726 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.668" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1372" Evaluating: 1372-7 Parameter: NUMWAT <- "1365" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1365" Comparing "1081" and "1365". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.668" Parameter: BOX -> "34.668" Parameter: BOX -> "34.668" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.66800 B = 34.66800 C = 34.66800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8479 2 1 -1 0 -1 6.2826 3 1 -1 1 -1 5.3252 4 1 0 -1 -1 3.1155 5 1 0 0 -1 2.1518 6 1 0 1 -1 3.7212 7 1 -1 -1 0 5.3019 8 1 -1 0 0 2.5663 9 1 -1 1 0 4.6502 10 1 0 -1 0 1.4143 11 1 0 1 0 1.4143 12 1 -1 -1 1 4.6037 13 1 -1 0 1 4.4559 14 1 -1 1 1 5.1995 15 1 0 -1 1 3.7212 16 1 0 0 1 2.1518 17 1 0 1 1 3.1155 18 1 1 1 1 4.8479 19 1 1 0 1 6.2826 20 1 1 -1 1 5.3252 21 1 1 1 0 5.3019 22 1 1 0 0 2.5663 23 1 1 -1 0 4.6502 24 1 1 1 -1 4.6037 25 1 1 0 -1 4.4559 26 1 1 -1 -1 5.1995 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4077 atoms have been selected out of 4151 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 684 228 228 0.00 3 C003 has 84 28 28 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1692 564 564 0.00 6 C006 has 507 169 169 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1746 582 582 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 0.00 Total of13648 atoms and 4541 groups and 4536 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4151 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1372 Number of atoms = 4151 Number of groups = 1377 Number of bonds = 4144 Number of angles = 1476 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1374 Number of HB donors = 2726 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1372 Number of atoms = 4151 Number of groups = 1377 Number of bonds = 4144 Number of angles = 1476 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1374 Number of HB donors = 2726 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.666" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1372" Evaluating: 1372-7 Parameter: NUMWAT <- "1365" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1365" Comparing "1081" and "1365". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.666" Parameter: BOX -> "34.666" Parameter: BOX -> "34.666" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.66600 B = 34.66600 C = 34.66600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8501 2 1 -1 0 -1 6.2838 3 1 -1 1 -1 5.3217 4 1 0 -1 -1 3.1136 5 1 0 0 -1 2.1498 6 1 0 1 -1 3.7184 7 1 -1 -1 0 5.2999 8 1 -1 0 0 2.5655 9 1 -1 1 0 4.6479 10 1 0 -1 0 1.4133 11 1 0 1 0 1.4133 12 1 -1 -1 1 4.6002 13 1 -1 0 1 4.4532 14 1 -1 1 1 5.1965 15 1 0 -1 1 3.7184 16 1 0 0 1 2.1498 17 1 0 1 1 3.1136 18 1 1 1 1 4.8501 19 1 1 0 1 6.2838 20 1 1 -1 1 5.3217 21 1 1 1 0 5.2999 22 1 1 0 0 2.5655 23 1 1 -1 0 4.6479 24 1 1 1 -1 4.6002 25 1 1 0 -1 4.4532 26 1 1 -1 -1 5.1965 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4077 atoms have been selected out of 4151 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 684 228 228 0.00 3 C003 has 84 28 28 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1692 564 564 0.00 6 C006 has 507 169 169 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1746 582 582 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 0.00 Total of13648 atoms and 4541 groups and 4536 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4151 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1372 Number of atoms = 4151 Number of groups = 1377 Number of bonds = 4144 Number of angles = 1476 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1374 Number of HB donors = 2726 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1372 Number of atoms = 4151 Number of groups = 1377 Number of bonds = 4144 Number of angles = 1476 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1374 Number of HB donors = 2726 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.664" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1372" Evaluating: 1372-7 Parameter: NUMWAT <- "1365" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1365" Comparing "1081" and "1365". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.664" Parameter: BOX -> "34.664" Parameter: BOX -> "34.664" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.66400 B = 34.66400 C = 34.66400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8522 2 1 -1 0 -1 6.2850 3 1 -1 1 -1 5.3183 4 1 0 -1 -1 3.1117 5 1 0 0 -1 2.1479 6 1 0 1 -1 3.7157 7 1 -1 -1 0 5.2980 8 1 -1 0 0 2.5648 9 1 -1 1 0 4.6457 10 1 0 -1 0 1.4122 11 1 0 1 0 1.4122 12 1 -1 -1 1 4.5968 13 1 -1 0 1 4.4504 14 1 -1 1 1 5.1934 15 1 0 -1 1 3.7157 16 1 0 0 1 2.1479 17 1 0 1 1 3.1117 18 1 1 1 1 4.8522 19 1 1 0 1 6.2850 20 1 1 -1 1 5.3183 21 1 1 1 0 5.2980 22 1 1 0 0 2.5648 23 1 1 -1 0 4.6457 24 1 1 1 -1 4.5968 25 1 1 0 -1 4.4504 26 1 1 -1 -1 5.1934 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4077 atoms have been selected out of 4151 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 761 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 504 168 168 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1746 582 582 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 0.00 Total of13645 atoms and 4540 groups and 4535 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4151 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1371 Number of atoms = 4148 Number of groups = 1376 Number of bonds = 4141 Number of angles = 1475 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1373 Number of HB donors = 2724 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1371 Number of atoms = 4148 Number of groups = 1376 Number of bonds = 4141 Number of angles = 1475 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1373 Number of HB donors = 2724 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.662" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1371" Evaluating: 1371-7 Parameter: NUMWAT <- "1364" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1364" Comparing "1081" and "1364". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.662" Parameter: BOX -> "34.662" Parameter: BOX -> "34.662" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.66200 B = 34.66200 C = 34.66200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8544 2 1 -1 0 -1 6.2862 3 1 -1 1 -1 5.3149 4 1 0 -1 -1 3.1098 5 1 0 0 -1 2.1459 6 1 0 1 -1 3.7129 7 1 -1 -1 0 5.2960 8 1 -1 0 0 2.5640 9 1 -1 1 0 4.6434 10 1 0 -1 0 1.4111 11 1 0 1 0 1.4111 12 1 -1 -1 1 4.5933 13 1 -1 0 1 4.4476 14 1 -1 1 1 5.1903 15 1 0 -1 1 3.7129 16 1 0 0 1 2.1459 17 1 0 1 1 3.1098 18 1 1 1 1 4.8544 19 1 1 0 1 6.2862 20 1 1 -1 1 5.3149 21 1 1 1 0 5.2960 22 1 1 0 0 2.5640 23 1 1 -1 0 4.6434 24 1 1 1 -1 4.5933 25 1 1 0 -1 4.4476 26 1 1 -1 -1 5.1903 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4074 atoms have been selected out of 4148 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 504 168 168 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1746 582 582 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 0.00 Total of13645 atoms and 4540 groups and 4535 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4148 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1371 Number of atoms = 4148 Number of groups = 1376 Number of bonds = 4141 Number of angles = 1475 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1373 Number of HB donors = 2724 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1371 Number of atoms = 4148 Number of groups = 1376 Number of bonds = 4141 Number of angles = 1475 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1373 Number of HB donors = 2724 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.66" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1371" Evaluating: 1371-7 Parameter: NUMWAT <- "1364" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1364" Comparing "1081" and "1364". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.66" Parameter: BOX -> "34.66" Parameter: BOX -> "34.66" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.66000 B = 34.66000 C = 34.66000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8566 2 1 -1 0 -1 6.2874 3 1 -1 1 -1 5.3114 4 1 0 -1 -1 3.1078 5 1 0 0 -1 2.1440 6 1 0 1 -1 3.7101 7 1 -1 -1 0 5.2940 8 1 -1 0 0 2.5633 9 1 -1 1 0 4.6411 10 1 0 -1 0 1.4100 11 1 0 1 0 1.4100 12 1 -1 -1 1 4.5899 13 1 -1 0 1 4.4448 14 1 -1 1 1 5.1873 15 1 0 -1 1 3.7101 16 1 0 0 1 2.1440 17 1 0 1 1 3.1078 18 1 1 1 1 4.8566 19 1 1 0 1 6.2874 20 1 1 -1 1 5.3114 21 1 1 1 0 5.2940 22 1 1 0 0 2.5633 23 1 1 -1 0 4.6411 24 1 1 1 -1 4.5899 25 1 1 0 -1 4.4448 26 1 1 -1 -1 5.1873 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4074 atoms have been selected out of 4148 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 504 168 168 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1746 582 582 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 0.00 Total of13645 atoms and 4540 groups and 4535 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4148 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1371 Number of atoms = 4148 Number of groups = 1376 Number of bonds = 4141 Number of angles = 1475 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1373 Number of HB donors = 2724 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1371 Number of atoms = 4148 Number of groups = 1376 Number of bonds = 4141 Number of angles = 1475 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1373 Number of HB donors = 2724 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.658" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1371" Evaluating: 1371-7 Parameter: NUMWAT <- "1364" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1364" Comparing "1081" and "1364". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.658" Parameter: BOX -> "34.658" Parameter: BOX -> "34.658" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.65800 B = 34.65800 C = 34.65800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8588 2 1 -1 0 -1 6.2886 3 1 -1 1 -1 5.3080 4 1 0 -1 -1 3.1059 5 1 0 0 -1 2.1421 6 1 0 1 -1 3.7074 7 1 -1 -1 0 5.2920 8 1 -1 0 0 2.5626 9 1 -1 1 0 4.6388 10 1 0 -1 0 1.4089 11 1 0 1 0 1.4089 12 1 -1 -1 1 4.5864 13 1 -1 0 1 4.4420 14 1 -1 1 1 5.1842 15 1 0 -1 1 3.7074 16 1 0 0 1 2.1421 17 1 0 1 1 3.1059 18 1 1 1 1 4.8588 19 1 1 0 1 6.2886 20 1 1 -1 1 5.3080 21 1 1 1 0 5.2920 22 1 1 0 0 2.5626 23 1 1 -1 0 4.6388 24 1 1 1 -1 4.5864 25 1 1 0 -1 4.4420 26 1 1 -1 -1 5.1842 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4074 atoms have been selected out of 4148 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1208 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 606 202 202 0.00 5 C005 has 1692 564 564 0.00 6 C006 has 504 168 168 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1746 582 582 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 0.00 Total of13645 atoms and 4540 groups and 4535 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4148 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.656" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1370" Evaluating: 1370-7 Parameter: NUMWAT <- "1363" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1363" Comparing "1081" and "1363". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.656" Parameter: BOX -> "34.656" Parameter: BOX -> "34.656" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.65600 B = 34.65600 C = 34.65600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8610 2 1 -1 0 -1 6.2898 3 1 -1 1 -1 5.3045 4 1 0 -1 -1 3.1040 5 1 0 0 -1 2.1401 6 1 0 1 -1 3.7046 7 1 -1 -1 0 5.2900 8 1 -1 0 0 2.5618 9 1 -1 1 0 4.6365 10 1 0 -1 0 1.4079 11 1 0 1 0 1.4079 12 1 -1 -1 1 4.5830 13 1 -1 0 1 4.4392 14 1 -1 1 1 5.1811 15 1 0 -1 1 3.7046 16 1 0 0 1 2.1401 17 1 0 1 1 3.1040 18 1 1 1 1 4.8610 19 1 1 0 1 6.2898 20 1 1 -1 1 5.3045 21 1 1 1 0 5.2900 22 1 1 0 0 2.5618 23 1 1 -1 0 4.6365 24 1 1 1 -1 4.5830 25 1 1 0 -1 4.4392 26 1 1 -1 -1 5.1811 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4071 atoms have been selected out of 4145 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 606 202 202 0.00 5 C005 has 1686 562 562 0.00 6 C006 has 504 168 168 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1743 581 581 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 0.00 Total of13630 atoms and 4535 groups and 4530 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4145 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.654" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1370" Evaluating: 1370-7 Parameter: NUMWAT <- "1363" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1363" Comparing "1081" and "1363". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.654" Parameter: BOX -> "34.654" Parameter: BOX -> "34.654" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.65400 B = 34.65400 C = 34.65400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8632 2 1 -1 0 -1 6.2910 3 1 -1 1 -1 5.3011 4 1 0 -1 -1 3.1021 5 1 0 0 -1 2.1382 6 1 0 1 -1 3.7018 7 1 -1 -1 0 5.2880 8 1 -1 0 0 2.5611 9 1 -1 1 0 4.6342 10 1 0 -1 0 1.4068 11 1 0 1 0 1.4068 12 1 -1 -1 1 4.5795 13 1 -1 0 1 4.4364 14 1 -1 1 1 5.1781 15 1 0 -1 1 3.7018 16 1 0 0 1 2.1382 17 1 0 1 1 3.1021 18 1 1 1 1 4.8632 19 1 1 0 1 6.2910 20 1 1 -1 1 5.3011 21 1 1 1 0 5.2880 22 1 1 0 0 2.5611 23 1 1 -1 0 4.6342 24 1 1 1 -1 4.5795 25 1 1 0 -1 4.4364 26 1 1 -1 -1 5.1781 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4071 atoms have been selected out of 4145 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 606 202 202 0.00 5 C005 has 1686 562 562 0.00 6 C006 has 504 168 168 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1743 581 581 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 0.00 Total of13630 atoms and 4535 groups and 4530 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4145 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.652" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1370" Evaluating: 1370-7 Parameter: NUMWAT <- "1363" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1363" Comparing "1081" and "1363". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.652" Parameter: BOX -> "34.652" Parameter: BOX -> "34.652" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.65200 B = 34.65200 C = 34.65200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8653 2 1 -1 0 -1 6.2922 3 1 -1 1 -1 5.2976 4 1 0 -1 -1 3.1002 5 1 0 0 -1 2.1363 6 1 0 1 -1 3.6991 7 1 -1 -1 0 5.2860 8 1 -1 0 0 2.5603 9 1 -1 1 0 4.6319 10 1 0 -1 0 1.4057 11 1 0 1 0 1.4057 12 1 -1 -1 1 4.5761 13 1 -1 0 1 4.4337 14 1 -1 1 1 5.1750 15 1 0 -1 1 3.6991 16 1 0 0 1 2.1363 17 1 0 1 1 3.1002 18 1 1 1 1 4.8653 19 1 1 0 1 6.2922 20 1 1 -1 1 5.2976 21 1 1 1 0 5.2860 22 1 1 0 0 2.5603 23 1 1 -1 0 4.6319 24 1 1 1 -1 4.5761 25 1 1 0 -1 4.4337 26 1 1 -1 -1 5.1750 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4071 atoms have been selected out of 4145 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 606 202 202 0.00 5 C005 has 1686 562 562 0.00 6 C006 has 504 168 168 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1743 581 581 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 0.00 Total of13630 atoms and 4535 groups and 4530 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4145 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.65" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1370" Evaluating: 1370-7 Parameter: NUMWAT <- "1363" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1363" Comparing "1081" and "1363". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.65" Parameter: BOX -> "34.65" Parameter: BOX -> "34.65" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.65000 B = 34.65000 C = 34.65000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8675 2 1 -1 0 -1 6.2934 3 1 -1 1 -1 5.2942 4 1 0 -1 -1 3.0983 5 1 0 0 -1 2.1343 6 1 0 1 -1 3.6963 7 1 -1 -1 0 5.2840 8 1 -1 0 0 2.5596 9 1 -1 1 0 4.6297 10 1 0 -1 0 1.4047 11 1 0 1 0 1.4047 12 1 -1 -1 1 4.5726 13 1 -1 0 1 4.4309 14 1 -1 1 1 5.1719 15 1 0 -1 1 3.6963 16 1 0 0 1 2.1343 17 1 0 1 1 3.0983 18 1 1 1 1 4.8675 19 1 1 0 1 6.2934 20 1 1 -1 1 5.2942 21 1 1 1 0 5.2840 22 1 1 0 0 2.5596 23 1 1 -1 0 4.6297 24 1 1 1 -1 4.5726 25 1 1 0 -1 4.4309 26 1 1 -1 -1 5.1719 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4071 atoms have been selected out of 4145 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1686 562 562 0.00 6 C006 has 504 168 168 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1743 581 581 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 0.00 Total of13633 atoms and 4536 groups and 4531 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4145 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.648" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1370" Evaluating: 1370-7 Parameter: NUMWAT <- "1363" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1363" Comparing "1081" and "1363". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.648" Parameter: BOX -> "34.648" Parameter: BOX -> "34.648" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.64800 B = 34.64800 C = 34.64800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8697 2 1 -1 0 -1 6.2946 3 1 -1 1 -1 5.2908 4 1 0 -1 -1 3.0963 5 1 0 0 -1 2.1324 6 1 0 1 -1 3.6935 7 1 -1 -1 0 5.2820 8 1 -1 0 0 2.5589 9 1 -1 1 0 4.6274 10 1 0 -1 0 1.4036 11 1 0 1 0 1.4036 12 1 -1 -1 1 4.5691 13 1 -1 0 1 4.4281 14 1 -1 1 1 5.1689 15 1 0 -1 1 3.6935 16 1 0 0 1 2.1324 17 1 0 1 1 3.0963 18 1 1 1 1 4.8697 19 1 1 0 1 6.2946 20 1 1 -1 1 5.2908 21 1 1 1 0 5.2820 22 1 1 0 0 2.5589 23 1 1 -1 0 4.6274 24 1 1 1 -1 4.5691 25 1 1 0 -1 4.4281 26 1 1 -1 -1 5.1689 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4071 atoms have been selected out of 4145 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1686 562 562 0.00 6 C006 has 504 168 168 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1743 581 581 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 0.00 Total of13633 atoms and 4536 groups and 4531 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4145 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.646" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1370" Evaluating: 1370-7 Parameter: NUMWAT <- "1363" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1363" Comparing "1081" and "1363". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.646" Parameter: BOX -> "34.646" Parameter: BOX -> "34.646" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.64600 B = 34.64600 C = 34.64600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8719 2 1 -1 0 -1 6.2958 3 1 -1 1 -1 5.2873 4 1 0 -1 -1 3.0944 5 1 0 0 -1 2.1305 6 1 0 1 -1 3.6908 7 1 -1 -1 0 5.2801 8 1 -1 0 0 2.5581 9 1 -1 1 0 4.6251 10 1 0 -1 0 1.4025 11 1 0 1 0 1.4025 12 1 -1 -1 1 4.5657 13 1 -1 0 1 4.4253 14 1 -1 1 1 5.1658 15 1 0 -1 1 3.6908 16 1 0 0 1 2.1305 17 1 0 1 1 3.0944 18 1 1 1 1 4.8719 19 1 1 0 1 6.2958 20 1 1 -1 1 5.2873 21 1 1 1 0 5.2801 22 1 1 0 0 2.5581 23 1 1 -1 0 4.6251 24 1 1 1 -1 4.5657 25 1 1 0 -1 4.4253 26 1 1 -1 -1 5.1658 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4071 atoms have been selected out of 4145 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 504 168 168 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1743 581 581 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13642 atoms and 4539 groups and 4534 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4145 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.644" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1370" Evaluating: 1370-7 Parameter: NUMWAT <- "1363" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1363" Comparing "1081" and "1363". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.644" Parameter: BOX -> "34.644" Parameter: BOX -> "34.644" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.64400 B = 34.64400 C = 34.64400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8741 2 1 -1 0 -1 6.2970 3 1 -1 1 -1 5.2839 4 1 0 -1 -1 3.0925 5 1 0 0 -1 2.1285 6 1 0 1 -1 3.6880 7 1 -1 -1 0 5.2781 8 1 -1 0 0 2.5574 9 1 -1 1 0 4.6228 10 1 0 -1 0 1.4015 11 1 0 1 0 1.4015 12 1 -1 -1 1 4.5622 13 1 -1 0 1 4.4225 14 1 -1 1 1 5.1628 15 1 0 -1 1 3.6880 16 1 0 0 1 2.1285 17 1 0 1 1 3.0925 18 1 1 1 1 4.8741 19 1 1 0 1 6.2970 20 1 1 -1 1 5.2839 21 1 1 1 0 5.2781 22 1 1 0 0 2.5574 23 1 1 -1 0 4.6228 24 1 1 1 -1 4.5622 25 1 1 0 -1 4.4225 26 1 1 -1 -1 5.1628 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4071 atoms have been selected out of 4145 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 507 169 169 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1743 581 581 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13648 atoms and 4541 groups and 4536 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4145 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.642" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1370" Evaluating: 1370-7 Parameter: NUMWAT <- "1363" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1363" Comparing "1081" and "1363". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.642" Parameter: BOX -> "34.642" Parameter: BOX -> "34.642" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.64200 B = 34.64200 C = 34.64200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8763 2 1 -1 0 -1 6.2982 3 1 -1 1 -1 5.2804 4 1 0 -1 -1 3.0906 5 1 0 0 -1 2.1266 6 1 0 1 -1 3.6852 7 1 -1 -1 0 5.2761 8 1 -1 0 0 2.5567 9 1 -1 1 0 4.6205 10 1 0 -1 0 1.4004 11 1 0 1 0 1.4004 12 1 -1 -1 1 4.5588 13 1 -1 0 1 4.4197 14 1 -1 1 1 5.1597 15 1 0 -1 1 3.6852 16 1 0 0 1 2.1266 17 1 0 1 1 3.0906 18 1 1 1 1 4.8763 19 1 1 0 1 6.2982 20 1 1 -1 1 5.2804 21 1 1 1 0 5.2761 22 1 1 0 0 2.5567 23 1 1 -1 0 4.6205 24 1 1 1 -1 4.5588 25 1 1 0 -1 4.4197 26 1 1 -1 -1 5.1597 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4071 atoms have been selected out of 4145 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 507 169 169 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1743 581 581 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13648 atoms and 4541 groups and 4536 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4145 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.64" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1370" Evaluating: 1370-7 Parameter: NUMWAT <- "1363" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1363" Comparing "1081" and "1363". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.64" Parameter: BOX -> "34.64" Parameter: BOX -> "34.64" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.64000 B = 34.64000 C = 34.64000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8785 2 1 -1 0 -1 6.2994 3 1 -1 1 -1 5.2770 4 1 0 -1 -1 3.0887 5 1 0 0 -1 2.1246 6 1 0 1 -1 3.6824 7 1 -1 -1 0 5.2741 8 1 -1 0 0 2.5559 9 1 -1 1 0 4.6183 10 1 0 -1 0 1.3994 11 1 0 1 0 1.3994 12 1 -1 -1 1 4.5553 13 1 -1 0 1 4.4170 14 1 -1 1 1 5.1566 15 1 0 -1 1 3.6824 16 1 0 0 1 2.1246 17 1 0 1 1 3.0887 18 1 1 1 1 4.8785 19 1 1 0 1 6.2994 20 1 1 -1 1 5.2770 21 1 1 1 0 5.2741 22 1 1 0 0 2.5559 23 1 1 -1 0 4.6183 24 1 1 1 -1 4.5553 25 1 1 0 -1 4.4170 26 1 1 -1 -1 5.1566 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4071 atoms have been selected out of 4145 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 510 170 170 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1746 582 582 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13654 atoms and 4543 groups and 4538 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4145 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.638" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1370" Evaluating: 1370-7 Parameter: NUMWAT <- "1363" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1363" Comparing "1081" and "1363". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.638" Parameter: BOX -> "34.638" Parameter: BOX -> "34.638" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.63800 B = 34.63800 C = 34.63800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8807 2 1 -1 0 -1 6.3006 3 1 -1 1 -1 5.2735 4 1 0 -1 -1 3.0868 5 1 0 0 -1 2.1227 6 1 0 1 -1 3.6797 7 1 -1 -1 0 5.2721 8 1 -1 0 0 2.5552 9 1 -1 1 0 4.6160 10 1 0 -1 0 1.3983 11 1 0 1 0 1.3983 12 1 -1 -1 1 4.5519 13 1 -1 0 1 4.4142 14 1 -1 1 1 5.1536 15 1 0 -1 1 3.6797 16 1 0 0 1 2.1227 17 1 0 1 1 3.0868 18 1 1 1 1 4.8807 19 1 1 0 1 6.3006 20 1 1 -1 1 5.2735 21 1 1 1 0 5.2721 22 1 1 0 0 2.5552 23 1 1 -1 0 4.6160 24 1 1 1 -1 4.5519 25 1 1 0 -1 4.4142 26 1 1 -1 -1 5.1536 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4071 atoms have been selected out of 4145 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 510 170 170 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1746 582 582 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13654 atoms and 4543 groups and 4538 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4145 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.636" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1370" Evaluating: 1370-7 Parameter: NUMWAT <- "1363" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1363" Comparing "1081" and "1363". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.636" Parameter: BOX -> "34.636" Parameter: BOX -> "34.636" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.63600 B = 34.63600 C = 34.63600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8829 2 1 -1 0 -1 6.3018 3 1 -1 1 -1 5.2701 4 1 0 -1 -1 3.0849 5 1 0 0 -1 2.1208 6 1 0 1 -1 3.6769 7 1 -1 -1 0 5.2701 8 1 -1 0 0 2.5545 9 1 -1 1 0 4.6137 10 1 0 -1 0 1.3973 11 1 0 1 0 1.3973 12 1 -1 -1 1 4.5484 13 1 -1 0 1 4.4114 14 1 -1 1 1 5.1505 15 1 0 -1 1 3.6769 16 1 0 0 1 2.1208 17 1 0 1 1 3.0849 18 1 1 1 1 4.8829 19 1 1 0 1 6.3018 20 1 1 -1 1 5.2701 21 1 1 1 0 5.2701 22 1 1 0 0 2.5545 23 1 1 -1 0 4.6137 24 1 1 1 -1 4.5484 25 1 1 0 -1 4.4114 26 1 1 -1 -1 5.1505 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4071 atoms have been selected out of 4145 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 510 170 170 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1746 582 582 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13654 atoms and 4543 groups and 4538 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4145 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.634" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1370" Evaluating: 1370-7 Parameter: NUMWAT <- "1363" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1363" Comparing "1081" and "1363". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.634" Parameter: BOX -> "34.634" Parameter: BOX -> "34.634" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.63400 B = 34.63400 C = 34.63400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8851 2 1 -1 0 -1 6.3030 3 1 -1 1 -1 5.2666 4 1 0 -1 -1 3.0830 5 1 0 0 -1 2.1188 6 1 0 1 -1 3.6741 7 1 -1 -1 0 5.2682 8 1 -1 0 0 2.5537 9 1 -1 1 0 4.6114 10 1 0 -1 0 1.3962 11 1 0 1 0 1.3962 12 1 -1 -1 1 4.5450 13 1 -1 0 1 4.4086 14 1 -1 1 1 5.1475 15 1 0 -1 1 3.6741 16 1 0 0 1 2.1188 17 1 0 1 1 3.0830 18 1 1 1 1 4.8851 19 1 1 0 1 6.3030 20 1 1 -1 1 5.2666 21 1 1 1 0 5.2682 22 1 1 0 0 2.5537 23 1 1 -1 0 4.6114 24 1 1 1 -1 4.5450 25 1 1 0 -1 4.4086 26 1 1 -1 -1 5.1475 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4071 atoms have been selected out of 4145 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 510 170 170 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1749 583 583 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13657 atoms and 4544 groups and 4539 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4145 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.632" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1370" Evaluating: 1370-7 Parameter: NUMWAT <- "1363" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1363" Comparing "1081" and "1363". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.632" Parameter: BOX -> "34.632" Parameter: BOX -> "34.632" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.63200 B = 34.63200 C = 34.63200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8873 2 1 -1 0 -1 6.3042 3 1 -1 1 -1 5.2632 4 1 0 -1 -1 3.0811 5 1 0 0 -1 2.1169 6 1 0 1 -1 3.6714 7 1 -1 -1 0 5.2662 8 1 -1 0 0 2.5530 9 1 -1 1 0 4.6091 10 1 0 -1 0 1.3952 11 1 0 1 0 1.3952 12 1 -1 -1 1 4.5415 13 1 -1 0 1 4.4058 14 1 -1 1 1 5.1444 15 1 0 -1 1 3.6714 16 1 0 0 1 2.1169 17 1 0 1 1 3.0811 18 1 1 1 1 4.8873 19 1 1 0 1 6.3042 20 1 1 -1 1 5.2632 21 1 1 1 0 5.2662 22 1 1 0 0 2.5530 23 1 1 -1 0 4.6091 24 1 1 1 -1 4.5415 25 1 1 0 -1 4.4058 26 1 1 -1 -1 5.1444 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4071 atoms have been selected out of 4145 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 510 170 170 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1749 583 583 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13660 atoms and 4545 groups and 4540 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4145 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.63" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1370" Evaluating: 1370-7 Parameter: NUMWAT <- "1363" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1363" Comparing "1081" and "1363". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.63" Parameter: BOX -> "34.63" Parameter: BOX -> "34.63" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.63000 B = 34.63000 C = 34.63000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8895 2 1 -1 0 -1 6.3054 3 1 -1 1 -1 5.2598 4 1 0 -1 -1 3.0792 5 1 0 0 -1 2.1150 6 1 0 1 -1 3.6686 7 1 -1 -1 0 5.2642 8 1 -1 0 0 2.5523 9 1 -1 1 0 4.6069 10 1 0 -1 0 1.3941 11 1 0 1 0 1.3941 12 1 -1 -1 1 4.5381 13 1 -1 0 1 4.4030 14 1 -1 1 1 5.1413 15 1 0 -1 1 3.6686 16 1 0 0 1 2.1150 17 1 0 1 1 3.0792 18 1 1 1 1 4.8895 19 1 1 0 1 6.3054 20 1 1 -1 1 5.2598 21 1 1 1 0 5.2642 22 1 1 0 0 2.5523 23 1 1 -1 0 4.6069 24 1 1 1 -1 4.5381 25 1 1 0 -1 4.4030 26 1 1 -1 -1 5.1413 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4071 atoms have been selected out of 4145 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 510 170 170 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1749 583 583 0.00 12 C012 has 117 39 39 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13663 atoms and 4546 groups and 4541 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4145 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.628" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1370" Evaluating: 1370-7 Parameter: NUMWAT <- "1363" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1363" Comparing "1081" and "1363". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.628" Parameter: BOX -> "34.628" Parameter: BOX -> "34.628" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.62800 B = 34.62800 C = 34.62800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8917 2 1 -1 0 -1 6.3066 3 1 -1 1 -1 5.2563 4 1 0 -1 -1 3.0773 5 1 0 0 -1 2.1130 6 1 0 1 -1 3.6658 7 1 -1 -1 0 5.2622 8 1 -1 0 0 2.5516 9 1 -1 1 0 4.6046 10 1 0 -1 0 1.3931 11 1 0 1 0 1.3931 12 1 -1 -1 1 4.5346 13 1 -1 0 1 4.4002 14 1 -1 1 1 5.1383 15 1 0 -1 1 3.6658 16 1 0 0 1 2.1130 17 1 0 1 1 3.0773 18 1 1 1 1 4.8917 19 1 1 0 1 6.3066 20 1 1 -1 1 5.2563 21 1 1 1 0 5.2622 22 1 1 0 0 2.5516 23 1 1 -1 0 4.6046 24 1 1 1 -1 4.5346 25 1 1 0 -1 4.4002 26 1 1 -1 -1 5.1383 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4071 atoms have been selected out of 4145 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 363 121 121 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 510 170 170 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1749 583 583 0.00 12 C012 has 117 39 39 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13663 atoms and 4546 groups and 4541 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4145 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.626" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1370" Evaluating: 1370-7 Parameter: NUMWAT <- "1363" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1363" Comparing "1081" and "1363". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.626" Parameter: BOX -> "34.626" Parameter: BOX -> "34.626" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.62600 B = 34.62600 C = 34.62600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8939 2 1 -1 0 -1 6.3078 3 1 -1 1 -1 5.2529 4 1 0 -1 -1 3.0754 5 1 0 0 -1 2.1111 6 1 0 1 -1 3.6631 7 1 -1 -1 0 5.2603 8 1 -1 0 0 2.5508 9 1 -1 1 0 4.6023 10 1 0 -1 0 1.3920 11 1 0 1 0 1.3920 12 1 -1 -1 1 4.5311 13 1 -1 0 1 4.3975 14 1 -1 1 1 5.1352 15 1 0 -1 1 3.6631 16 1 0 0 1 2.1111 17 1 0 1 1 3.0754 18 1 1 1 1 4.8939 19 1 1 0 1 6.3078 20 1 1 -1 1 5.2529 21 1 1 1 0 5.2603 22 1 1 0 0 2.5508 23 1 1 -1 0 4.6023 24 1 1 1 -1 4.5311 25 1 1 0 -1 4.3975 26 1 1 -1 -1 5.1352 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4071 atoms have been selected out of 4145 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 510 170 170 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1850 615 615 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1752 584 584 0.00 12 C012 has 117 39 39 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13672 atoms and 4549 groups and 4544 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4145 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1370 Number of atoms = 4145 Number of groups = 1375 Number of bonds = 4138 Number of angles = 1474 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1372 Number of HB donors = 2722 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.624" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1370" Evaluating: 1370-7 Parameter: NUMWAT <- "1363" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1363" Comparing "1081" and "1363". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.624" Parameter: BOX -> "34.624" Parameter: BOX -> "34.624" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.62400 B = 34.62400 C = 34.62400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8961 2 1 -1 0 -1 6.3090 3 1 -1 1 -1 5.2494 4 1 0 -1 -1 3.0735 5 1 0 0 -1 2.1092 6 1 0 1 -1 3.6603 7 1 -1 -1 0 5.2583 8 1 -1 0 0 2.5501 9 1 -1 1 0 4.6000 10 1 0 -1 0 1.3910 11 1 0 1 0 1.3910 12 1 -1 -1 1 4.5277 13 1 -1 0 1 4.3947 14 1 -1 1 1 5.1322 15 1 0 -1 1 3.6603 16 1 0 0 1 2.1092 17 1 0 1 1 3.0735 18 1 1 1 1 4.8961 19 1 1 0 1 6.3090 20 1 1 -1 1 5.2494 21 1 1 1 0 5.2583 22 1 1 0 0 2.5501 23 1 1 -1 0 4.6000 24 1 1 1 -1 4.5277 25 1 1 0 -1 4.3947 26 1 1 -1 -1 5.1322 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4071 atoms have been selected out of 4145 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 155 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1692 564 564 0.00 6 C006 has 513 171 171 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1850 615 615 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1752 584 584 0.00 12 C012 has 117 39 39 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13684 atoms and 4553 groups and 4548 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4145 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1369 Number of atoms = 4142 Number of groups = 1374 Number of bonds = 4135 Number of angles = 1473 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1371 Number of HB donors = 2720 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1369 Number of atoms = 4142 Number of groups = 1374 Number of bonds = 4135 Number of angles = 1473 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1371 Number of HB donors = 2720 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.622" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1369" Evaluating: 1369-7 Parameter: NUMWAT <- "1362" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1362" Comparing "1081" and "1362". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.622" Parameter: BOX -> "34.622" Parameter: BOX -> "34.622" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.62200 B = 34.62200 C = 34.62200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.8984 2 1 -1 0 -1 6.3103 3 1 -1 1 -1 5.2460 4 1 0 -1 -1 3.0716 5 1 0 0 -1 2.1072 6 1 0 1 -1 3.6575 7 1 -1 -1 0 5.2563 8 1 -1 0 0 2.5494 9 1 -1 1 0 4.5978 10 1 0 -1 0 1.3900 11 1 0 1 0 1.3900 12 1 -1 -1 1 4.5242 13 1 -1 0 1 4.3919 14 1 -1 1 1 5.1291 15 1 0 -1 1 3.6575 16 1 0 0 1 2.1072 17 1 0 1 1 3.0716 18 1 1 1 1 4.8984 19 1 1 0 1 6.3103 20 1 1 -1 1 5.2460 21 1 1 1 0 5.2563 22 1 1 0 0 2.5494 23 1 1 -1 0 4.5978 24 1 1 1 -1 4.5242 25 1 1 0 -1 4.3919 26 1 1 -1 -1 5.1291 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4068 atoms have been selected out of 4142 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 510 170 170 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1850 615 615 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1752 584 584 0.00 12 C012 has 117 39 39 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13678 atoms and 4551 groups and 4546 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4142 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1369 Number of atoms = 4142 Number of groups = 1374 Number of bonds = 4135 Number of angles = 1473 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1371 Number of HB donors = 2720 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1369 Number of atoms = 4142 Number of groups = 1374 Number of bonds = 4135 Number of angles = 1473 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1371 Number of HB donors = 2720 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.62" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1369" Evaluating: 1369-7 Parameter: NUMWAT <- "1362" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1362" Comparing "1081" and "1362". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.62" Parameter: BOX -> "34.62" Parameter: BOX -> "34.62" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.62000 B = 34.62000 C = 34.62000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9006 2 1 -1 0 -1 6.3115 3 1 -1 1 -1 5.2425 4 1 0 -1 -1 3.0697 5 1 0 0 -1 2.1053 6 1 0 1 -1 3.6548 7 1 -1 -1 0 5.2543 8 1 -1 0 0 2.5487 9 1 -1 1 0 4.5955 10 1 0 -1 0 1.3889 11 1 0 1 0 1.3889 12 1 -1 -1 1 4.5208 13 1 -1 0 1 4.3891 14 1 -1 1 1 5.1261 15 1 0 -1 1 3.6548 16 1 0 0 1 2.1053 17 1 0 1 1 3.0697 18 1 1 1 1 4.9006 19 1 1 0 1 6.3115 20 1 1 -1 1 5.2425 21 1 1 1 0 5.2543 22 1 1 0 0 2.5487 23 1 1 -1 0 4.5955 24 1 1 1 -1 4.5208 25 1 1 0 -1 4.3891 26 1 1 -1 -1 5.1261 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4068 atoms have been selected out of 4142 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 513 171 171 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1850 615 615 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1752 584 584 0.00 12 C012 has 117 39 39 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13681 atoms and 4552 groups and 4547 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4142 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1369 Number of atoms = 4142 Number of groups = 1374 Number of bonds = 4135 Number of angles = 1473 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1371 Number of HB donors = 2720 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1369 Number of atoms = 4142 Number of groups = 1374 Number of bonds = 4135 Number of angles = 1473 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1371 Number of HB donors = 2720 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.618" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1369" Evaluating: 1369-7 Parameter: NUMWAT <- "1362" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1362" Comparing "1081" and "1362". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.618" Parameter: BOX -> "34.618" Parameter: BOX -> "34.618" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.61800 B = 34.61800 C = 34.61800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9028 2 1 -1 0 -1 6.3127 3 1 -1 1 -1 5.2391 4 1 0 -1 -1 3.0678 5 1 0 0 -1 2.1034 6 1 0 1 -1 3.6520 7 1 -1 -1 0 5.2524 8 1 -1 0 0 2.5480 9 1 -1 1 0 4.5932 10 1 0 -1 0 1.3879 11 1 0 1 0 1.3879 12 1 -1 -1 1 4.5173 13 1 -1 0 1 4.3863 14 1 -1 1 1 5.1230 15 1 0 -1 1 3.6520 16 1 0 0 1 2.1034 17 1 0 1 1 3.0678 18 1 1 1 1 4.9028 19 1 1 0 1 6.3127 20 1 1 -1 1 5.2391 21 1 1 1 0 5.2524 22 1 1 0 0 2.5480 23 1 1 -1 0 4.5932 24 1 1 1 -1 4.5173 25 1 1 0 -1 4.3863 26 1 1 -1 -1 5.1230 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4068 atoms have been selected out of 4142 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 513 171 171 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1850 615 615 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 117 39 39 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13684 atoms and 4553 groups and 4548 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4142 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1369 Number of atoms = 4142 Number of groups = 1374 Number of bonds = 4135 Number of angles = 1473 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1371 Number of HB donors = 2720 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1369 Number of atoms = 4142 Number of groups = 1374 Number of bonds = 4135 Number of angles = 1473 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1371 Number of HB donors = 2720 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.616" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1369" Evaluating: 1369-7 Parameter: NUMWAT <- "1362" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1362" Comparing "1081" and "1362". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.616" Parameter: BOX -> "34.616" Parameter: BOX -> "34.616" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.61600 B = 34.61600 C = 34.61600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9050 2 1 -1 0 -1 6.3139 3 1 -1 1 -1 5.2356 4 1 0 -1 -1 3.0660 5 1 0 0 -1 2.1014 6 1 0 1 -1 3.6492 7 1 -1 -1 0 5.2504 8 1 -1 0 0 2.5472 9 1 -1 1 0 4.5910 10 1 0 -1 0 1.3869 11 1 0 1 0 1.3869 12 1 -1 -1 1 4.5139 13 1 -1 0 1 4.3835 14 1 -1 1 1 5.1200 15 1 0 -1 1 3.6492 16 1 0 0 1 2.1014 17 1 0 1 1 3.0660 18 1 1 1 1 4.9050 19 1 1 0 1 6.3139 20 1 1 -1 1 5.2356 21 1 1 1 0 5.2504 22 1 1 0 0 2.5472 23 1 1 -1 0 4.5910 24 1 1 1 -1 4.5139 25 1 1 0 -1 4.3835 26 1 1 -1 -1 5.1200 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4068 atoms have been selected out of 4142 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 516 172 172 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1850 615 615 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 117 39 39 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13687 atoms and 4554 groups and 4549 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4142 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1369 Number of atoms = 4142 Number of groups = 1374 Number of bonds = 4135 Number of angles = 1473 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1371 Number of HB donors = 2720 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1369 Number of atoms = 4142 Number of groups = 1374 Number of bonds = 4135 Number of angles = 1473 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1371 Number of HB donors = 2720 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.614" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1369" Evaluating: 1369-7 Parameter: NUMWAT <- "1362" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1362" Comparing "1081" and "1362". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.614" Parameter: BOX -> "34.614" Parameter: BOX -> "34.614" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.61400 B = 34.61400 C = 34.61400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9072 2 1 -1 0 -1 6.3151 3 1 -1 1 -1 5.2322 4 1 0 -1 -1 3.0641 5 1 0 0 -1 2.0995 6 1 0 1 -1 3.6465 7 1 -1 -1 0 5.2484 8 1 -1 0 0 2.5465 9 1 -1 1 0 4.5887 10 1 0 -1 0 1.3858 11 1 0 1 0 1.3858 12 1 -1 -1 1 4.5104 13 1 -1 0 1 4.3808 14 1 -1 1 1 5.1169 15 1 0 -1 1 3.6465 16 1 0 0 1 2.0995 17 1 0 1 1 3.0641 18 1 1 1 1 4.9072 19 1 1 0 1 6.3151 20 1 1 -1 1 5.2322 21 1 1 1 0 5.2484 22 1 1 0 0 2.5465 23 1 1 -1 0 4.5887 24 1 1 1 -1 4.5104 25 1 1 0 -1 4.3808 26 1 1 -1 -1 5.1169 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4068 atoms have been selected out of 4142 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 516 172 172 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1850 615 615 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 117 39 39 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13690 atoms and 4555 groups and 4550 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4142 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1369 Number of atoms = 4142 Number of groups = 1374 Number of bonds = 4135 Number of angles = 1473 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1371 Number of HB donors = 2720 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1369 Number of atoms = 4142 Number of groups = 1374 Number of bonds = 4135 Number of angles = 1473 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1371 Number of HB donors = 2720 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.612" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1369" Evaluating: 1369-7 Parameter: NUMWAT <- "1362" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1362" Comparing "1081" and "1362". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.612" Parameter: BOX -> "34.612" Parameter: BOX -> "34.612" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.61200 B = 34.61200 C = 34.61200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9094 2 1 -1 0 -1 6.3163 3 1 -1 1 -1 5.2288 4 1 0 -1 -1 3.0622 5 1 0 0 -1 2.0975 6 1 0 1 -1 3.6437 7 1 -1 -1 0 5.2464 8 1 -1 0 0 2.5458 9 1 -1 1 0 4.5864 10 1 0 -1 0 1.3848 11 1 0 1 0 1.3848 12 1 -1 -1 1 4.5070 13 1 -1 0 1 4.3780 14 1 -1 1 1 5.1139 15 1 0 -1 1 3.6437 16 1 0 0 1 2.0975 17 1 0 1 1 3.0622 18 1 1 1 1 4.9094 19 1 1 0 1 6.3163 20 1 1 -1 1 5.2288 21 1 1 1 0 5.2464 22 1 1 0 0 2.5458 23 1 1 -1 0 4.5864 24 1 1 1 -1 4.5070 25 1 1 0 -1 4.3780 26 1 1 -1 -1 5.1139 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4068 atoms have been selected out of 4142 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1016 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1692 564 564 0.00 6 C006 has 516 172 172 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1853 616 616 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 117 39 39 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13690 atoms and 4555 groups and 4550 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4142 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1368 Number of atoms = 4139 Number of groups = 1373 Number of bonds = 4132 Number of angles = 1472 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1370 Number of HB donors = 2718 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1368 Number of atoms = 4139 Number of groups = 1373 Number of bonds = 4132 Number of angles = 1472 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1370 Number of HB donors = 2718 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.61" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1368" Evaluating: 1368-7 Parameter: NUMWAT <- "1361" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1361" Comparing "1081" and "1361". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.61" Parameter: BOX -> "34.61" Parameter: BOX -> "34.61" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.61000 B = 34.61000 C = 34.61000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9117 2 1 -1 0 -1 6.3176 3 1 -1 1 -1 5.2253 4 1 0 -1 -1 3.0603 5 1 0 0 -1 2.0956 6 1 0 1 -1 3.6409 7 1 -1 -1 0 5.2445 8 1 -1 0 0 2.5451 9 1 -1 1 0 4.5841 10 1 0 -1 0 1.3838 11 1 0 1 0 1.3838 12 1 -1 -1 1 4.5035 13 1 -1 0 1 4.3752 14 1 -1 1 1 5.1108 15 1 0 -1 1 3.6409 16 1 0 0 1 2.0956 17 1 0 1 1 3.0603 18 1 1 1 1 4.9117 19 1 1 0 1 6.3176 20 1 1 -1 1 5.2253 21 1 1 1 0 5.2445 22 1 1 0 0 2.5451 23 1 1 -1 0 4.5841 24 1 1 1 -1 4.5035 25 1 1 0 -1 4.3752 26 1 1 -1 -1 5.1108 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4065 atoms have been selected out of 4139 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 516 172 172 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 117 39 39 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13678 atoms and 4551 groups and 4546 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4139 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1368 Number of atoms = 4139 Number of groups = 1373 Number of bonds = 4132 Number of angles = 1472 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1370 Number of HB donors = 2718 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1368 Number of atoms = 4139 Number of groups = 1373 Number of bonds = 4132 Number of angles = 1472 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1370 Number of HB donors = 2718 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.608" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1368" Evaluating: 1368-7 Parameter: NUMWAT <- "1361" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1361" Comparing "1081" and "1361". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.608" Parameter: BOX -> "34.608" Parameter: BOX -> "34.608" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.60800 B = 34.60800 C = 34.60800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9139 2 1 -1 0 -1 6.3188 3 1 -1 1 -1 5.2219 4 1 0 -1 -1 3.0584 5 1 0 0 -1 2.0937 6 1 0 1 -1 3.6382 7 1 -1 -1 0 5.2425 8 1 -1 0 0 2.5444 9 1 -1 1 0 4.5819 10 1 0 -1 0 1.3828 11 1 0 1 0 1.3828 12 1 -1 -1 1 4.5001 13 1 -1 0 1 4.3724 14 1 -1 1 1 5.1078 15 1 0 -1 1 3.6382 16 1 0 0 1 2.0937 17 1 0 1 1 3.0584 18 1 1 1 1 4.9139 19 1 1 0 1 6.3188 20 1 1 -1 1 5.2219 21 1 1 1 0 5.2425 22 1 1 0 0 2.5444 23 1 1 -1 0 4.5819 24 1 1 1 -1 4.5001 25 1 1 0 -1 4.3724 26 1 1 -1 -1 5.1078 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4065 atoms have been selected out of 4139 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 516 172 172 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 117 39 39 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13681 atoms and 4552 groups and 4547 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4139 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1368 Number of atoms = 4139 Number of groups = 1373 Number of bonds = 4132 Number of angles = 1472 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1370 Number of HB donors = 2718 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1368 Number of atoms = 4139 Number of groups = 1373 Number of bonds = 4132 Number of angles = 1472 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1370 Number of HB donors = 2718 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.606" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1368" Evaluating: 1368-7 Parameter: NUMWAT <- "1361" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1361" Comparing "1081" and "1361". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.606" Parameter: BOX -> "34.606" Parameter: BOX -> "34.606" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.60600 B = 34.60600 C = 34.60600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9161 2 1 -1 0 -1 6.3200 3 1 -1 1 -1 5.2184 4 1 0 -1 -1 3.0565 5 1 0 0 -1 2.0917 6 1 0 1 -1 3.6354 7 1 -1 -1 0 5.2405 8 1 -1 0 0 2.5437 9 1 -1 1 0 4.5796 10 1 0 -1 0 1.3817 11 1 0 1 0 1.3817 12 1 -1 -1 1 4.4966 13 1 -1 0 1 4.3696 14 1 -1 1 1 5.1047 15 1 0 -1 1 3.6354 16 1 0 0 1 2.0917 17 1 0 1 1 3.0565 18 1 1 1 1 4.9161 19 1 1 0 1 6.3200 20 1 1 -1 1 5.2184 21 1 1 1 0 5.2405 22 1 1 0 0 2.5437 23 1 1 -1 0 4.5796 24 1 1 1 -1 4.4966 25 1 1 0 -1 4.3696 26 1 1 -1 -1 5.1047 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4065 atoms have been selected out of 4139 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 516 172 172 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1850 615 615 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 117 39 39 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13684 atoms and 4553 groups and 4548 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4139 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1368 Number of atoms = 4139 Number of groups = 1373 Number of bonds = 4132 Number of angles = 1472 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1370 Number of HB donors = 2718 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1368 Number of atoms = 4139 Number of groups = 1373 Number of bonds = 4132 Number of angles = 1472 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1370 Number of HB donors = 2718 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.604" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1368" Evaluating: 1368-7 Parameter: NUMWAT <- "1361" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1361" Comparing "1081" and "1361". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.604" Parameter: BOX -> "34.604" Parameter: BOX -> "34.604" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.60400 B = 34.60400 C = 34.60400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9183 2 1 -1 0 -1 6.3212 3 1 -1 1 -1 5.2150 4 1 0 -1 -1 3.0546 5 1 0 0 -1 2.0898 6 1 0 1 -1 3.6326 7 1 -1 -1 0 5.2386 8 1 -1 0 0 2.5430 9 1 -1 1 0 4.5773 10 1 0 -1 0 1.3807 11 1 0 1 0 1.3807 12 1 -1 -1 1 4.4932 13 1 -1 0 1 4.3668 14 1 -1 1 1 5.1017 15 1 0 -1 1 3.6326 16 1 0 0 1 2.0898 17 1 0 1 1 3.0546 18 1 1 1 1 4.9183 19 1 1 0 1 6.3212 20 1 1 -1 1 5.2150 21 1 1 1 0 5.2386 22 1 1 0 0 2.5430 23 1 1 -1 0 4.5773 24 1 1 1 -1 4.4932 25 1 1 0 -1 4.3668 26 1 1 -1 -1 5.1017 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4065 atoms have been selected out of 4139 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 516 172 172 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1850 615 615 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1761 587 587 0.00 12 C012 has 117 39 39 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13687 atoms and 4554 groups and 4549 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4139 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1368 Number of atoms = 4139 Number of groups = 1373 Number of bonds = 4132 Number of angles = 1472 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1370 Number of HB donors = 2718 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1368 Number of atoms = 4139 Number of groups = 1373 Number of bonds = 4132 Number of angles = 1472 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1370 Number of HB donors = 2718 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.602" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1368" Evaluating: 1368-7 Parameter: NUMWAT <- "1361" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1361" Comparing "1081" and "1361". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.602" Parameter: BOX -> "34.602" Parameter: BOX -> "34.602" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.60200 B = 34.60200 C = 34.60200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9205 2 1 -1 0 -1 6.3224 3 1 -1 1 -1 5.2115 4 1 0 -1 -1 3.0528 5 1 0 0 -1 2.0879 6 1 0 1 -1 3.6299 7 1 -1 -1 0 5.2366 8 1 -1 0 0 2.5423 9 1 -1 1 0 4.5751 10 1 0 -1 0 1.3797 11 1 0 1 0 1.3797 12 1 -1 -1 1 4.4897 13 1 -1 0 1 4.3641 14 1 -1 1 1 5.0986 15 1 0 -1 1 3.6299 16 1 0 0 1 2.0879 17 1 0 1 1 3.0528 18 1 1 1 1 4.9205 19 1 1 0 1 6.3224 20 1 1 -1 1 5.2115 21 1 1 1 0 5.2366 22 1 1 0 0 2.5423 23 1 1 -1 0 4.5751 24 1 1 1 -1 4.4897 25 1 1 0 -1 4.3641 26 1 1 -1 -1 5.0986 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4065 atoms have been selected out of 4139 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 516 172 172 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1850 615 615 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1761 587 587 0.00 12 C012 has 117 39 39 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13687 atoms and 4554 groups and 4549 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4139 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1368 Number of atoms = 4139 Number of groups = 1373 Number of bonds = 4132 Number of angles = 1472 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1370 Number of HB donors = 2718 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1368 Number of atoms = 4139 Number of groups = 1373 Number of bonds = 4132 Number of angles = 1472 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1370 Number of HB donors = 2718 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.6" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1368" Evaluating: 1368-7 Parameter: NUMWAT <- "1361" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1361" Comparing "1081" and "1361". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.6" Parameter: BOX -> "34.6" Parameter: BOX -> "34.6" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.60000 B = 34.60000 C = 34.60000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9228 2 1 -1 0 -1 6.3237 3 1 -1 1 -1 5.2081 4 1 0 -1 -1 3.0509 5 1 0 0 -1 2.0859 6 1 0 1 -1 3.6271 7 1 -1 -1 0 5.2346 8 1 -1 0 0 2.5416 9 1 -1 1 0 4.5728 10 1 0 -1 0 1.3787 11 1 0 1 0 1.3787 12 1 -1 -1 1 4.4862 13 1 -1 0 1 4.3613 14 1 -1 1 1 5.0956 15 1 0 -1 1 3.6271 16 1 0 0 1 2.0859 17 1 0 1 1 3.0509 18 1 1 1 1 4.9228 19 1 1 0 1 6.3237 20 1 1 -1 1 5.2081 21 1 1 1 0 5.2346 22 1 1 0 0 2.5416 23 1 1 -1 0 4.5728 24 1 1 1 -1 4.4862 25 1 1 0 -1 4.3613 26 1 1 -1 -1 5.0956 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4065 atoms have been selected out of 4139 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 712 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 513 171 171 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1850 615 615 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1764 588 588 0.00 12 C012 has 117 39 39 0.00 13 C013 has 483 161 161 0.00 14 C014 has 108 36 36 0.00 Total of13693 atoms and 4556 groups and 4551 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4139 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1367 Number of atoms = 4136 Number of groups = 1372 Number of bonds = 4129 Number of angles = 1471 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1369 Number of HB donors = 2716 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1367 Number of atoms = 4136 Number of groups = 1372 Number of bonds = 4129 Number of angles = 1471 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1369 Number of HB donors = 2716 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.598" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1367" Evaluating: 1367-7 Parameter: NUMWAT <- "1360" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1360" Comparing "1081" and "1360". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.598" Parameter: BOX -> "34.598" Parameter: BOX -> "34.598" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.59800 B = 34.59800 C = 34.59800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9250 2 1 -1 0 -1 6.3249 3 1 -1 1 -1 5.2047 4 1 0 -1 -1 3.0490 5 1 0 0 -1 2.0840 6 1 0 1 -1 3.6243 7 1 -1 -1 0 5.2327 8 1 -1 0 0 2.5409 9 1 -1 1 0 4.5705 10 1 0 -1 0 1.3777 11 1 0 1 0 1.3777 12 1 -1 -1 1 4.4828 13 1 -1 0 1 4.3585 14 1 -1 1 1 5.0925 15 1 0 -1 1 3.6243 16 1 0 0 1 2.0840 17 1 0 1 1 3.0490 18 1 1 1 1 4.9250 19 1 1 0 1 6.3249 20 1 1 -1 1 5.2047 21 1 1 1 0 5.2327 22 1 1 0 0 2.5409 23 1 1 -1 0 4.5705 24 1 1 1 -1 4.4828 25 1 1 0 -1 4.3585 26 1 1 -1 -1 5.0925 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4062 atoms have been selected out of 4136 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1686 562 562 0.00 6 C006 has 513 171 171 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1850 615 615 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1761 587 587 0.00 12 C012 has 117 39 39 0.00 13 C013 has 483 161 161 0.00 14 C014 has 108 36 36 0.00 Total of13681 atoms and 4552 groups and 4547 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4136 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1367 Number of atoms = 4136 Number of groups = 1372 Number of bonds = 4129 Number of angles = 1471 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1369 Number of HB donors = 2716 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1367 Number of atoms = 4136 Number of groups = 1372 Number of bonds = 4129 Number of angles = 1471 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1369 Number of HB donors = 2716 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.596" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1367" Evaluating: 1367-7 Parameter: NUMWAT <- "1360" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1360" Comparing "1081" and "1360". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.596" Parameter: BOX -> "34.596" Parameter: BOX -> "34.596" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.59600 B = 34.59600 C = 34.59600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9272 2 1 -1 0 -1 6.3261 3 1 -1 1 -1 5.2012 4 1 0 -1 -1 3.0471 5 1 0 0 -1 2.0821 6 1 0 1 -1 3.6216 7 1 -1 -1 0 5.2307 8 1 -1 0 0 2.5402 9 1 -1 1 0 4.5683 10 1 0 -1 0 1.3767 11 1 0 1 0 1.3767 12 1 -1 -1 1 4.4793 13 1 -1 0 1 4.3557 14 1 -1 1 1 5.0895 15 1 0 -1 1 3.6216 16 1 0 0 1 2.0821 17 1 0 1 1 3.0471 18 1 1 1 1 4.9272 19 1 1 0 1 6.3261 20 1 1 -1 1 5.2012 21 1 1 1 0 5.2307 22 1 1 0 0 2.5402 23 1 1 -1 0 4.5683 24 1 1 1 -1 4.4793 25 1 1 0 -1 4.3557 26 1 1 -1 -1 5.0895 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4062 atoms have been selected out of 4136 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 185 OPERATED ON BY TRANSFORMATION C016 RESIDUE 530 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 369 123 123 0.00 2 C002 has 696 232 232 0.00 3 C003 has 87 29 29 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1692 564 564 0.00 6 C006 has 516 172 172 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1850 615 615 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1761 587 587 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 105 35 35 0.00 Total of13690 atoms and 4555 groups and 4550 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 4136 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1365 Number of atoms = 4130 Number of groups = 1370 Number of bonds = 4123 Number of angles = 1469 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1367 Number of HB donors = 2712 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1365 Number of atoms = 4130 Number of groups = 1370 Number of bonds = 4123 Number of angles = 1469 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1367 Number of HB donors = 2712 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.594" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1365" Evaluating: 1365-7 Parameter: NUMWAT <- "1358" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1358" Comparing "1081" and "1358". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.594" Parameter: BOX -> "34.594" Parameter: BOX -> "34.594" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.59400 B = 34.59400 C = 34.59400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9295 2 1 -1 0 -1 6.3273 3 1 -1 1 -1 5.1978 4 1 0 -1 -1 3.0453 5 1 0 0 -1 2.0801 6 1 0 1 -1 3.6188 7 1 -1 -1 0 5.2287 8 1 -1 0 0 2.5395 9 1 -1 1 0 4.5660 10 1 0 -1 0 1.3757 11 1 0 1 0 1.3757 12 1 -1 -1 1 4.4759 13 1 -1 0 1 4.3529 14 1 -1 1 1 5.0864 15 1 0 -1 1 3.6188 16 1 0 0 1 2.0801 17 1 0 1 1 3.0453 18 1 1 1 1 4.9295 19 1 1 0 1 6.3273 20 1 1 -1 1 5.1978 21 1 1 1 0 5.2287 22 1 1 0 0 2.5395 23 1 1 -1 0 4.5660 24 1 1 1 -1 4.4759 25 1 1 0 -1 4.3529 26 1 1 -1 -1 5.0864 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4056 atoms have been selected out of 4130 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 325 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1686 562 562 0.00 6 C006 has 513 171 171 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1841 612 612 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 114 38 38 0.00 13 C013 has 474 158 158 0.00 14 C014 has 102 34 34 0.00 Total of13633 atoms and 4536 groups and 4531 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4130 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1364 Number of atoms = 4127 Number of groups = 1369 Number of bonds = 4120 Number of angles = 1468 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1366 Number of HB donors = 2710 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1364 Number of atoms = 4127 Number of groups = 1369 Number of bonds = 4120 Number of angles = 1468 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1366 Number of HB donors = 2710 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.592" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1364" Evaluating: 1364-7 Parameter: NUMWAT <- "1357" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1357" Comparing "1081" and "1357". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.592" Parameter: BOX -> "34.592" Parameter: BOX -> "34.592" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.59200 B = 34.59200 C = 34.59200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9317 2 1 -1 0 -1 6.3286 3 1 -1 1 -1 5.1943 4 1 0 -1 -1 3.0434 5 1 0 0 -1 2.0782 6 1 0 1 -1 3.6161 7 1 -1 -1 0 5.2268 8 1 -1 0 0 2.5388 9 1 -1 1 0 4.5637 10 1 0 -1 0 1.3747 11 1 0 1 0 1.3747 12 1 -1 -1 1 4.4724 13 1 -1 0 1 4.3501 14 1 -1 1 1 5.0834 15 1 0 -1 1 3.6161 16 1 0 0 1 2.0782 17 1 0 1 1 3.0434 18 1 1 1 1 4.9317 19 1 1 0 1 6.3286 20 1 1 -1 1 5.1943 21 1 1 1 0 5.2268 22 1 1 0 0 2.5388 23 1 1 -1 0 4.5637 24 1 1 1 -1 4.4724 25 1 1 0 -1 4.3501 26 1 1 -1 -1 5.0834 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4053 atoms have been selected out of 4127 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1686 562 562 0.00 6 C006 has 513 171 171 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1841 612 612 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13633 atoms and 4536 groups and 4531 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4127 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1364 Number of atoms = 4127 Number of groups = 1369 Number of bonds = 4120 Number of angles = 1468 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1366 Number of HB donors = 2710 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1364 Number of atoms = 4127 Number of groups = 1369 Number of bonds = 4120 Number of angles = 1468 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1366 Number of HB donors = 2710 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.59" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1364" Evaluating: 1364-7 Parameter: NUMWAT <- "1357" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1357" Comparing "1081" and "1357". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.59" Parameter: BOX -> "34.59" Parameter: BOX -> "34.59" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.59000 B = 34.59000 C = 34.59000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9339 2 1 -1 0 -1 6.3298 3 1 -1 1 -1 5.1909 4 1 0 -1 -1 3.0415 5 1 0 0 -1 2.0763 6 1 0 1 -1 3.6133 7 1 -1 -1 0 5.2248 8 1 -1 0 0 2.5381 9 1 -1 1 0 4.5615 10 1 0 -1 0 1.3737 11 1 0 1 0 1.3737 12 1 -1 -1 1 4.4690 13 1 -1 0 1 4.3474 14 1 -1 1 1 5.0803 15 1 0 -1 1 3.6133 16 1 0 0 1 2.0763 17 1 0 1 1 3.0415 18 1 1 1 1 4.9339 19 1 1 0 1 6.3298 20 1 1 -1 1 5.1909 21 1 1 1 0 5.2248 22 1 1 0 0 2.5381 23 1 1 -1 0 4.5615 24 1 1 1 -1 4.4690 25 1 1 0 -1 4.3474 26 1 1 -1 -1 5.0803 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4053 atoms have been selected out of 4127 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 513 171 171 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1841 612 612 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13639 atoms and 4538 groups and 4533 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4127 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1364 Number of atoms = 4127 Number of groups = 1369 Number of bonds = 4120 Number of angles = 1468 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1366 Number of HB donors = 2710 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1364 Number of atoms = 4127 Number of groups = 1369 Number of bonds = 4120 Number of angles = 1468 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1366 Number of HB donors = 2710 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.588" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1364" Evaluating: 1364-7 Parameter: NUMWAT <- "1357" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1357" Comparing "1081" and "1357". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.588" Parameter: BOX -> "34.588" Parameter: BOX -> "34.588" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.58800 B = 34.58800 C = 34.58800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9362 2 1 -1 0 -1 6.3310 3 1 -1 1 -1 5.1874 4 1 0 -1 -1 3.0397 5 1 0 0 -1 2.0743 6 1 0 1 -1 3.6105 7 1 -1 -1 0 5.2228 8 1 -1 0 0 2.5374 9 1 -1 1 0 4.5592 10 1 0 -1 0 1.3727 11 1 0 1 0 1.3727 12 1 -1 -1 1 4.4655 13 1 -1 0 1 4.3446 14 1 -1 1 1 5.0773 15 1 0 -1 1 3.6105 16 1 0 0 1 2.0743 17 1 0 1 1 3.0397 18 1 1 1 1 4.9362 19 1 1 0 1 6.3310 20 1 1 -1 1 5.1874 21 1 1 1 0 5.2228 22 1 1 0 0 2.5374 23 1 1 -1 0 4.5592 24 1 1 1 -1 4.4655 25 1 1 0 -1 4.3446 26 1 1 -1 -1 5.0773 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4053 atoms have been selected out of 4127 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 513 171 171 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1841 612 612 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1761 587 587 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13645 atoms and 4540 groups and 4535 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4127 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1364 Number of atoms = 4127 Number of groups = 1369 Number of bonds = 4120 Number of angles = 1468 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1366 Number of HB donors = 2710 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1364 Number of atoms = 4127 Number of groups = 1369 Number of bonds = 4120 Number of angles = 1468 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1366 Number of HB donors = 2710 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.586" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1364" Evaluating: 1364-7 Parameter: NUMWAT <- "1357" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1357" Comparing "1081" and "1357". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.586" Parameter: BOX -> "34.586" Parameter: BOX -> "34.586" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.58600 B = 34.58600 C = 34.58600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9384 2 1 -1 0 -1 6.3323 3 1 -1 1 -1 5.1840 4 1 0 -1 -1 3.0378 5 1 0 0 -1 2.0724 6 1 0 1 -1 3.6078 7 1 -1 -1 0 5.2209 8 1 -1 0 0 2.5367 9 1 -1 1 0 4.5569 10 1 0 -1 0 1.3717 11 1 0 1 0 1.3717 12 1 -1 -1 1 4.4621 13 1 -1 0 1 4.3418 14 1 -1 1 1 5.0742 15 1 0 -1 1 3.6078 16 1 0 0 1 2.0724 17 1 0 1 1 3.0378 18 1 1 1 1 4.9384 19 1 1 0 1 6.3323 20 1 1 -1 1 5.1840 21 1 1 1 0 5.2209 22 1 1 0 0 2.5367 23 1 1 -1 0 4.5569 24 1 1 1 -1 4.4621 25 1 1 0 -1 4.3418 26 1 1 -1 -1 5.0742 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4053 atoms have been selected out of 4127 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1024 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 369 123 123 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1689 563 563 0.00 6 C006 has 513 171 171 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1841 612 612 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1761 587 587 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13657 atoms and 4544 groups and 4539 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4127 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1363 Number of atoms = 4124 Number of groups = 1368 Number of bonds = 4117 Number of angles = 1467 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1365 Number of HB donors = 2708 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1363 Number of atoms = 4124 Number of groups = 1368 Number of bonds = 4117 Number of angles = 1467 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1365 Number of HB donors = 2708 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.584" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1363" Evaluating: 1363-7 Parameter: NUMWAT <- "1356" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1356" Comparing "1081" and "1356". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.584" Parameter: BOX -> "34.584" Parameter: BOX -> "34.584" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.58400 B = 34.58400 C = 34.58400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9406 2 1 -1 0 -1 6.3335 3 1 -1 1 -1 5.1806 4 1 0 -1 -1 3.0359 5 1 0 0 -1 2.0705 6 1 0 1 -1 3.6050 7 1 -1 -1 0 5.2189 8 1 -1 0 0 2.5360 9 1 -1 1 0 4.5547 10 1 0 -1 0 1.3707 11 1 0 1 0 1.3707 12 1 -1 -1 1 4.4586 13 1 -1 0 1 4.3390 14 1 -1 1 1 5.0712 15 1 0 -1 1 3.6050 16 1 0 0 1 2.0705 17 1 0 1 1 3.0359 18 1 1 1 1 4.9406 19 1 1 0 1 6.3335 20 1 1 -1 1 5.1806 21 1 1 1 0 5.2189 22 1 1 0 0 2.5360 23 1 1 -1 0 4.5547 24 1 1 1 -1 4.4586 25 1 1 0 -1 4.3390 26 1 1 -1 -1 5.0712 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4050 atoms have been selected out of 4124 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1686 562 562 0.00 6 C006 has 513 171 171 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1841 612 612 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13639 atoms and 4538 groups and 4533 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4124 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1363 Number of atoms = 4124 Number of groups = 1368 Number of bonds = 4117 Number of angles = 1467 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1365 Number of HB donors = 2708 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1363 Number of atoms = 4124 Number of groups = 1368 Number of bonds = 4117 Number of angles = 1467 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1365 Number of HB donors = 2708 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.582" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1363" Evaluating: 1363-7 Parameter: NUMWAT <- "1356" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1356" Comparing "1081" and "1356". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.582" Parameter: BOX -> "34.582" Parameter: BOX -> "34.582" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.58200 B = 34.58200 C = 34.58200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9429 2 1 -1 0 -1 6.3347 3 1 -1 1 -1 5.1771 4 1 0 -1 -1 3.0341 5 1 0 0 -1 2.0685 6 1 0 1 -1 3.6022 7 1 -1 -1 0 5.2169 8 1 -1 0 0 2.5353 9 1 -1 1 0 4.5524 10 1 0 -1 0 1.3697 11 1 0 1 0 1.3697 12 1 -1 -1 1 4.4552 13 1 -1 0 1 4.3362 14 1 -1 1 1 5.0681 15 1 0 -1 1 3.6022 16 1 0 0 1 2.0685 17 1 0 1 1 3.0341 18 1 1 1 1 4.9429 19 1 1 0 1 6.3347 20 1 1 -1 1 5.1771 21 1 1 1 0 5.2169 22 1 1 0 0 2.5353 23 1 1 -1 0 4.5524 24 1 1 1 -1 4.4552 25 1 1 0 -1 4.3362 26 1 1 -1 -1 5.0681 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4050 atoms have been selected out of 4124 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1686 562 562 0.00 6 C006 has 513 171 171 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1841 612 612 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13642 atoms and 4539 groups and 4534 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4124 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1363 Number of atoms = 4124 Number of groups = 1368 Number of bonds = 4117 Number of angles = 1467 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1365 Number of HB donors = 2708 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1363 Number of atoms = 4124 Number of groups = 1368 Number of bonds = 4117 Number of angles = 1467 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1365 Number of HB donors = 2708 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.58" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1363" Evaluating: 1363-7 Parameter: NUMWAT <- "1356" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1356" Comparing "1081" and "1356". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.58" Parameter: BOX -> "34.58" Parameter: BOX -> "34.58" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.58000 B = 34.58000 C = 34.58000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9451 2 1 -1 0 -1 6.3360 3 1 -1 1 -1 5.1737 4 1 0 -1 -1 3.0322 5 1 0 0 -1 2.0666 6 1 0 1 -1 3.5995 7 1 -1 -1 0 5.2150 8 1 -1 0 0 2.5346 9 1 -1 1 0 4.5502 10 1 0 -1 0 1.3687 11 1 0 1 0 1.3687 12 1 -1 -1 1 4.4517 13 1 -1 0 1 4.3334 14 1 -1 1 1 5.0651 15 1 0 -1 1 3.5995 16 1 0 0 1 2.0666 17 1 0 1 1 3.0322 18 1 1 1 1 4.9451 19 1 1 0 1 6.3360 20 1 1 -1 1 5.1737 21 1 1 1 0 5.2150 22 1 1 0 0 2.5346 23 1 1 -1 0 4.5502 24 1 1 1 -1 4.4517 25 1 1 0 -1 4.3334 26 1 1 -1 -1 5.0651 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4050 atoms have been selected out of 4124 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1686 562 562 0.00 6 C006 has 513 171 171 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1841 612 612 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13642 atoms and 4539 groups and 4534 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4124 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1363 Number of atoms = 4124 Number of groups = 1368 Number of bonds = 4117 Number of angles = 1467 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1365 Number of HB donors = 2708 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1363 Number of atoms = 4124 Number of groups = 1368 Number of bonds = 4117 Number of angles = 1467 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1365 Number of HB donors = 2708 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.578" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1363" Evaluating: 1363-7 Parameter: NUMWAT <- "1356" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1356" Comparing "1081" and "1356". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.578" Parameter: BOX -> "34.578" Parameter: BOX -> "34.578" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.57800 B = 34.57800 C = 34.57800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9474 2 1 -1 0 -1 6.3372 3 1 -1 1 -1 5.1702 4 1 0 -1 -1 3.0303 5 1 0 0 -1 2.0647 6 1 0 1 -1 3.5967 7 1 -1 -1 0 5.2130 8 1 -1 0 0 2.5339 9 1 -1 1 0 4.5479 10 1 0 -1 0 1.3677 11 1 0 1 0 1.3677 12 1 -1 -1 1 4.4483 13 1 -1 0 1 4.3307 14 1 -1 1 1 5.0621 15 1 0 -1 1 3.5967 16 1 0 0 1 2.0647 17 1 0 1 1 3.0303 18 1 1 1 1 4.9474 19 1 1 0 1 6.3372 20 1 1 -1 1 5.1702 21 1 1 1 0 5.2130 22 1 1 0 0 2.5339 23 1 1 -1 0 4.5479 24 1 1 1 -1 4.4483 25 1 1 0 -1 4.3307 26 1 1 -1 -1 5.0621 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4050 atoms have been selected out of 4124 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1686 562 562 0.00 6 C006 has 513 171 171 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13648 atoms and 4541 groups and 4536 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4124 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1363 Number of atoms = 4124 Number of groups = 1368 Number of bonds = 4117 Number of angles = 1467 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1365 Number of HB donors = 2708 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1363 Number of atoms = 4124 Number of groups = 1368 Number of bonds = 4117 Number of angles = 1467 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1365 Number of HB donors = 2708 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.576" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1363" Evaluating: 1363-7 Parameter: NUMWAT <- "1356" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1356" Comparing "1081" and "1356". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.576" Parameter: BOX -> "34.576" Parameter: BOX -> "34.576" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.57600 B = 34.57600 C = 34.57600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9496 2 1 -1 0 -1 6.3384 3 1 -1 1 -1 5.1668 4 1 0 -1 -1 3.0285 5 1 0 0 -1 2.0627 6 1 0 1 -1 3.5939 7 1 -1 -1 0 5.2111 8 1 -1 0 0 2.5332 9 1 -1 1 0 4.5456 10 1 0 -1 0 1.3667 11 1 0 1 0 1.3667 12 1 -1 -1 1 4.4448 13 1 -1 0 1 4.3279 14 1 -1 1 1 5.0590 15 1 0 -1 1 3.5939 16 1 0 0 1 2.0627 17 1 0 1 1 3.0285 18 1 1 1 1 4.9496 19 1 1 0 1 6.3384 20 1 1 -1 1 5.1668 21 1 1 1 0 5.2111 22 1 1 0 0 2.5332 23 1 1 -1 0 4.5456 24 1 1 1 -1 4.4448 25 1 1 0 -1 4.3279 26 1 1 -1 -1 5.0590 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4050 atoms have been selected out of 4124 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1686 562 562 0.00 6 C006 has 513 171 171 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13648 atoms and 4541 groups and 4536 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4124 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1363 Number of atoms = 4124 Number of groups = 1368 Number of bonds = 4117 Number of angles = 1467 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1365 Number of HB donors = 2708 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1363 Number of atoms = 4124 Number of groups = 1368 Number of bonds = 4117 Number of angles = 1467 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1365 Number of HB donors = 2708 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.574" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1363" Evaluating: 1363-7 Parameter: NUMWAT <- "1356" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1356" Comparing "1081" and "1356". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.574" Parameter: BOX -> "34.574" Parameter: BOX -> "34.574" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.57400 B = 34.57400 C = 34.57400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9518 2 1 -1 0 -1 6.3397 3 1 -1 1 -1 5.1633 4 1 0 -1 -1 3.0266 5 1 0 0 -1 2.0608 6 1 0 1 -1 3.5912 7 1 -1 -1 0 5.2091 8 1 -1 0 0 2.5325 9 1 -1 1 0 4.5434 10 1 0 -1 0 1.3657 11 1 0 1 0 1.3657 12 1 -1 -1 1 4.4413 13 1 -1 0 1 4.3251 14 1 -1 1 1 5.0560 15 1 0 -1 1 3.5912 16 1 0 0 1 2.0608 17 1 0 1 1 3.0266 18 1 1 1 1 4.9518 19 1 1 0 1 6.3397 20 1 1 -1 1 5.1633 21 1 1 1 0 5.2091 22 1 1 0 0 2.5325 23 1 1 -1 0 4.5434 24 1 1 1 -1 4.4413 25 1 1 0 -1 4.3251 26 1 1 -1 -1 5.0560 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4050 atoms have been selected out of 4124 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 369 123 123 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1686 562 562 0.00 6 C006 has 513 171 171 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13651 atoms and 4542 groups and 4537 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4124 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1363 Number of atoms = 4124 Number of groups = 1368 Number of bonds = 4117 Number of angles = 1467 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1365 Number of HB donors = 2708 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1363 Number of atoms = 4124 Number of groups = 1368 Number of bonds = 4117 Number of angles = 1467 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1365 Number of HB donors = 2708 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.572" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1363" Evaluating: 1363-7 Parameter: NUMWAT <- "1356" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1356" Comparing "1081" and "1356". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.572" Parameter: BOX -> "34.572" Parameter: BOX -> "34.572" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.57200 B = 34.57200 C = 34.57200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9541 2 1 -1 0 -1 6.3409 3 1 -1 1 -1 5.1599 4 1 0 -1 -1 3.0248 5 1 0 0 -1 2.0589 6 1 0 1 -1 3.5884 7 1 -1 -1 0 5.2072 8 1 -1 0 0 2.5319 9 1 -1 1 0 4.5411 10 1 0 -1 0 1.3647 11 1 0 1 0 1.3647 12 1 -1 -1 1 4.4379 13 1 -1 0 1 4.3223 14 1 -1 1 1 5.0529 15 1 0 -1 1 3.5884 16 1 0 0 1 2.0589 17 1 0 1 1 3.0248 18 1 1 1 1 4.9541 19 1 1 0 1 6.3409 20 1 1 -1 1 5.1599 21 1 1 1 0 5.2072 22 1 1 0 0 2.5319 23 1 1 -1 0 4.5411 24 1 1 1 -1 4.4379 25 1 1 0 -1 4.3223 26 1 1 -1 -1 5.0529 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4050 atoms have been selected out of 4124 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 369 123 123 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1686 562 562 0.00 6 C006 has 513 171 171 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13651 atoms and 4542 groups and 4537 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4124 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1363 Number of atoms = 4124 Number of groups = 1368 Number of bonds = 4117 Number of angles = 1467 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1365 Number of HB donors = 2708 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1363 Number of atoms = 4124 Number of groups = 1368 Number of bonds = 4117 Number of angles = 1467 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1365 Number of HB donors = 2708 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.57" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1363" Evaluating: 1363-7 Parameter: NUMWAT <- "1356" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1356" Comparing "1081" and "1356". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.57" Parameter: BOX -> "34.57" Parameter: BOX -> "34.57" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.57000 B = 34.57000 C = 34.57000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9563 2 1 -1 0 -1 6.3421 3 1 -1 1 -1 5.1565 4 1 0 -1 -1 3.0229 5 1 0 0 -1 2.0570 6 1 0 1 -1 3.5856 7 1 -1 -1 0 5.2052 8 1 -1 0 0 2.5312 9 1 -1 1 0 4.5389 10 1 0 -1 0 1.3638 11 1 0 1 0 1.3638 12 1 -1 -1 1 4.4344 13 1 -1 0 1 4.3195 14 1 -1 1 1 5.0499 15 1 0 -1 1 3.5856 16 1 0 0 1 2.0570 17 1 0 1 1 3.0229 18 1 1 1 1 4.9563 19 1 1 0 1 6.3421 20 1 1 -1 1 5.1565 21 1 1 1 0 5.2052 22 1 1 0 0 2.5312 23 1 1 -1 0 4.5389 24 1 1 1 -1 4.4344 25 1 1 0 -1 4.3195 26 1 1 -1 -1 5.0499 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4050 atoms have been selected out of 4124 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 369 123 123 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1686 562 562 0.00 6 C006 has 513 171 171 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13651 atoms and 4542 groups and 4537 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4124 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1363 Number of atoms = 4124 Number of groups = 1368 Number of bonds = 4117 Number of angles = 1467 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1365 Number of HB donors = 2708 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1363 Number of atoms = 4124 Number of groups = 1368 Number of bonds = 4117 Number of angles = 1467 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1365 Number of HB donors = 2708 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.568" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1363" Evaluating: 1363-7 Parameter: NUMWAT <- "1356" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1356" Comparing "1081" and "1356". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.568" Parameter: BOX -> "34.568" Parameter: BOX -> "34.568" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.56800 B = 34.56800 C = 34.56800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9586 2 1 -1 0 -1 6.3434 3 1 -1 1 -1 5.1530 4 1 0 -1 -1 3.0211 5 1 0 0 -1 2.0550 6 1 0 1 -1 3.5829 7 1 -1 -1 0 5.2033 8 1 -1 0 0 2.5305 9 1 -1 1 0 4.5366 10 1 0 -1 0 1.3628 11 1 0 1 0 1.3628 12 1 -1 -1 1 4.4310 13 1 -1 0 1 4.3167 14 1 -1 1 1 5.0468 15 1 0 -1 1 3.5829 16 1 0 0 1 2.0550 17 1 0 1 1 3.0211 18 1 1 1 1 4.9586 19 1 1 0 1 6.3434 20 1 1 -1 1 5.1530 21 1 1 1 0 5.2033 22 1 1 0 0 2.5305 23 1 1 -1 0 4.5366 24 1 1 1 -1 4.4310 25 1 1 0 -1 4.3167 26 1 1 -1 -1 5.0468 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4050 atoms have been selected out of 4124 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 369 123 123 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1686 562 562 0.00 6 C006 has 513 171 171 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13657 atoms and 4544 groups and 4539 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4124 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1363 Number of atoms = 4124 Number of groups = 1368 Number of bonds = 4117 Number of angles = 1467 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1365 Number of HB donors = 2708 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1363 Number of atoms = 4124 Number of groups = 1368 Number of bonds = 4117 Number of angles = 1467 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1365 Number of HB donors = 2708 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.566" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1363" Evaluating: 1363-7 Parameter: NUMWAT <- "1356" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1356" Comparing "1081" and "1356". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.566" Parameter: BOX -> "34.566" Parameter: BOX -> "34.566" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.56600 B = 34.56600 C = 34.56600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9608 2 1 -1 0 -1 6.3446 3 1 -1 1 -1 5.1496 4 1 0 -1 -1 3.0192 5 1 0 0 -1 2.0531 6 1 0 1 -1 3.5801 7 1 -1 -1 0 5.2013 8 1 -1 0 0 2.5298 9 1 -1 1 0 4.5344 10 1 0 -1 0 1.3618 11 1 0 1 0 1.3618 12 1 -1 -1 1 4.4275 13 1 -1 0 1 4.3140 14 1 -1 1 1 5.0438 15 1 0 -1 1 3.5801 16 1 0 0 1 2.0531 17 1 0 1 1 3.0192 18 1 1 1 1 4.9608 19 1 1 0 1 6.3446 20 1 1 -1 1 5.1496 21 1 1 1 0 5.2013 22 1 1 0 0 2.5298 23 1 1 -1 0 4.5344 24 1 1 1 -1 4.4275 25 1 1 0 -1 4.3140 26 1 1 -1 -1 5.0438 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4050 atoms have been selected out of 4124 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 880 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1207 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 81 27 27 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1686 562 562 0.00 6 C006 has 513 171 171 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 120 40 40 0.00 13 C013 has 480 160 160 0.00 14 C014 has 114 38 38 0.00 Total of13681 atoms and 4552 groups and 4547 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 4124 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1361 Number of atoms = 4118 Number of groups = 1366 Number of bonds = 4111 Number of angles = 1465 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1363 Number of HB donors = 2704 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1361 Number of atoms = 4118 Number of groups = 1366 Number of bonds = 4111 Number of angles = 1465 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1363 Number of HB donors = 2704 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.564" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1361" Evaluating: 1361-7 Parameter: NUMWAT <- "1354" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1354" Comparing "1081" and "1354". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.564" Parameter: BOX -> "34.564" Parameter: BOX -> "34.564" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.56400 B = 34.56400 C = 34.56400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9631 2 1 -1 0 -1 6.3459 3 1 -1 1 -1 5.1461 4 1 0 -1 -1 3.0174 5 1 0 0 -1 2.0512 6 1 0 1 -1 3.5773 7 1 -1 -1 0 5.1993 8 1 -1 0 0 2.5291 9 1 -1 1 0 4.5321 10 1 0 -1 0 1.3608 11 1 0 1 0 1.3608 12 1 -1 -1 1 4.4241 13 1 -1 0 1 4.3112 14 1 -1 1 1 5.0408 15 1 0 -1 1 3.5773 16 1 0 0 1 2.0512 17 1 0 1 1 3.0174 18 1 1 1 1 4.9631 19 1 1 0 1 6.3459 20 1 1 -1 1 5.1461 21 1 1 1 0 5.1993 22 1 1 0 0 2.5291 23 1 1 -1 0 4.5321 24 1 1 1 -1 4.4241 25 1 1 0 -1 4.3112 26 1 1 -1 -1 5.0408 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4044 atoms have been selected out of 4118 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 81 27 27 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1838 611 611 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13615 atoms and 4530 groups and 4525 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4118 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1361 Number of atoms = 4118 Number of groups = 1366 Number of bonds = 4111 Number of angles = 1465 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1363 Number of HB donors = 2704 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1361 Number of atoms = 4118 Number of groups = 1366 Number of bonds = 4111 Number of angles = 1465 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1363 Number of HB donors = 2704 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.562" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1361" Evaluating: 1361-7 Parameter: NUMWAT <- "1354" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1354" Comparing "1081" and "1354". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.562" Parameter: BOX -> "34.562" Parameter: BOX -> "34.562" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.56200 B = 34.56200 C = 34.56200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9653 2 1 -1 0 -1 6.3471 3 1 -1 1 -1 5.1427 4 1 0 -1 -1 3.0155 5 1 0 0 -1 2.0492 6 1 0 1 -1 3.5746 7 1 -1 -1 0 5.1974 8 1 -1 0 0 2.5285 9 1 -1 1 0 4.5298 10 1 0 -1 0 1.3599 11 1 0 1 0 1.3599 12 1 -1 -1 1 4.4206 13 1 -1 0 1 4.3084 14 1 -1 1 1 5.0377 15 1 0 -1 1 3.5746 16 1 0 0 1 2.0492 17 1 0 1 1 3.0155 18 1 1 1 1 4.9653 19 1 1 0 1 6.3471 20 1 1 -1 1 5.1427 21 1 1 1 0 5.1974 22 1 1 0 0 2.5285 23 1 1 -1 0 4.5298 24 1 1 1 -1 4.4206 25 1 1 0 -1 4.3084 26 1 1 -1 -1 5.0377 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4044 atoms have been selected out of 4118 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 81 27 27 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1838 611 611 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13618 atoms and 4531 groups and 4526 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4118 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1361 Number of atoms = 4118 Number of groups = 1366 Number of bonds = 4111 Number of angles = 1465 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1363 Number of HB donors = 2704 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1361 Number of atoms = 4118 Number of groups = 1366 Number of bonds = 4111 Number of angles = 1465 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1363 Number of HB donors = 2704 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.56" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1361" Evaluating: 1361-7 Parameter: NUMWAT <- "1354" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1354" Comparing "1081" and "1354". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.56" Parameter: BOX -> "34.56" Parameter: BOX -> "34.56" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.56000 B = 34.56000 C = 34.56000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9676 2 1 -1 0 -1 6.3483 3 1 -1 1 -1 5.1392 4 1 0 -1 -1 3.0137 5 1 0 0 -1 2.0473 6 1 0 1 -1 3.5718 7 1 -1 -1 0 5.1954 8 1 -1 0 0 2.5278 9 1 -1 1 0 4.5276 10 1 0 -1 0 1.3589 11 1 0 1 0 1.3589 12 1 -1 -1 1 4.4172 13 1 -1 0 1 4.3056 14 1 -1 1 1 5.0347 15 1 0 -1 1 3.5718 16 1 0 0 1 2.0473 17 1 0 1 1 3.0137 18 1 1 1 1 4.9676 19 1 1 0 1 6.3483 20 1 1 -1 1 5.1392 21 1 1 1 0 5.1954 22 1 1 0 0 2.5278 23 1 1 -1 0 4.5276 24 1 1 1 -1 4.4172 25 1 1 0 -1 4.3056 26 1 1 -1 -1 5.0347 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4044 atoms have been selected out of 4118 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 81 27 27 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1838 611 611 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13618 atoms and 4531 groups and 4526 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4118 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1361 Number of atoms = 4118 Number of groups = 1366 Number of bonds = 4111 Number of angles = 1465 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1363 Number of HB donors = 2704 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1361 Number of atoms = 4118 Number of groups = 1366 Number of bonds = 4111 Number of angles = 1465 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1363 Number of HB donors = 2704 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.558" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1361" Evaluating: 1361-7 Parameter: NUMWAT <- "1354" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1354" Comparing "1081" and "1354". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.558" Parameter: BOX -> "34.558" Parameter: BOX -> "34.558" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.55800 B = 34.55800 C = 34.55800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9699 2 1 -1 0 -1 6.3496 3 1 -1 1 -1 5.1358 4 1 0 -1 -1 3.0118 5 1 0 0 -1 2.0454 6 1 0 1 -1 3.5691 7 1 -1 -1 0 5.1935 8 1 -1 0 0 2.5271 9 1 -1 1 0 4.5253 10 1 0 -1 0 1.3579 11 1 0 1 0 1.3579 12 1 -1 -1 1 4.4137 13 1 -1 0 1 4.3028 14 1 -1 1 1 5.0317 15 1 0 -1 1 3.5691 16 1 0 0 1 2.0454 17 1 0 1 1 3.0118 18 1 1 1 1 4.9699 19 1 1 0 1 6.3496 20 1 1 -1 1 5.1358 21 1 1 1 0 5.1935 22 1 1 0 0 2.5271 23 1 1 -1 0 4.5253 24 1 1 1 -1 4.4137 25 1 1 0 -1 4.3028 26 1 1 -1 -1 5.0317 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4044 atoms have been selected out of 4118 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 81 27 27 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1838 611 611 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13621 atoms and 4532 groups and 4527 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4118 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1361 Number of atoms = 4118 Number of groups = 1366 Number of bonds = 4111 Number of angles = 1465 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1363 Number of HB donors = 2704 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1361 Number of atoms = 4118 Number of groups = 1366 Number of bonds = 4111 Number of angles = 1465 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1363 Number of HB donors = 2704 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.556" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1361" Evaluating: 1361-7 Parameter: NUMWAT <- "1354" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1354" Comparing "1081" and "1354". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.556" Parameter: BOX -> "34.556" Parameter: BOX -> "34.556" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.55600 B = 34.55600 C = 34.55600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9721 2 1 -1 0 -1 6.3508 3 1 -1 1 -1 5.1324 4 1 0 -1 -1 3.0100 5 1 0 0 -1 2.0434 6 1 0 1 -1 3.5663 7 1 -1 -1 0 5.1915 8 1 -1 0 0 2.5264 9 1 -1 1 0 4.5231 10 1 0 -1 0 1.3570 11 1 0 1 0 1.3570 12 1 -1 -1 1 4.4103 13 1 -1 0 1 4.3000 14 1 -1 1 1 5.0286 15 1 0 -1 1 3.5663 16 1 0 0 1 2.0434 17 1 0 1 1 3.0100 18 1 1 1 1 4.9721 19 1 1 0 1 6.3508 20 1 1 -1 1 5.1324 21 1 1 1 0 5.1915 22 1 1 0 0 2.5264 23 1 1 -1 0 4.5231 24 1 1 1 -1 4.4103 25 1 1 0 -1 4.3000 26 1 1 -1 -1 5.0286 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4044 atoms have been selected out of 4118 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 113 OPERATED ON BY TRANSFORMATION C022 RESIDUE 451 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 81 27 27 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1841 612 612 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13615 atoms and 4530 groups and 4525 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 4118 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1359 Number of atoms = 4112 Number of groups = 1364 Number of bonds = 4105 Number of angles = 1463 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1361 Number of HB donors = 2700 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1359 Number of atoms = 4112 Number of groups = 1364 Number of bonds = 4105 Number of angles = 1463 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1361 Number of HB donors = 2700 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.554" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1359" Evaluating: 1359-7 Parameter: NUMWAT <- "1352" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1352" Comparing "1081" and "1352". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.554" Parameter: BOX -> "34.554" Parameter: BOX -> "34.554" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.55400 B = 34.55400 C = 34.55400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9744 2 1 -1 0 -1 6.3521 3 1 -1 1 -1 5.1289 4 1 0 -1 -1 3.0081 5 1 0 0 -1 2.0415 6 1 0 1 -1 3.5635 7 1 -1 -1 0 5.1896 8 1 -1 0 0 2.5258 9 1 -1 1 0 4.5208 10 1 0 -1 0 1.3560 11 1 0 1 0 1.3560 12 1 -1 -1 1 4.4068 13 1 -1 0 1 4.2973 14 1 -1 1 1 5.0256 15 1 0 -1 1 3.5635 16 1 0 0 1 2.0415 17 1 0 1 1 3.0081 18 1 1 1 1 4.9744 19 1 1 0 1 6.3521 20 1 1 -1 1 5.1289 21 1 1 1 0 5.1896 22 1 1 0 0 2.5258 23 1 1 -1 0 4.5208 24 1 1 1 -1 4.4068 25 1 1 0 -1 4.2973 26 1 1 -1 -1 5.0256 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4038 atoms have been selected out of 4112 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 294 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 81 27 27 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1835 610 610 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 114 38 38 0.00 13 C013 has 477 159 159 0.00 14 C014 has 102 34 34 0.00 Total of13594 atoms and 4523 groups and 4518 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4112 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.552" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1358" Evaluating: 1358-7 Parameter: NUMWAT <- "1351" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1351" Comparing "1081" and "1351". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.552" Parameter: BOX -> "34.552" Parameter: BOX -> "34.552" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.55200 B = 34.55200 C = 34.55200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9766 2 1 -1 0 -1 6.3533 3 1 -1 1 -1 5.1255 4 1 0 -1 -1 3.0063 5 1 0 0 -1 2.0396 6 1 0 1 -1 3.5608 7 1 -1 -1 0 5.1876 8 1 -1 0 0 2.5251 9 1 -1 1 0 4.5186 10 1 0 -1 0 1.3550 11 1 0 1 0 1.3550 12 1 -1 -1 1 4.4034 13 1 -1 0 1 4.2945 14 1 -1 1 1 5.0225 15 1 0 -1 1 3.5608 16 1 0 0 1 2.0396 17 1 0 1 1 3.0063 18 1 1 1 1 4.9766 19 1 1 0 1 6.3533 20 1 1 -1 1 5.1255 21 1 1 1 0 5.1876 22 1 1 0 0 2.5251 23 1 1 -1 0 4.5186 24 1 1 1 -1 4.4034 25 1 1 0 -1 4.2945 26 1 1 -1 -1 5.0225 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4035 atoms have been selected out of 4109 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 81 27 27 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 102 34 34 0.00 Total of13597 atoms and 4524 groups and 4519 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4109 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.55" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1358" Evaluating: 1358-7 Parameter: NUMWAT <- "1351" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1351" Comparing "1081" and "1351". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.55" Parameter: BOX -> "34.55" Parameter: BOX -> "34.55" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.55000 B = 34.55000 C = 34.55000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9789 2 1 -1 0 -1 6.3546 3 1 -1 1 -1 5.1220 4 1 0 -1 -1 3.0044 5 1 0 0 -1 2.0376 6 1 0 1 -1 3.5580 7 1 -1 -1 0 5.1857 8 1 -1 0 0 2.5244 9 1 -1 1 0 4.5163 10 1 0 -1 0 1.3541 11 1 0 1 0 1.3541 12 1 -1 -1 1 4.3999 13 1 -1 0 1 4.2917 14 1 -1 1 1 5.0195 15 1 0 -1 1 3.5580 16 1 0 0 1 2.0376 17 1 0 1 1 3.0044 18 1 1 1 1 4.9789 19 1 1 0 1 6.3546 20 1 1 -1 1 5.1220 21 1 1 1 0 5.1857 22 1 1 0 0 2.5244 23 1 1 -1 0 4.5163 24 1 1 1 -1 4.3999 25 1 1 0 -1 4.2917 26 1 1 -1 -1 5.0195 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4035 atoms have been selected out of 4109 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 81 27 27 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 102 34 34 0.00 Total of13597 atoms and 4524 groups and 4519 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4109 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.548" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1358" Evaluating: 1358-7 Parameter: NUMWAT <- "1351" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1351" Comparing "1081" and "1351". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.548" Parameter: BOX -> "34.548" Parameter: BOX -> "34.548" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.54800 B = 34.54800 C = 34.54800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9812 2 1 -1 0 -1 6.3558 3 1 -1 1 -1 5.1186 4 1 0 -1 -1 3.0026 5 1 0 0 -1 2.0357 6 1 0 1 -1 3.5552 7 1 -1 -1 0 5.1838 8 1 -1 0 0 2.5238 9 1 -1 1 0 4.5141 10 1 0 -1 0 1.3531 11 1 0 1 0 1.3531 12 1 -1 -1 1 4.3964 13 1 -1 0 1 4.2889 14 1 -1 1 1 5.0165 15 1 0 -1 1 3.5552 16 1 0 0 1 2.0357 17 1 0 1 1 3.0026 18 1 1 1 1 4.9812 19 1 1 0 1 6.3558 20 1 1 -1 1 5.1186 21 1 1 1 0 5.1838 22 1 1 0 0 2.5238 23 1 1 -1 0 4.5141 24 1 1 1 -1 4.3964 25 1 1 0 -1 4.2889 26 1 1 -1 -1 5.0165 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4035 atoms have been selected out of 4109 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 81 27 27 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 102 34 34 0.00 Total of13597 atoms and 4524 groups and 4519 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4109 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.546" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1358" Evaluating: 1358-7 Parameter: NUMWAT <- "1351" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1351" Comparing "1081" and "1351". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.546" Parameter: BOX -> "34.546" Parameter: BOX -> "34.546" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.54600 B = 34.54600 C = 34.54600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9834 2 1 -1 0 -1 6.3571 3 1 -1 1 -1 5.1151 4 1 0 -1 -1 3.0008 5 1 0 0 -1 2.0338 6 1 0 1 -1 3.5525 7 1 -1 -1 0 5.1818 8 1 -1 0 0 2.5231 9 1 -1 1 0 4.5118 10 1 0 -1 0 1.3522 11 1 0 1 0 1.3522 12 1 -1 -1 1 4.3930 13 1 -1 0 1 4.2861 14 1 -1 1 1 5.0134 15 1 0 -1 1 3.5525 16 1 0 0 1 2.0338 17 1 0 1 1 3.0008 18 1 1 1 1 4.9834 19 1 1 0 1 6.3571 20 1 1 -1 1 5.1151 21 1 1 1 0 5.1818 22 1 1 0 0 2.5231 23 1 1 -1 0 4.5118 24 1 1 1 -1 4.3930 25 1 1 0 -1 4.2861 26 1 1 -1 -1 5.0134 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4035 atoms have been selected out of 4109 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 102 34 34 0.00 Total of13600 atoms and 4525 groups and 4520 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4109 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.544" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1358" Evaluating: 1358-7 Parameter: NUMWAT <- "1351" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1351" Comparing "1081" and "1351". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.544" Parameter: BOX -> "34.544" Parameter: BOX -> "34.544" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.54400 B = 34.54400 C = 34.54400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9857 2 1 -1 0 -1 6.3583 3 1 -1 1 -1 5.1117 4 1 0 -1 -1 2.9989 5 1 0 0 -1 2.0318 6 1 0 1 -1 3.5497 7 1 -1 -1 0 5.1799 8 1 -1 0 0 2.5224 9 1 -1 1 0 4.5096 10 1 0 -1 0 1.3512 11 1 0 1 0 1.3512 12 1 -1 -1 1 4.3895 13 1 -1 0 1 4.2834 14 1 -1 1 1 5.0104 15 1 0 -1 1 3.5497 16 1 0 0 1 2.0318 17 1 0 1 1 2.9989 18 1 1 1 1 4.9857 19 1 1 0 1 6.3583 20 1 1 -1 1 5.1117 21 1 1 1 0 5.1799 22 1 1 0 0 2.5224 23 1 1 -1 0 4.5096 24 1 1 1 -1 4.3895 25 1 1 0 -1 4.2834 26 1 1 -1 -1 5.0104 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4035 atoms have been selected out of 4109 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 102 34 34 0.00 Total of13600 atoms and 4525 groups and 4520 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4109 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.542" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1358" Evaluating: 1358-7 Parameter: NUMWAT <- "1351" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1351" Comparing "1081" and "1351". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.542" Parameter: BOX -> "34.542" Parameter: BOX -> "34.542" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.54200 B = 34.54200 C = 34.54200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9880 2 1 -1 0 -1 6.3596 3 1 -1 1 -1 5.1083 4 1 0 -1 -1 2.9971 5 1 0 0 -1 2.0299 6 1 0 1 -1 3.5469 7 1 -1 -1 0 5.1779 8 1 -1 0 0 2.5218 9 1 -1 1 0 4.5073 10 1 0 -1 0 1.3503 11 1 0 1 0 1.3503 12 1 -1 -1 1 4.3861 13 1 -1 0 1 4.2806 14 1 -1 1 1 5.0074 15 1 0 -1 1 3.5469 16 1 0 0 1 2.0299 17 1 0 1 1 2.9971 18 1 1 1 1 4.9880 19 1 1 0 1 6.3596 20 1 1 -1 1 5.1083 21 1 1 1 0 5.1779 22 1 1 0 0 2.5218 23 1 1 -1 0 4.5073 24 1 1 1 -1 4.3861 25 1 1 0 -1 4.2806 26 1 1 -1 -1 5.0074 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4035 atoms have been selected out of 4109 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 102 34 34 0.00 Total of13600 atoms and 4525 groups and 4520 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4109 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.54" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1358" Evaluating: 1358-7 Parameter: NUMWAT <- "1351" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1351" Comparing "1081" and "1351". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.54" Parameter: BOX -> "34.54" Parameter: BOX -> "34.54" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.54000 B = 34.54000 C = 34.54000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9902 2 1 -1 0 -1 6.3608 3 1 -1 1 -1 5.1048 4 1 0 -1 -1 2.9953 5 1 0 0 -1 2.0280 6 1 0 1 -1 3.5442 7 1 -1 -1 0 5.1760 8 1 -1 0 0 2.5211 9 1 -1 1 0 4.5051 10 1 0 -1 0 1.3493 11 1 0 1 0 1.3493 12 1 -1 -1 1 4.3826 13 1 -1 0 1 4.2778 14 1 -1 1 1 5.0043 15 1 0 -1 1 3.5442 16 1 0 0 1 2.0280 17 1 0 1 1 2.9953 18 1 1 1 1 4.9902 19 1 1 0 1 6.3608 20 1 1 -1 1 5.1048 21 1 1 1 0 5.1760 22 1 1 0 0 2.5211 23 1 1 -1 0 4.5051 24 1 1 1 -1 4.3826 25 1 1 0 -1 4.2778 26 1 1 -1 -1 5.0043 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4035 atoms have been selected out of 4109 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1761 587 587 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 102 34 34 0.00 Total of13603 atoms and 4526 groups and 4521 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4109 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.538" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1358" Evaluating: 1358-7 Parameter: NUMWAT <- "1351" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1351" Comparing "1081" and "1351". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.538" Parameter: BOX -> "34.538" Parameter: BOX -> "34.538" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.53800 B = 34.53800 C = 34.53800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9925 2 1 -1 0 -1 6.3621 3 1 -1 1 -1 5.1014 4 1 0 -1 -1 2.9934 5 1 0 0 -1 2.0261 6 1 0 1 -1 3.5414 7 1 -1 -1 0 5.1740 8 1 -1 0 0 2.5204 9 1 -1 1 0 4.5028 10 1 0 -1 0 1.3484 11 1 0 1 0 1.3484 12 1 -1 -1 1 4.3792 13 1 -1 0 1 4.2750 14 1 -1 1 1 5.0013 15 1 0 -1 1 3.5414 16 1 0 0 1 2.0261 17 1 0 1 1 2.9934 18 1 1 1 1 4.9925 19 1 1 0 1 6.3621 20 1 1 -1 1 5.1014 21 1 1 1 0 5.1740 22 1 1 0 0 2.5204 23 1 1 -1 0 4.5028 24 1 1 1 -1 4.3792 25 1 1 0 -1 4.2750 26 1 1 -1 -1 5.0013 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4035 atoms have been selected out of 4109 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1767 589 589 0.00 12 C012 has 117 39 39 0.00 13 C013 has 480 160 160 0.00 14 C014 has 102 34 34 0.00 Total of13612 atoms and 4529 groups and 4524 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4109 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.536" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1358" Evaluating: 1358-7 Parameter: NUMWAT <- "1351" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1351" Comparing "1081" and "1351". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.536" Parameter: BOX -> "34.536" Parameter: BOX -> "34.536" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.53600 B = 34.53600 C = 34.53600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9948 2 1 -1 0 -1 6.3634 3 1 -1 1 -1 5.0979 4 1 0 -1 -1 2.9916 5 1 0 0 -1 2.0241 6 1 0 1 -1 3.5387 7 1 -1 -1 0 5.1721 8 1 -1 0 0 2.5198 9 1 -1 1 0 4.5006 10 1 0 -1 0 1.3474 11 1 0 1 0 1.3474 12 1 -1 -1 1 4.3757 13 1 -1 0 1 4.2722 14 1 -1 1 1 4.9983 15 1 0 -1 1 3.5387 16 1 0 0 1 2.0241 17 1 0 1 1 2.9916 18 1 1 1 1 4.9948 19 1 1 0 1 6.3634 20 1 1 -1 1 5.0979 21 1 1 1 0 5.1721 22 1 1 0 0 2.5198 23 1 1 -1 0 4.5006 24 1 1 1 -1 4.3757 25 1 1 0 -1 4.2722 26 1 1 -1 -1 4.9983 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4035 atoms have been selected out of 4109 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1767 589 589 0.00 12 C012 has 117 39 39 0.00 13 C013 has 480 160 160 0.00 14 C014 has 102 34 34 0.00 Total of13612 atoms and 4529 groups and 4524 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4109 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.534" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1358" Evaluating: 1358-7 Parameter: NUMWAT <- "1351" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1351" Comparing "1081" and "1351". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.534" Parameter: BOX -> "34.534" Parameter: BOX -> "34.534" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.53400 B = 34.53400 C = 34.53400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9970 2 1 -1 0 -1 6.3646 3 1 -1 1 -1 5.0945 4 1 0 -1 -1 2.9898 5 1 0 0 -1 2.0222 6 1 0 1 -1 3.5359 7 1 -1 -1 0 5.1701 8 1 -1 0 0 2.5191 9 1 -1 1 0 4.4983 10 1 0 -1 0 1.3465 11 1 0 1 0 1.3465 12 1 -1 -1 1 4.3723 13 1 -1 0 1 4.2694 14 1 -1 1 1 4.9952 15 1 0 -1 1 3.5359 16 1 0 0 1 2.0222 17 1 0 1 1 2.9898 18 1 1 1 1 4.9970 19 1 1 0 1 6.3646 20 1 1 -1 1 5.0945 21 1 1 1 0 5.1701 22 1 1 0 0 2.5191 23 1 1 -1 0 4.4983 24 1 1 1 -1 4.3723 25 1 1 0 -1 4.2694 26 1 1 -1 -1 4.9952 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4035 atoms have been selected out of 4109 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1767 589 589 0.00 12 C012 has 117 39 39 0.00 13 C013 has 480 160 160 0.00 14 C014 has 102 34 34 0.00 Total of13612 atoms and 4529 groups and 4524 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4109 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.532" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1358" Evaluating: 1358-7 Parameter: NUMWAT <- "1351" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1351" Comparing "1081" and "1351". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.532" Parameter: BOX -> "34.532" Parameter: BOX -> "34.532" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.53200 B = 34.53200 C = 34.53200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 4.9993 2 1 -1 0 -1 6.3659 3 1 -1 1 -1 5.0910 4 1 0 -1 -1 2.9880 5 1 0 0 -1 2.0203 6 1 0 1 -1 3.5331 7 1 -1 -1 0 5.1682 8 1 -1 0 0 2.5185 9 1 -1 1 0 4.4961 10 1 0 -1 0 1.3456 11 1 0 1 0 1.3456 12 1 -1 -1 1 4.3688 13 1 -1 0 1 4.2667 14 1 -1 1 1 4.9922 15 1 0 -1 1 3.5331 16 1 0 0 1 2.0203 17 1 0 1 1 2.9880 18 1 1 1 1 4.9993 19 1 1 0 1 6.3659 20 1 1 -1 1 5.0910 21 1 1 1 0 5.1682 22 1 1 0 0 2.5185 23 1 1 -1 0 4.4961 24 1 1 1 -1 4.3688 25 1 1 0 -1 4.2667 26 1 1 -1 -1 4.9922 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4035 atoms have been selected out of 4109 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1767 589 589 0.00 12 C012 has 117 39 39 0.00 13 C013 has 480 160 160 0.00 14 C014 has 102 34 34 0.00 Total of13612 atoms and 4529 groups and 4524 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4109 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.53" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1358" Evaluating: 1358-7 Parameter: NUMWAT <- "1351" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1351" Comparing "1081" and "1351". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.53" Parameter: BOX -> "34.53" Parameter: BOX -> "34.53" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.53000 B = 34.53000 C = 34.53000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0016 2 1 -1 0 -1 6.3671 3 1 -1 1 -1 5.0876 4 1 0 -1 -1 2.9861 5 1 0 0 -1 2.0183 6 1 0 1 -1 3.5304 7 1 -1 -1 0 5.1663 8 1 -1 0 0 2.5178 9 1 -1 1 0 4.4939 10 1 0 -1 0 1.3446 11 1 0 1 0 1.3446 12 1 -1 -1 1 4.3654 13 1 -1 0 1 4.2639 14 1 -1 1 1 4.9892 15 1 0 -1 1 3.5304 16 1 0 0 1 2.0183 17 1 0 1 1 2.9861 18 1 1 1 1 5.0016 19 1 1 0 1 6.3671 20 1 1 -1 1 5.0876 21 1 1 1 0 5.1663 22 1 1 0 0 2.5178 23 1 1 -1 0 4.4939 24 1 1 1 -1 4.3654 25 1 1 0 -1 4.2639 26 1 1 -1 -1 4.9892 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4035 atoms have been selected out of 4109 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1767 589 589 0.00 12 C012 has 117 39 39 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13615 atoms and 4530 groups and 4525 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4109 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.528" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1358" Evaluating: 1358-7 Parameter: NUMWAT <- "1351" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1351" Comparing "1081" and "1351". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.528" Parameter: BOX -> "34.528" Parameter: BOX -> "34.528" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.52800 B = 34.52800 C = 34.52800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0039 2 1 -1 0 -1 6.3684 3 1 -1 1 -1 5.0842 4 1 0 -1 -1 2.9843 5 1 0 0 -1 2.0164 6 1 0 1 -1 3.5276 7 1 -1 -1 0 5.1643 8 1 -1 0 0 2.5172 9 1 -1 1 0 4.4916 10 1 0 -1 0 1.3437 11 1 0 1 0 1.3437 12 1 -1 -1 1 4.3619 13 1 -1 0 1 4.2611 14 1 -1 1 1 4.9862 15 1 0 -1 1 3.5276 16 1 0 0 1 2.0164 17 1 0 1 1 2.9843 18 1 1 1 1 5.0039 19 1 1 0 1 6.3684 20 1 1 -1 1 5.0842 21 1 1 1 0 5.1643 22 1 1 0 0 2.5172 23 1 1 -1 0 4.4916 24 1 1 1 -1 4.3619 25 1 1 0 -1 4.2611 26 1 1 -1 -1 4.9862 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4035 atoms have been selected out of 4109 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1767 589 589 0.00 12 C012 has 117 39 39 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13618 atoms and 4531 groups and 4526 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4109 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1358 Number of atoms = 4109 Number of groups = 1363 Number of bonds = 4102 Number of angles = 1462 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1360 Number of HB donors = 2698 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.526" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1358" Evaluating: 1358-7 Parameter: NUMWAT <- "1351" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1351" Comparing "1081" and "1351". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.526" Parameter: BOX -> "34.526" Parameter: BOX -> "34.526" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.52600 B = 34.52600 C = 34.52600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0061 2 1 -1 0 -1 6.3697 3 1 -1 1 -1 5.0807 4 1 0 -1 -1 2.9825 5 1 0 0 -1 2.0145 6 1 0 1 -1 3.5248 7 1 -1 -1 0 5.1624 8 1 -1 0 0 2.5165 9 1 -1 1 0 4.4894 10 1 0 -1 0 1.3428 11 1 0 1 0 1.3428 12 1 -1 -1 1 4.3585 13 1 -1 0 1 4.2583 14 1 -1 1 1 4.9831 15 1 0 -1 1 3.5248 16 1 0 0 1 2.0145 17 1 0 1 1 2.9825 18 1 1 1 1 5.0061 19 1 1 0 1 6.3697 20 1 1 -1 1 5.0807 21 1 1 1 0 5.1624 22 1 1 0 0 2.5165 23 1 1 -1 0 4.4894 24 1 1 1 -1 4.3585 25 1 1 0 -1 4.2583 26 1 1 -1 -1 4.9831 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4035 atoms have been selected out of 4109 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 38 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1835 610 610 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1767 589 589 0.00 12 C012 has 117 39 39 0.00 13 C013 has 486 162 162 0.00 14 C014 has 105 35 35 0.00 Total of13633 atoms and 4536 groups and 4531 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4109 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1357 Number of atoms = 4106 Number of groups = 1362 Number of bonds = 4099 Number of angles = 1461 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1359 Number of HB donors = 2696 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1357 Number of atoms = 4106 Number of groups = 1362 Number of bonds = 4099 Number of angles = 1461 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1359 Number of HB donors = 2696 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.524" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1357" Evaluating: 1357-7 Parameter: NUMWAT <- "1350" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1350" Comparing "1081" and "1350". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.524" Parameter: BOX -> "34.524" Parameter: BOX -> "34.524" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.52400 B = 34.52400 C = 34.52400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0084 2 1 -1 0 -1 6.3709 3 1 -1 1 -1 5.0773 4 1 0 -1 -1 2.9807 5 1 0 0 -1 2.0126 6 1 0 1 -1 3.5221 7 1 -1 -1 0 5.1605 8 1 -1 0 0 2.5159 9 1 -1 1 0 4.4871 10 1 0 -1 0 1.3418 11 1 0 1 0 1.3418 12 1 -1 -1 1 4.3550 13 1 -1 0 1 4.2555 14 1 -1 1 1 4.9801 15 1 0 -1 1 3.5221 16 1 0 0 1 2.0126 17 1 0 1 1 2.9807 18 1 1 1 1 5.0084 19 1 1 0 1 6.3709 20 1 1 -1 1 5.0773 21 1 1 1 0 5.1605 22 1 1 0 0 2.5159 23 1 1 -1 0 4.4871 24 1 1 1 -1 4.3550 25 1 1 0 -1 4.2555 26 1 1 -1 -1 4.9801 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4032 atoms have been selected out of 4106 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1767 589 589 0.00 12 C012 has 117 39 39 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13618 atoms and 4531 groups and 4526 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4106 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1357 Number of atoms = 4106 Number of groups = 1362 Number of bonds = 4099 Number of angles = 1461 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1359 Number of HB donors = 2696 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1357 Number of atoms = 4106 Number of groups = 1362 Number of bonds = 4099 Number of angles = 1461 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1359 Number of HB donors = 2696 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.522" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1357" Evaluating: 1357-7 Parameter: NUMWAT <- "1350" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1350" Comparing "1081" and "1350". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.522" Parameter: BOX -> "34.522" Parameter: BOX -> "34.522" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.52200 B = 34.52200 C = 34.52200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0107 2 1 -1 0 -1 6.3722 3 1 -1 1 -1 5.0738 4 1 0 -1 -1 2.9788 5 1 0 0 -1 2.0106 6 1 0 1 -1 3.5193 7 1 -1 -1 0 5.1585 8 1 -1 0 0 2.5152 9 1 -1 1 0 4.4849 10 1 0 -1 0 1.3409 11 1 0 1 0 1.3409 12 1 -1 -1 1 4.3516 13 1 -1 0 1 4.2528 14 1 -1 1 1 4.9771 15 1 0 -1 1 3.5193 16 1 0 0 1 2.0106 17 1 0 1 1 2.9788 18 1 1 1 1 5.0107 19 1 1 0 1 6.3722 20 1 1 -1 1 5.0738 21 1 1 1 0 5.1585 22 1 1 0 0 2.5152 23 1 1 -1 0 4.4849 24 1 1 1 -1 4.3516 25 1 1 0 -1 4.2528 26 1 1 -1 -1 4.9771 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4032 atoms have been selected out of 4106 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1767 589 589 0.00 12 C012 has 117 39 39 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13618 atoms and 4531 groups and 4526 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4106 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1357 Number of atoms = 4106 Number of groups = 1362 Number of bonds = 4099 Number of angles = 1461 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1359 Number of HB donors = 2696 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1357 Number of atoms = 4106 Number of groups = 1362 Number of bonds = 4099 Number of angles = 1461 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1359 Number of HB donors = 2696 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.52" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1357" Evaluating: 1357-7 Parameter: NUMWAT <- "1350" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1350" Comparing "1081" and "1350". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.52" Parameter: BOX -> "34.52" Parameter: BOX -> "34.52" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.52000 B = 34.52000 C = 34.52000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0130 2 1 -1 0 -1 6.3734 3 1 -1 1 -1 5.0704 4 1 0 -1 -1 2.9770 5 1 0 0 -1 2.0087 6 1 0 1 -1 3.5166 7 1 -1 -1 0 5.1566 8 1 -1 0 0 2.5146 9 1 -1 1 0 4.4826 10 1 0 -1 0 1.3400 11 1 0 1 0 1.3400 12 1 -1 -1 1 4.3481 13 1 -1 0 1 4.2500 14 1 -1 1 1 4.9740 15 1 0 -1 1 3.5166 16 1 0 0 1 2.0087 17 1 0 1 1 2.9770 18 1 1 1 1 5.0130 19 1 1 0 1 6.3734 20 1 1 -1 1 5.0704 21 1 1 1 0 5.1566 22 1 1 0 0 2.5146 23 1 1 -1 0 4.4826 24 1 1 1 -1 4.3481 25 1 1 0 -1 4.2500 26 1 1 -1 -1 4.9740 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4032 atoms have been selected out of 4106 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1767 589 589 0.00 12 C012 has 117 39 39 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13618 atoms and 4531 groups and 4526 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4106 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1357 Number of atoms = 4106 Number of groups = 1362 Number of bonds = 4099 Number of angles = 1461 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1359 Number of HB donors = 2696 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1357 Number of atoms = 4106 Number of groups = 1362 Number of bonds = 4099 Number of angles = 1461 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1359 Number of HB donors = 2696 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.518" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1357" Evaluating: 1357-7 Parameter: NUMWAT <- "1350" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1350" Comparing "1081" and "1350". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.518" Parameter: BOX -> "34.518" Parameter: BOX -> "34.518" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.51800 B = 34.51800 C = 34.51800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0153 2 1 -1 0 -1 6.3747 3 1 -1 1 -1 5.0669 4 1 0 -1 -1 2.9752 5 1 0 0 -1 2.0068 6 1 0 1 -1 3.5138 7 1 -1 -1 0 5.1547 8 1 -1 0 0 2.5139 9 1 -1 1 0 4.4804 10 1 0 -1 0 1.3391 11 1 0 1 0 1.3391 12 1 -1 -1 1 4.3446 13 1 -1 0 1 4.2472 14 1 -1 1 1 4.9710 15 1 0 -1 1 3.5138 16 1 0 0 1 2.0068 17 1 0 1 1 2.9752 18 1 1 1 1 5.0153 19 1 1 0 1 6.3747 20 1 1 -1 1 5.0669 21 1 1 1 0 5.1547 22 1 1 0 0 2.5139 23 1 1 -1 0 4.4804 24 1 1 1 -1 4.3446 25 1 1 0 -1 4.2472 26 1 1 -1 -1 4.9710 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4032 atoms have been selected out of 4106 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1767 589 589 0.00 12 C012 has 120 40 40 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13624 atoms and 4533 groups and 4528 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4106 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1357 Number of atoms = 4106 Number of groups = 1362 Number of bonds = 4099 Number of angles = 1461 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1359 Number of HB donors = 2696 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1357 Number of atoms = 4106 Number of groups = 1362 Number of bonds = 4099 Number of angles = 1461 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1359 Number of HB donors = 2696 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.516" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1357" Evaluating: 1357-7 Parameter: NUMWAT <- "1350" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1350" Comparing "1081" and "1350". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.516" Parameter: BOX -> "34.516" Parameter: BOX -> "34.516" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.51600 B = 34.51600 C = 34.51600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0176 2 1 -1 0 -1 6.3760 3 1 -1 1 -1 5.0635 4 1 0 -1 -1 2.9734 5 1 0 0 -1 2.0048 6 1 0 1 -1 3.5110 7 1 -1 -1 0 5.1527 8 1 -1 0 0 2.5133 9 1 -1 1 0 4.4782 10 1 0 -1 0 1.3381 11 1 0 1 0 1.3381 12 1 -1 -1 1 4.3412 13 1 -1 0 1 4.2444 14 1 -1 1 1 4.9680 15 1 0 -1 1 3.5110 16 1 0 0 1 2.0048 17 1 0 1 1 2.9734 18 1 1 1 1 5.0176 19 1 1 0 1 6.3760 20 1 1 -1 1 5.0635 21 1 1 1 0 5.1527 22 1 1 0 0 2.5133 23 1 1 -1 0 4.4782 24 1 1 1 -1 4.3412 25 1 1 0 -1 4.2444 26 1 1 -1 -1 4.9680 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4032 atoms have been selected out of 4106 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1767 589 589 0.00 12 C012 has 120 40 40 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13627 atoms and 4534 groups and 4529 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4106 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1357 Number of atoms = 4106 Number of groups = 1362 Number of bonds = 4099 Number of angles = 1461 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1359 Number of HB donors = 2696 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1357 Number of atoms = 4106 Number of groups = 1362 Number of bonds = 4099 Number of angles = 1461 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1359 Number of HB donors = 2696 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.514" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1357" Evaluating: 1357-7 Parameter: NUMWAT <- "1350" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1350" Comparing "1081" and "1350". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.514" Parameter: BOX -> "34.514" Parameter: BOX -> "34.514" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.51400 B = 34.51400 C = 34.51400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0198 2 1 -1 0 -1 6.3772 3 1 -1 1 -1 5.0601 4 1 0 -1 -1 2.9716 5 1 0 0 -1 2.0029 6 1 0 1 -1 3.5083 7 1 -1 -1 0 5.1508 8 1 -1 0 0 2.5126 9 1 -1 1 0 4.4759 10 1 0 -1 0 1.3372 11 1 0 1 0 1.3372 12 1 -1 -1 1 4.3377 13 1 -1 0 1 4.2416 14 1 -1 1 1 4.9650 15 1 0 -1 1 3.5083 16 1 0 0 1 2.0029 17 1 0 1 1 2.9716 18 1 1 1 1 5.0198 19 1 1 0 1 6.3772 20 1 1 -1 1 5.0601 21 1 1 1 0 5.1508 22 1 1 0 0 2.5126 23 1 1 -1 0 4.4759 24 1 1 1 -1 4.3377 25 1 1 0 -1 4.2416 26 1 1 -1 -1 4.9650 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4032 atoms have been selected out of 4106 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 369 123 123 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1838 611 611 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1767 589 589 0.00 12 C012 has 120 40 40 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13636 atoms and 4537 groups and 4532 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4106 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1357 Number of atoms = 4106 Number of groups = 1362 Number of bonds = 4099 Number of angles = 1461 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1359 Number of HB donors = 2696 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1357 Number of atoms = 4106 Number of groups = 1362 Number of bonds = 4099 Number of angles = 1461 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1359 Number of HB donors = 2696 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.512" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1357" Evaluating: 1357-7 Parameter: NUMWAT <- "1350" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1350" Comparing "1081" and "1350". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.512" Parameter: BOX -> "34.512" Parameter: BOX -> "34.512" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.51200 B = 34.51200 C = 34.51200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0221 2 1 -1 0 -1 6.3785 3 1 -1 1 -1 5.0566 4 1 0 -1 -1 2.9698 5 1 0 0 -1 2.0010 6 1 0 1 -1 3.5055 7 1 -1 -1 0 5.1489 8 1 -1 0 0 2.5120 9 1 -1 1 0 4.4737 10 1 0 -1 0 1.3363 11 1 0 1 0 1.3363 12 1 -1 -1 1 4.3343 13 1 -1 0 1 4.2389 14 1 -1 1 1 4.9619 15 1 0 -1 1 3.5055 16 1 0 0 1 2.0010 17 1 0 1 1 2.9698 18 1 1 1 1 5.0221 19 1 1 0 1 6.3785 20 1 1 -1 1 5.0566 21 1 1 1 0 5.1489 22 1 1 0 0 2.5120 23 1 1 -1 0 4.4737 24 1 1 1 -1 4.3343 25 1 1 0 -1 4.2389 26 1 1 -1 -1 4.9619 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4032 atoms have been selected out of 4106 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 369 123 123 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1838 611 611 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1767 589 589 0.00 12 C012 has 120 40 40 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13636 atoms and 4537 groups and 4532 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4106 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1357 Number of atoms = 4106 Number of groups = 1362 Number of bonds = 4099 Number of angles = 1461 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1359 Number of HB donors = 2696 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1357 Number of atoms = 4106 Number of groups = 1362 Number of bonds = 4099 Number of angles = 1461 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1359 Number of HB donors = 2696 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.51" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1357" Evaluating: 1357-7 Parameter: NUMWAT <- "1350" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1350" Comparing "1081" and "1350". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.51" Parameter: BOX -> "34.51" Parameter: BOX -> "34.51" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.51000 B = 34.51000 C = 34.51000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0244 2 1 -1 0 -1 6.3798 3 1 -1 1 -1 5.0532 4 1 0 -1 -1 2.9680 5 1 0 0 -1 1.9991 6 1 0 1 -1 3.5028 7 1 -1 -1 0 5.1469 8 1 -1 0 0 2.5113 9 1 -1 1 0 4.4714 10 1 0 -1 0 1.3354 11 1 0 1 0 1.3354 12 1 -1 -1 1 4.3308 13 1 -1 0 1 4.2361 14 1 -1 1 1 4.9589 15 1 0 -1 1 3.5028 16 1 0 0 1 1.9991 17 1 0 1 1 2.9680 18 1 1 1 1 5.0244 19 1 1 0 1 6.3798 20 1 1 -1 1 5.0532 21 1 1 1 0 5.1469 22 1 1 0 0 2.5113 23 1 1 -1 0 4.4714 24 1 1 1 -1 4.3308 25 1 1 0 -1 4.2361 26 1 1 -1 -1 4.9589 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4032 atoms have been selected out of 4106 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 369 123 123 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1838 611 611 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1770 590 590 0.00 12 C012 has 120 40 40 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13639 atoms and 4538 groups and 4533 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4106 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1357 Number of atoms = 4106 Number of groups = 1362 Number of bonds = 4099 Number of angles = 1461 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1359 Number of HB donors = 2696 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1357 Number of atoms = 4106 Number of groups = 1362 Number of bonds = 4099 Number of angles = 1461 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1359 Number of HB donors = 2696 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.508" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1357" Evaluating: 1357-7 Parameter: NUMWAT <- "1350" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1350" Comparing "1081" and "1350". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.508" Parameter: BOX -> "34.508" Parameter: BOX -> "34.508" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.50800 B = 34.50800 C = 34.50800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0267 2 1 -1 0 -1 6.3810 3 1 -1 1 -1 5.0497 4 1 0 -1 -1 2.9662 5 1 0 0 -1 1.9971 6 1 0 1 -1 3.5000 7 1 -1 -1 0 5.1450 8 1 -1 0 0 2.5107 9 1 -1 1 0 4.4692 10 1 0 -1 0 1.3345 11 1 0 1 0 1.3345 12 1 -1 -1 1 4.3274 13 1 -1 0 1 4.2333 14 1 -1 1 1 4.9559 15 1 0 -1 1 3.5000 16 1 0 0 1 1.9971 17 1 0 1 1 2.9662 18 1 1 1 1 5.0267 19 1 1 0 1 6.3810 20 1 1 -1 1 5.0497 21 1 1 1 0 5.1450 22 1 1 0 0 2.5107 23 1 1 -1 0 4.4692 24 1 1 1 -1 4.3274 25 1 1 0 -1 4.2333 26 1 1 -1 -1 4.9559 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4032 atoms have been selected out of 4106 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 369 123 123 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 510 170 170 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1838 611 611 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 120 40 40 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13642 atoms and 4539 groups and 4534 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4106 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1357 Number of atoms = 4106 Number of groups = 1362 Number of bonds = 4099 Number of angles = 1461 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1359 Number of HB donors = 2696 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1357 Number of atoms = 4106 Number of groups = 1362 Number of bonds = 4099 Number of angles = 1461 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1359 Number of HB donors = 2696 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.506" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1357" Evaluating: 1357-7 Parameter: NUMWAT <- "1350" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1350" Comparing "1081" and "1350". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.506" Parameter: BOX -> "34.506" Parameter: BOX -> "34.506" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.50600 B = 34.50600 C = 34.50600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0290 2 1 -1 0 -1 6.3823 3 1 -1 1 -1 5.0463 4 1 0 -1 -1 2.9644 5 1 0 0 -1 1.9952 6 1 0 1 -1 3.4972 7 1 -1 -1 0 5.1431 8 1 -1 0 0 2.5101 9 1 -1 1 0 4.4670 10 1 0 -1 0 1.3336 11 1 0 1 0 1.3336 12 1 -1 -1 1 4.3239 13 1 -1 0 1 4.2305 14 1 -1 1 1 4.9529 15 1 0 -1 1 3.4972 16 1 0 0 1 1.9952 17 1 0 1 1 2.9644 18 1 1 1 1 5.0290 19 1 1 0 1 6.3823 20 1 1 -1 1 5.0463 21 1 1 1 0 5.1431 22 1 1 0 0 2.5101 23 1 1 -1 0 4.4670 24 1 1 1 -1 4.3239 25 1 1 0 -1 4.2305 26 1 1 -1 -1 4.9529 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4032 atoms have been selected out of 4106 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1302 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1683 561 561 0.00 6 C006 has 513 171 171 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1838 611 611 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1770 590 590 0.00 12 C012 has 120 40 40 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13639 atoms and 4538 groups and 4533 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4106 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1356 Number of atoms = 4103 Number of groups = 1361 Number of bonds = 4096 Number of angles = 1460 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1358 Number of HB donors = 2694 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1356 Number of atoms = 4103 Number of groups = 1361 Number of bonds = 4096 Number of angles = 1460 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1358 Number of HB donors = 2694 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.504" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1356" Evaluating: 1356-7 Parameter: NUMWAT <- "1349" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1349" Comparing "1081" and "1349". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.504" Parameter: BOX -> "34.504" Parameter: BOX -> "34.504" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.50400 B = 34.50400 C = 34.50400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0313 2 1 -1 0 -1 6.3836 3 1 -1 1 -1 5.0429 4 1 0 -1 -1 2.9626 5 1 0 0 -1 1.9933 6 1 0 1 -1 3.4945 7 1 -1 -1 0 5.1411 8 1 -1 0 0 2.5094 9 1 -1 1 0 4.4647 10 1 0 -1 0 1.3327 11 1 0 1 0 1.3327 12 1 -1 -1 1 4.3205 13 1 -1 0 1 4.2277 14 1 -1 1 1 4.9498 15 1 0 -1 1 3.4945 16 1 0 0 1 1.9933 17 1 0 1 1 2.9626 18 1 1 1 1 5.0313 19 1 1 0 1 6.3836 20 1 1 -1 1 5.0429 21 1 1 1 0 5.1411 22 1 1 0 0 2.5094 23 1 1 -1 0 4.4647 24 1 1 1 -1 4.3205 25 1 1 0 -1 4.2277 26 1 1 -1 -1 4.9498 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4029 atoms have been selected out of 4103 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 81 OPERATED ON BY TRANSFORMATION C011 RESIDUE 779 OPERATED ON BY TRANSFORMATION C022 RESIDUE 844 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 690 230 230 0.00 3 C003 has 87 29 29 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 510 170 170 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1835 610 610 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 120 40 40 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13642 atoms and 4539 groups and 4534 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 9 atoms have been selected out of 4103 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 3 residues deleted. DELTIC: 9 bonds deleted DELTIC: 3 angles deleted DELTIC: 6 donors deleted DELTIC: 3 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.502" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1353" Evaluating: 1353-7 Parameter: NUMWAT <- "1346" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1346" Comparing "1081" and "1346". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.502" Parameter: BOX -> "34.502" Parameter: BOX -> "34.502" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.50200 B = 34.50200 C = 34.50200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0336 2 1 -1 0 -1 6.3831 3 1 -1 1 -1 5.0394 4 1 0 -1 -1 2.9607 5 1 0 0 -1 1.9913 6 1 0 1 -1 3.4917 7 1 -1 -1 0 5.1392 8 1 -1 0 0 2.5088 9 1 -1 1 0 4.4625 10 1 0 -1 0 1.3318 11 1 0 1 0 1.3318 12 1 -1 -1 1 4.3170 13 1 -1 0 1 4.2250 14 1 -1 1 1 4.9468 15 1 0 -1 1 3.4917 16 1 0 0 1 1.9913 17 1 0 1 1 2.9607 18 1 1 1 1 5.0336 19 1 1 0 1 6.3831 20 1 1 -1 1 5.0394 21 1 1 1 0 5.1392 22 1 1 0 0 2.5088 23 1 1 -1 0 4.4625 24 1 1 1 -1 4.3170 25 1 1 0 -1 4.2250 26 1 1 -1 -1 4.9468 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4020 atoms have been selected out of 4094 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 366 122 122 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 507 169 169 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1770 590 590 0.00 12 C012 has 120 40 40 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13612 atoms and 4529 groups and 4524 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4094 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.5" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1353" Evaluating: 1353-7 Parameter: NUMWAT <- "1346" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1346" Comparing "1081" and "1346". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.5" Parameter: BOX -> "34.5" Parameter: BOX -> "34.5" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.50000 B = 34.50000 C = 34.50000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0359 2 1 -1 0 -1 6.3808 3 1 -1 1 -1 5.0360 4 1 0 -1 -1 2.9589 5 1 0 0 -1 1.9894 6 1 0 1 -1 3.4890 7 1 -1 -1 0 5.1373 8 1 -1 0 0 2.5082 9 1 -1 1 0 4.4603 10 1 0 -1 0 1.3309 11 1 0 1 0 1.3309 12 1 -1 -1 1 4.3136 13 1 -1 0 1 4.2222 14 1 -1 1 1 4.9438 15 1 0 -1 1 3.4890 16 1 0 0 1 1.9894 17 1 0 1 1 2.9589 18 1 1 1 1 5.0359 19 1 1 0 1 6.3808 20 1 1 -1 1 5.0360 21 1 1 1 0 5.1373 22 1 1 0 0 2.5082 23 1 1 -1 0 4.4603 24 1 1 1 -1 4.3136 25 1 1 0 -1 4.2222 26 1 1 -1 -1 4.9438 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4020 atoms have been selected out of 4094 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 369 123 123 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 507 169 169 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1770 590 590 0.00 12 C012 has 120 40 40 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13615 atoms and 4530 groups and 4525 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4094 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.498" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1353" Evaluating: 1353-7 Parameter: NUMWAT <- "1346" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1346" Comparing "1081" and "1346". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.498" Parameter: BOX -> "34.498" Parameter: BOX -> "34.498" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.49800 B = 34.49800 C = 34.49800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0382 2 1 -1 0 -1 6.3784 3 1 -1 1 -1 5.0325 4 1 0 -1 -1 2.9571 5 1 0 0 -1 1.9875 6 1 0 1 -1 3.4862 7 1 -1 -1 0 5.1354 8 1 -1 0 0 2.5075 9 1 -1 1 0 4.4580 10 1 0 -1 0 1.3300 11 1 0 1 0 1.3300 12 1 -1 -1 1 4.3101 13 1 -1 0 1 4.2194 14 1 -1 1 1 4.9408 15 1 0 -1 1 3.4862 16 1 0 0 1 1.9875 17 1 0 1 1 2.9571 18 1 1 1 1 5.0382 19 1 1 0 1 6.3784 20 1 1 -1 1 5.0325 21 1 1 1 0 5.1354 22 1 1 0 0 2.5075 23 1 1 -1 0 4.4580 24 1 1 1 -1 4.3101 25 1 1 0 -1 4.2194 26 1 1 -1 -1 4.9408 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4020 atoms have been selected out of 4094 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 369 123 123 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 507 169 169 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1770 590 590 0.00 12 C012 has 120 40 40 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13615 atoms and 4530 groups and 4525 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4094 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.496" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1353" Evaluating: 1353-7 Parameter: NUMWAT <- "1346" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1346" Comparing "1081" and "1346". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.496" Parameter: BOX -> "34.496" Parameter: BOX -> "34.496" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.49600 B = 34.49600 C = 34.49600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0405 2 1 -1 0 -1 6.3761 3 1 -1 1 -1 5.0291 4 1 0 -1 -1 2.9554 5 1 0 0 -1 1.9856 6 1 0 1 -1 3.4834 7 1 -1 -1 0 5.1334 8 1 -1 0 0 2.5069 9 1 -1 1 0 4.4558 10 1 0 -1 0 1.3291 11 1 0 1 0 1.3291 12 1 -1 -1 1 4.3067 13 1 -1 0 1 4.2166 14 1 -1 1 1 4.9378 15 1 0 -1 1 3.4834 16 1 0 0 1 1.9856 17 1 0 1 1 2.9554 18 1 1 1 1 5.0405 19 1 1 0 1 6.3761 20 1 1 -1 1 5.0291 21 1 1 1 0 5.1334 22 1 1 0 0 2.5069 23 1 1 -1 0 4.4558 24 1 1 1 -1 4.3067 25 1 1 0 -1 4.2166 26 1 1 -1 -1 4.9378 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4020 atoms have been selected out of 4094 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 369 123 123 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 507 169 169 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1770 590 590 0.00 12 C012 has 120 40 40 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13615 atoms and 4530 groups and 4525 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4094 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.494" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1353" Evaluating: 1353-7 Parameter: NUMWAT <- "1346" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1346" Comparing "1081" and "1346". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.494" Parameter: BOX -> "34.494" Parameter: BOX -> "34.494" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.49400 B = 34.49400 C = 34.49400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0428 2 1 -1 0 -1 6.3738 3 1 -1 1 -1 5.0256 4 1 0 -1 -1 2.9536 5 1 0 0 -1 1.9836 6 1 0 1 -1 3.4807 7 1 -1 -1 0 5.1315 8 1 -1 0 0 2.5063 9 1 -1 1 0 4.4536 10 1 0 -1 0 1.3282 11 1 0 1 0 1.3282 12 1 -1 -1 1 4.3032 13 1 -1 0 1 4.2138 14 1 -1 1 1 4.9347 15 1 0 -1 1 3.4807 16 1 0 0 1 1.9836 17 1 0 1 1 2.9536 18 1 1 1 1 5.0428 19 1 1 0 1 6.3738 20 1 1 -1 1 5.0256 21 1 1 1 0 5.1315 22 1 1 0 0 2.5063 23 1 1 -1 0 4.4536 24 1 1 1 -1 4.3032 25 1 1 0 -1 4.2138 26 1 1 -1 -1 4.9347 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4020 atoms have been selected out of 4094 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 369 123 123 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 507 169 169 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1835 610 610 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1770 590 590 0.00 12 C012 has 120 40 40 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13618 atoms and 4531 groups and 4526 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4094 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.492" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1353" Evaluating: 1353-7 Parameter: NUMWAT <- "1346" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1346" Comparing "1081" and "1346". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.492" Parameter: BOX -> "34.492" Parameter: BOX -> "34.492" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.49200 B = 34.49200 C = 34.49200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0451 2 1 -1 0 -1 6.3714 3 1 -1 1 -1 5.0222 4 1 0 -1 -1 2.9518 5 1 0 0 -1 1.9817 6 1 0 1 -1 3.4779 7 1 -1 -1 0 5.1296 8 1 -1 0 0 2.5056 9 1 -1 1 0 4.4513 10 1 0 -1 0 1.3273 11 1 0 1 0 1.3273 12 1 -1 -1 1 4.2998 13 1 -1 0 1 4.2110 14 1 -1 1 1 4.9317 15 1 0 -1 1 3.4779 16 1 0 0 1 1.9817 17 1 0 1 1 2.9518 18 1 1 1 1 5.0451 19 1 1 0 1 6.3714 20 1 1 -1 1 5.0222 21 1 1 1 0 5.1296 22 1 1 0 0 2.5056 23 1 1 -1 0 4.4513 24 1 1 1 -1 4.2998 25 1 1 0 -1 4.2110 26 1 1 -1 -1 4.9317 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4020 atoms have been selected out of 4094 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 369 123 123 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 507 169 169 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1835 610 610 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1770 590 590 0.00 12 C012 has 120 40 40 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13621 atoms and 4532 groups and 4527 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4094 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.49" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1353" Evaluating: 1353-7 Parameter: NUMWAT <- "1346" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1346" Comparing "1081" and "1346". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.49" Parameter: BOX -> "34.49" Parameter: BOX -> "34.49" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.49000 B = 34.49000 C = 34.49000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0474 2 1 -1 0 -1 6.3691 3 1 -1 1 -1 5.0188 4 1 0 -1 -1 2.9500 5 1 0 0 -1 1.9798 6 1 0 1 -1 3.4752 7 1 -1 -1 0 5.1277 8 1 -1 0 0 2.5050 9 1 -1 1 0 4.4491 10 1 0 -1 0 1.3264 11 1 0 1 0 1.3264 12 1 -1 -1 1 4.2963 13 1 -1 0 1 4.2083 14 1 -1 1 1 4.9287 15 1 0 -1 1 3.4752 16 1 0 0 1 1.9798 17 1 0 1 1 2.9500 18 1 1 1 1 5.0474 19 1 1 0 1 6.3691 20 1 1 -1 1 5.0188 21 1 1 1 0 5.1277 22 1 1 0 0 2.5050 23 1 1 -1 0 4.4491 24 1 1 1 -1 4.2963 25 1 1 0 -1 4.2083 26 1 1 -1 -1 4.9287 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4020 atoms have been selected out of 4094 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 369 123 123 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 507 169 169 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1835 610 610 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1770 590 590 0.00 12 C012 has 120 40 40 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13621 atoms and 4532 groups and 4527 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4094 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.488" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1353" Evaluating: 1353-7 Parameter: NUMWAT <- "1346" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1346" Comparing "1081" and "1346". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.488" Parameter: BOX -> "34.488" Parameter: BOX -> "34.488" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.48800 B = 34.48800 C = 34.48800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0497 2 1 -1 0 -1 6.3667 3 1 -1 1 -1 5.0153 4 1 0 -1 -1 2.9482 5 1 0 0 -1 1.9779 6 1 0 1 -1 3.4724 7 1 -1 -1 0 5.1257 8 1 -1 0 0 2.5044 9 1 -1 1 0 4.4469 10 1 0 -1 0 1.3255 11 1 0 1 0 1.3255 12 1 -1 -1 1 4.2928 13 1 -1 0 1 4.2055 14 1 -1 1 1 4.9257 15 1 0 -1 1 3.4724 16 1 0 0 1 1.9779 17 1 0 1 1 2.9482 18 1 1 1 1 5.0497 19 1 1 0 1 6.3667 20 1 1 -1 1 5.0153 21 1 1 1 0 5.1257 22 1 1 0 0 2.5044 23 1 1 -1 0 4.4469 24 1 1 1 -1 4.2928 25 1 1 0 -1 4.2055 26 1 1 -1 -1 4.9257 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4020 atoms have been selected out of 4094 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 369 123 123 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 510 170 170 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1835 610 610 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1770 590 590 0.00 12 C012 has 120 40 40 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13624 atoms and 4533 groups and 4528 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4094 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.486" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1353" Evaluating: 1353-7 Parameter: NUMWAT <- "1346" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1346" Comparing "1081" and "1346". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.486" Parameter: BOX -> "34.486" Parameter: BOX -> "34.486" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.48600 B = 34.48600 C = 34.48600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0520 2 1 -1 0 -1 6.3644 3 1 -1 1 -1 5.0119 4 1 0 -1 -1 2.9464 5 1 0 0 -1 1.9759 6 1 0 1 -1 3.4696 7 1 -1 -1 0 5.1238 8 1 -1 0 0 2.5038 9 1 -1 1 0 4.4446 10 1 0 -1 0 1.3246 11 1 0 1 0 1.3246 12 1 -1 -1 1 4.2894 13 1 -1 0 1 4.2027 14 1 -1 1 1 4.9227 15 1 0 -1 1 3.4696 16 1 0 0 1 1.9759 17 1 0 1 1 2.9464 18 1 1 1 1 5.0520 19 1 1 0 1 6.3644 20 1 1 -1 1 5.0119 21 1 1 1 0 5.1238 22 1 1 0 0 2.5038 23 1 1 -1 0 4.4446 24 1 1 1 -1 4.2894 25 1 1 0 -1 4.2027 26 1 1 -1 -1 4.9227 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4020 atoms have been selected out of 4094 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 369 123 123 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 510 170 170 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1835 610 610 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 120 40 40 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13627 atoms and 4534 groups and 4529 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4094 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.484" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1353" Evaluating: 1353-7 Parameter: NUMWAT <- "1346" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1346" Comparing "1081" and "1346". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.484" Parameter: BOX -> "34.484" Parameter: BOX -> "34.484" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.48400 B = 34.48400 C = 34.48400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0543 2 1 -1 0 -1 6.3621 3 1 -1 1 -1 5.0084 4 1 0 -1 -1 2.9446 5 1 0 0 -1 1.9740 6 1 0 1 -1 3.4669 7 1 -1 -1 0 5.1219 8 1 -1 0 0 2.5031 9 1 -1 1 0 4.4424 10 1 0 -1 0 1.3238 11 1 0 1 0 1.3238 12 1 -1 -1 1 4.2859 13 1 -1 0 1 4.1999 14 1 -1 1 1 4.9197 15 1 0 -1 1 3.4669 16 1 0 0 1 1.9740 17 1 0 1 1 2.9446 18 1 1 1 1 5.0543 19 1 1 0 1 6.3621 20 1 1 -1 1 5.0084 21 1 1 1 0 5.1219 22 1 1 0 0 2.5031 23 1 1 -1 0 4.4424 24 1 1 1 -1 4.2859 25 1 1 0 -1 4.1999 26 1 1 -1 -1 4.9197 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4020 atoms have been selected out of 4094 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 369 123 123 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 510 170 170 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1835 610 610 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 120 40 40 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13627 atoms and 4534 groups and 4529 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4094 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.482" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1353" Evaluating: 1353-7 Parameter: NUMWAT <- "1346" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1346" Comparing "1081" and "1346". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.482" Parameter: BOX -> "34.482" Parameter: BOX -> "34.482" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.48200 B = 34.48200 C = 34.48200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0566 2 1 -1 0 -1 6.3597 3 1 -1 1 -1 5.0050 4 1 0 -1 -1 2.9428 5 1 0 0 -1 1.9721 6 1 0 1 -1 3.4641 7 1 -1 -1 0 5.1200 8 1 -1 0 0 2.5025 9 1 -1 1 0 4.4402 10 1 0 -1 0 1.3229 11 1 0 1 0 1.3229 12 1 -1 -1 1 4.2825 13 1 -1 0 1 4.1971 14 1 -1 1 1 4.9166 15 1 0 -1 1 3.4641 16 1 0 0 1 1.9721 17 1 0 1 1 2.9428 18 1 1 1 1 5.0566 19 1 1 0 1 6.3597 20 1 1 -1 1 5.0050 21 1 1 1 0 5.1200 22 1 1 0 0 2.5025 23 1 1 -1 0 4.4402 24 1 1 1 -1 4.2825 25 1 1 0 -1 4.1971 26 1 1 -1 -1 4.9166 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4020 atoms have been selected out of 4094 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 369 123 123 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 510 170 170 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1835 610 610 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 120 40 40 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13627 atoms and 4534 groups and 4529 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4094 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.48" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1353" Evaluating: 1353-7 Parameter: NUMWAT <- "1346" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1346" Comparing "1081" and "1346". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.48" Parameter: BOX -> "34.48" Parameter: BOX -> "34.48" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.48000 B = 34.48000 C = 34.48000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0589 2 1 -1 0 -1 6.3574 3 1 -1 1 -1 5.0016 4 1 0 -1 -1 2.9410 5 1 0 0 -1 1.9702 6 1 0 1 -1 3.4614 7 1 -1 -1 0 5.1181 8 1 -1 0 0 2.5019 9 1 -1 1 0 4.4380 10 1 0 -1 0 1.3220 11 1 0 1 0 1.3220 12 1 -1 -1 1 4.2790 13 1 -1 0 1 4.1944 14 1 -1 1 1 4.9136 15 1 0 -1 1 3.4614 16 1 0 0 1 1.9702 17 1 0 1 1 2.9410 18 1 1 1 1 5.0589 19 1 1 0 1 6.3574 20 1 1 -1 1 5.0016 21 1 1 1 0 5.1181 22 1 1 0 0 2.5019 23 1 1 -1 0 4.4380 24 1 1 1 -1 4.2790 25 1 1 0 -1 4.1944 26 1 1 -1 -1 4.9136 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4020 atoms have been selected out of 4094 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 369 123 123 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 510 170 170 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1835 610 610 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 120 40 40 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13627 atoms and 4534 groups and 4529 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4094 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.478" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1353" Evaluating: 1353-7 Parameter: NUMWAT <- "1346" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1346" Comparing "1081" and "1346". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.478" Parameter: BOX -> "34.478" Parameter: BOX -> "34.478" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.47800 B = 34.47800 C = 34.47800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0612 2 1 -1 0 -1 6.3551 3 1 -1 1 -1 4.9981 4 1 0 -1 -1 2.9392 5 1 0 0 -1 1.9682 6 1 0 1 -1 3.4586 7 1 -1 -1 0 5.1161 8 1 -1 0 0 2.5013 9 1 -1 1 0 4.4357 10 1 0 -1 0 1.3211 11 1 0 1 0 1.3211 12 1 -1 -1 1 4.2756 13 1 -1 0 1 4.1916 14 1 -1 1 1 4.9106 15 1 0 -1 1 3.4586 16 1 0 0 1 1.9682 17 1 0 1 1 2.9392 18 1 1 1 1 5.0612 19 1 1 0 1 6.3551 20 1 1 -1 1 4.9981 21 1 1 1 0 5.1161 22 1 1 0 0 2.5013 23 1 1 -1 0 4.4357 24 1 1 1 -1 4.2756 25 1 1 0 -1 4.1916 26 1 1 -1 -1 4.9106 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4020 atoms have been selected out of 4094 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 510 170 170 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1835 610 610 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1773 591 591 0.00 12 C012 has 120 40 40 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13633 atoms and 4536 groups and 4531 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4094 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.476" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1353" Evaluating: 1353-7 Parameter: NUMWAT <- "1346" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1346" Comparing "1081" and "1346". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.476" Parameter: BOX -> "34.476" Parameter: BOX -> "34.476" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.47600 B = 34.47600 C = 34.47600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0635 2 1 -1 0 -1 6.3527 3 1 -1 1 -1 4.9947 4 1 0 -1 -1 2.9375 5 1 0 0 -1 1.9663 6 1 0 1 -1 3.4558 7 1 -1 -1 0 5.1142 8 1 -1 0 0 2.5007 9 1 -1 1 0 4.4335 10 1 0 -1 0 1.3203 11 1 0 1 0 1.3203 12 1 -1 -1 1 4.2721 13 1 -1 0 1 4.1888 14 1 -1 1 1 4.9076 15 1 0 -1 1 3.4558 16 1 0 0 1 1.9663 17 1 0 1 1 2.9375 18 1 1 1 1 5.0635 19 1 1 0 1 6.3527 20 1 1 -1 1 4.9947 21 1 1 1 0 5.1142 22 1 1 0 0 2.5007 23 1 1 -1 0 4.4335 24 1 1 1 -1 4.2721 25 1 1 0 -1 4.1888 26 1 1 -1 -1 4.9076 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4020 atoms have been selected out of 4094 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 510 170 170 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1835 610 610 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 120 40 40 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13636 atoms and 4537 groups and 4532 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4094 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.474" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1353" Evaluating: 1353-7 Parameter: NUMWAT <- "1346" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1346" Comparing "1081" and "1346". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.474" Parameter: BOX -> "34.474" Parameter: BOX -> "34.474" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.47400 B = 34.47400 C = 34.47400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0659 2 1 -1 0 -1 6.3504 3 1 -1 1 -1 4.9912 4 1 0 -1 -1 2.9357 5 1 0 0 -1 1.9644 6 1 0 1 -1 3.4531 7 1 -1 -1 0 5.1123 8 1 -1 0 0 2.5000 9 1 -1 1 0 4.4313 10 1 0 -1 0 1.3194 11 1 0 1 0 1.3194 12 1 -1 -1 1 4.2687 13 1 -1 0 1 4.1860 14 1 -1 1 1 4.9046 15 1 0 -1 1 3.4531 16 1 0 0 1 1.9644 17 1 0 1 1 2.9357 18 1 1 1 1 5.0659 19 1 1 0 1 6.3504 20 1 1 -1 1 4.9912 21 1 1 1 0 5.1123 22 1 1 0 0 2.5000 23 1 1 -1 0 4.4313 24 1 1 1 -1 4.2687 25 1 1 0 -1 4.1860 26 1 1 -1 -1 4.9046 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4020 atoms have been selected out of 4094 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 687 229 229 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 510 170 170 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1835 610 610 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 120 40 40 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13636 atoms and 4537 groups and 4532 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4094 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.472" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1353" Evaluating: 1353-7 Parameter: NUMWAT <- "1346" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1346" Comparing "1081" and "1346". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.472" Parameter: BOX -> "34.472" Parameter: BOX -> "34.472" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.47200 B = 34.47200 C = 34.47200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0682 2 1 -1 0 -1 6.3481 3 1 -1 1 -1 4.9878 4 1 0 -1 -1 2.9339 5 1 0 0 -1 1.9625 6 1 0 1 -1 3.4503 7 1 -1 -1 0 5.1104 8 1 -1 0 0 2.4994 9 1 -1 1 0 4.4290 10 1 0 -1 0 1.3185 11 1 0 1 0 1.3185 12 1 -1 -1 1 4.2652 13 1 -1 0 1 4.1832 14 1 -1 1 1 4.9016 15 1 0 -1 1 3.4503 16 1 0 0 1 1.9625 17 1 0 1 1 2.9339 18 1 1 1 1 5.0682 19 1 1 0 1 6.3481 20 1 1 -1 1 4.9878 21 1 1 1 0 5.1104 22 1 1 0 0 2.4994 23 1 1 -1 0 4.4290 24 1 1 1 -1 4.2652 25 1 1 0 -1 4.1832 26 1 1 -1 -1 4.9016 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4020 atoms have been selected out of 4094 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 513 171 171 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1835 610 610 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 120 40 40 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13642 atoms and 4539 groups and 4534 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4094 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.47" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1353" Evaluating: 1353-7 Parameter: NUMWAT <- "1346" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1346" Comparing "1081" and "1346". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.47" Parameter: BOX -> "34.47" Parameter: BOX -> "34.47" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.47000 B = 34.47000 C = 34.47000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0705 2 1 -1 0 -1 6.3458 3 1 -1 1 -1 4.9843 4 1 0 -1 -1 2.9321 5 1 0 0 -1 1.9605 6 1 0 1 -1 3.4476 7 1 -1 -1 0 5.1085 8 1 -1 0 0 2.4988 9 1 -1 1 0 4.4268 10 1 0 -1 0 1.3177 11 1 0 1 0 1.3177 12 1 -1 -1 1 4.2618 13 1 -1 0 1 4.1805 14 1 -1 1 1 4.8986 15 1 0 -1 1 3.4476 16 1 0 0 1 1.9605 17 1 0 1 1 2.9321 18 1 1 1 1 5.0705 19 1 1 0 1 6.3458 20 1 1 -1 1 4.9843 21 1 1 1 0 5.1085 22 1 1 0 0 2.4988 23 1 1 -1 0 4.4268 24 1 1 1 -1 4.2618 25 1 1 0 -1 4.1805 26 1 1 -1 -1 4.8986 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4020 atoms have been selected out of 4094 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 513 171 171 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1835 610 610 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 120 40 40 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13642 atoms and 4539 groups and 4534 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4094 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.468" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1353" Evaluating: 1353-7 Parameter: NUMWAT <- "1346" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1346" Comparing "1081" and "1346". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.468" Parameter: BOX -> "34.468" Parameter: BOX -> "34.468" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.46800 B = 34.46800 C = 34.46800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0728 2 1 -1 0 -1 6.3434 3 1 -1 1 -1 4.9809 4 1 0 -1 -1 2.9304 5 1 0 0 -1 1.9586 6 1 0 1 -1 3.4448 7 1 -1 -1 0 5.1066 8 1 -1 0 0 2.4982 9 1 -1 1 0 4.4246 10 1 0 -1 0 1.3168 11 1 0 1 0 1.3168 12 1 -1 -1 1 4.2583 13 1 -1 0 1 4.1777 14 1 -1 1 1 4.8955 15 1 0 -1 1 3.4448 16 1 0 0 1 1.9586 17 1 0 1 1 2.9304 18 1 1 1 1 5.0728 19 1 1 0 1 6.3434 20 1 1 -1 1 4.9809 21 1 1 1 0 5.1066 22 1 1 0 0 2.4982 23 1 1 -1 0 4.4246 24 1 1 1 -1 4.2583 25 1 1 0 -1 4.1777 26 1 1 -1 -1 4.8955 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4020 atoms have been selected out of 4094 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 513 171 171 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1835 610 610 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 120 40 40 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13642 atoms and 4539 groups and 4534 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4094 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.466" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1353" Evaluating: 1353-7 Parameter: NUMWAT <- "1346" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1346" Comparing "1081" and "1346". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.466" Parameter: BOX -> "34.466" Parameter: BOX -> "34.466" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.46600 B = 34.46600 C = 34.46600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0751 2 1 -1 0 -1 6.3411 3 1 -1 1 -1 4.9775 4 1 0 -1 -1 2.9286 5 1 0 0 -1 1.9567 6 1 0 1 -1 3.4420 7 1 -1 -1 0 5.1047 8 1 -1 0 0 2.4976 9 1 -1 1 0 4.4224 10 1 0 -1 0 1.3159 11 1 0 1 0 1.3159 12 1 -1 -1 1 4.2549 13 1 -1 0 1 4.1749 14 1 -1 1 1 4.8925 15 1 0 -1 1 3.4420 16 1 0 0 1 1.9567 17 1 0 1 1 2.9286 18 1 1 1 1 5.0751 19 1 1 0 1 6.3411 20 1 1 -1 1 4.9775 21 1 1 1 0 5.1047 22 1 1 0 0 2.4976 23 1 1 -1 0 4.4224 24 1 1 1 -1 4.2549 25 1 1 0 -1 4.1749 26 1 1 -1 -1 4.8925 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4020 atoms have been selected out of 4094 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 513 171 171 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1838 611 611 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 120 40 40 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13645 atoms and 4540 groups and 4535 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4094 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.464" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1353" Evaluating: 1353-7 Parameter: NUMWAT <- "1346" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1346" Comparing "1081" and "1346". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.464" Parameter: BOX -> "34.464" Parameter: BOX -> "34.464" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.46400 B = 34.46400 C = 34.46400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0774 2 1 -1 0 -1 6.3388 3 1 -1 1 -1 4.9740 4 1 0 -1 -1 2.9268 5 1 0 0 -1 1.9548 6 1 0 1 -1 3.4393 7 1 -1 -1 0 5.1027 8 1 -1 0 0 2.4970 9 1 -1 1 0 4.4202 10 1 0 -1 0 1.3151 11 1 0 1 0 1.3151 12 1 -1 -1 1 4.2514 13 1 -1 0 1 4.1721 14 1 -1 1 1 4.8895 15 1 0 -1 1 3.4393 16 1 0 0 1 1.9548 17 1 0 1 1 2.9268 18 1 1 1 1 5.0774 19 1 1 0 1 6.3388 20 1 1 -1 1 4.9740 21 1 1 1 0 5.1027 22 1 1 0 0 2.4970 23 1 1 -1 0 4.4202 24 1 1 1 -1 4.2514 25 1 1 0 -1 4.1721 26 1 1 -1 -1 4.8895 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4020 atoms have been selected out of 4094 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 513 171 171 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1841 612 612 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1776 592 592 0.00 12 C012 has 120 40 40 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13651 atoms and 4542 groups and 4537 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4094 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1353 Number of atoms = 4094 Number of groups = 1358 Number of bonds = 4087 Number of angles = 1457 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1355 Number of HB donors = 2688 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.462" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1353" Evaluating: 1353-7 Parameter: NUMWAT <- "1346" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1346" Comparing "1081" and "1346". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.462" Parameter: BOX -> "34.462" Parameter: BOX -> "34.462" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.46200 B = 34.46200 C = 34.46200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0798 2 1 -1 0 -1 6.3364 3 1 -1 1 -1 4.9706 4 1 0 -1 -1 2.9250 5 1 0 0 -1 1.9528 6 1 0 1 -1 3.4365 7 1 -1 -1 0 5.1008 8 1 -1 0 0 2.4964 9 1 -1 1 0 4.4179 10 1 0 -1 0 1.3142 11 1 0 1 0 1.3142 12 1 -1 -1 1 4.2480 13 1 -1 0 1 4.1694 14 1 -1 1 1 4.8865 15 1 0 -1 1 3.4365 16 1 0 0 1 1.9528 17 1 0 1 1 2.9250 18 1 1 1 1 5.0798 19 1 1 0 1 6.3364 20 1 1 -1 1 4.9706 21 1 1 1 0 5.1008 22 1 1 0 0 2.4964 23 1 1 -1 0 4.4179 24 1 1 1 -1 4.2480 25 1 1 0 -1 4.1694 26 1 1 -1 -1 4.8865 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4020 atoms have been selected out of 4094 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 270 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 513 171 171 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1764 588 588 0.00 12 C012 has 120 40 40 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13642 atoms and 4539 groups and 4534 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4094 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1352 Number of atoms = 4091 Number of groups = 1357 Number of bonds = 4084 Number of angles = 1456 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1354 Number of HB donors = 2686 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1352 Number of atoms = 4091 Number of groups = 1357 Number of bonds = 4084 Number of angles = 1456 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1354 Number of HB donors = 2686 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.46" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1352" Evaluating: 1352-7 Parameter: NUMWAT <- "1345" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1345" Comparing "1081" and "1345". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.46" Parameter: BOX -> "34.46" Parameter: BOX -> "34.46" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.46000 B = 34.46000 C = 34.46000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0821 2 1 -1 0 -1 6.3341 3 1 -1 1 -1 4.9671 4 1 0 -1 -1 2.9233 5 1 0 0 -1 1.9509 6 1 0 1 -1 3.4338 7 1 -1 -1 0 5.0989 8 1 -1 0 0 2.4958 9 1 -1 1 0 4.4157 10 1 0 -1 0 1.3134 11 1 0 1 0 1.3134 12 1 -1 -1 1 4.2445 13 1 -1 0 1 4.1666 14 1 -1 1 1 4.8835 15 1 0 -1 1 3.4338 16 1 0 0 1 1.9509 17 1 0 1 1 2.9233 18 1 1 1 1 5.0821 19 1 1 0 1 6.3341 20 1 1 -1 1 4.9671 21 1 1 1 0 5.0989 22 1 1 0 0 2.4958 23 1 1 -1 0 4.4157 24 1 1 1 -1 4.2445 25 1 1 0 -1 4.1666 26 1 1 -1 -1 4.8835 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4017 atoms have been selected out of 4091 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 513 171 171 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1764 588 588 0.00 12 C012 has 120 40 40 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13636 atoms and 4537 groups and 4532 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4091 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1352 Number of atoms = 4091 Number of groups = 1357 Number of bonds = 4084 Number of angles = 1456 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1354 Number of HB donors = 2686 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1352 Number of atoms = 4091 Number of groups = 1357 Number of bonds = 4084 Number of angles = 1456 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1354 Number of HB donors = 2686 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.458" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1352" Evaluating: 1352-7 Parameter: NUMWAT <- "1345" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1345" Comparing "1081" and "1345". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.458" Parameter: BOX -> "34.458" Parameter: BOX -> "34.458" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.45800 B = 34.45800 C = 34.45800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0844 2 1 -1 0 -1 6.3318 3 1 -1 1 -1 4.9637 4 1 0 -1 -1 2.9215 5 1 0 0 -1 1.9490 6 1 0 1 -1 3.4310 7 1 -1 -1 0 5.0970 8 1 -1 0 0 2.4952 9 1 -1 1 0 4.4135 10 1 0 -1 0 1.3125 11 1 0 1 0 1.3125 12 1 -1 -1 1 4.2411 13 1 -1 0 1 4.1638 14 1 -1 1 1 4.8805 15 1 0 -1 1 3.4310 16 1 0 0 1 1.9490 17 1 0 1 1 2.9215 18 1 1 1 1 5.0844 19 1 1 0 1 6.3318 20 1 1 -1 1 4.9637 21 1 1 1 0 5.0970 22 1 1 0 0 2.4952 23 1 1 -1 0 4.4135 24 1 1 1 -1 4.2411 25 1 1 0 -1 4.1638 26 1 1 -1 -1 4.8805 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4017 atoms have been selected out of 4091 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 513 171 171 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1764 588 588 0.00 12 C012 has 120 40 40 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13636 atoms and 4537 groups and 4532 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4091 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1352 Number of atoms = 4091 Number of groups = 1357 Number of bonds = 4084 Number of angles = 1456 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1354 Number of HB donors = 2686 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1352 Number of atoms = 4091 Number of groups = 1357 Number of bonds = 4084 Number of angles = 1456 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1354 Number of HB donors = 2686 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.456" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1352" Evaluating: 1352-7 Parameter: NUMWAT <- "1345" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1345" Comparing "1081" and "1345". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.456" Parameter: BOX -> "34.456" Parameter: BOX -> "34.456" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.45600 B = 34.45600 C = 34.45600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0867 2 1 -1 0 -1 6.3294 3 1 -1 1 -1 4.9603 4 1 0 -1 -1 2.9197 5 1 0 0 -1 1.9471 6 1 0 1 -1 3.4282 7 1 -1 -1 0 5.0951 8 1 -1 0 0 2.4946 9 1 -1 1 0 4.4113 10 1 0 -1 0 1.3117 11 1 0 1 0 1.3117 12 1 -1 -1 1 4.2376 13 1 -1 0 1 4.1610 14 1 -1 1 1 4.8775 15 1 0 -1 1 3.4282 16 1 0 0 1 1.9471 17 1 0 1 1 2.9197 18 1 1 1 1 5.0867 19 1 1 0 1 6.3294 20 1 1 -1 1 4.9603 21 1 1 1 0 5.0951 22 1 1 0 0 2.4946 23 1 1 -1 0 4.4113 24 1 1 1 -1 4.2376 25 1 1 0 -1 4.1610 26 1 1 -1 -1 4.8775 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4017 atoms have been selected out of 4091 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 106 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 690 230 230 0.00 3 C003 has 84 28 28 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 513 171 171 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1850 615 615 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1761 587 587 0.00 12 C012 has 120 40 40 0.00 13 C013 has 489 163 163 0.00 14 C014 has 102 34 34 0.00 Total of13648 atoms and 4541 groups and 4536 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4091 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1351 Number of atoms = 4088 Number of groups = 1356 Number of bonds = 4081 Number of angles = 1455 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1353 Number of HB donors = 2684 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1351 Number of atoms = 4088 Number of groups = 1356 Number of bonds = 4081 Number of angles = 1455 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1353 Number of HB donors = 2684 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.454" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1351" Evaluating: 1351-7 Parameter: NUMWAT <- "1344" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1344" Comparing "1081" and "1344". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.454" Parameter: BOX -> "34.454" Parameter: BOX -> "34.454" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.45400 B = 34.45400 C = 34.45400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0891 2 1 -1 0 -1 6.3271 3 1 -1 1 -1 4.9568 4 1 0 -1 -1 2.9180 5 1 0 0 -1 1.9451 6 1 0 1 -1 3.4255 7 1 -1 -1 0 5.0932 8 1 -1 0 0 2.4940 9 1 -1 1 0 4.4091 10 1 0 -1 0 1.3108 11 1 0 1 0 1.3108 12 1 -1 -1 1 4.2342 13 1 -1 0 1 4.1582 14 1 -1 1 1 4.8745 15 1 0 -1 1 3.4255 16 1 0 0 1 1.9451 17 1 0 1 1 2.9180 18 1 1 1 1 5.0891 19 1 1 0 1 6.3271 20 1 1 -1 1 4.9568 21 1 1 1 0 5.0932 22 1 1 0 0 2.4940 23 1 1 -1 0 4.4091 24 1 1 1 -1 4.2342 25 1 1 0 -1 4.1582 26 1 1 -1 -1 4.8745 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4014 atoms have been selected out of 4088 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 513 171 171 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1761 587 587 0.00 12 C012 has 120 40 40 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13639 atoms and 4538 groups and 4533 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4088 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1351 Number of atoms = 4088 Number of groups = 1356 Number of bonds = 4081 Number of angles = 1455 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1353 Number of HB donors = 2684 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1351 Number of atoms = 4088 Number of groups = 1356 Number of bonds = 4081 Number of angles = 1455 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1353 Number of HB donors = 2684 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.452" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1351" Evaluating: 1351-7 Parameter: NUMWAT <- "1344" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1344" Comparing "1081" and "1344". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.452" Parameter: BOX -> "34.452" Parameter: BOX -> "34.452" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.45200 B = 34.45200 C = 34.45200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0914 2 1 -1 0 -1 6.3248 3 1 -1 1 -1 4.9534 4 1 0 -1 -1 2.9162 5 1 0 0 -1 1.9432 6 1 0 1 -1 3.4227 7 1 -1 -1 0 5.0913 8 1 -1 0 0 2.4934 9 1 -1 1 0 4.4068 10 1 0 -1 0 1.3100 11 1 0 1 0 1.3100 12 1 -1 -1 1 4.2307 13 1 -1 0 1 4.1555 14 1 -1 1 1 4.8715 15 1 0 -1 1 3.4227 16 1 0 0 1 1.9432 17 1 0 1 1 2.9162 18 1 1 1 1 5.0914 19 1 1 0 1 6.3248 20 1 1 -1 1 4.9534 21 1 1 1 0 5.0913 22 1 1 0 0 2.4934 23 1 1 -1 0 4.4068 24 1 1 1 -1 4.2307 25 1 1 0 -1 4.1555 26 1 1 -1 -1 4.8715 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4014 atoms have been selected out of 4088 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 513 171 171 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1761 587 587 0.00 12 C012 has 120 40 40 0.00 13 C013 has 486 162 162 0.00 14 C014 has 102 34 34 0.00 Total of13645 atoms and 4540 groups and 4535 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4088 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1351 Number of atoms = 4088 Number of groups = 1356 Number of bonds = 4081 Number of angles = 1455 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1353 Number of HB donors = 2684 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1351 Number of atoms = 4088 Number of groups = 1356 Number of bonds = 4081 Number of angles = 1455 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1353 Number of HB donors = 2684 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.45" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1351" Evaluating: 1351-7 Parameter: NUMWAT <- "1344" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1344" Comparing "1081" and "1344". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.45" Parameter: BOX -> "34.45" Parameter: BOX -> "34.45" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.45000 B = 34.45000 C = 34.45000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0937 2 1 -1 0 -1 6.3225 3 1 -1 1 -1 4.9499 4 1 0 -1 -1 2.9145 5 1 0 0 -1 1.9413 6 1 0 1 -1 3.4200 7 1 -1 -1 0 5.0894 8 1 -1 0 0 2.4928 9 1 -1 1 0 4.4046 10 1 0 -1 0 1.3092 11 1 0 1 0 1.3092 12 1 -1 -1 1 4.2272 13 1 -1 0 1 4.1527 14 1 -1 1 1 4.8685 15 1 0 -1 1 3.4200 16 1 0 0 1 1.9413 17 1 0 1 1 2.9145 18 1 1 1 1 5.0937 19 1 1 0 1 6.3225 20 1 1 -1 1 4.9499 21 1 1 1 0 5.0894 22 1 1 0 0 2.4928 23 1 1 -1 0 4.4046 24 1 1 1 -1 4.2272 25 1 1 0 -1 4.1527 26 1 1 -1 -1 4.8685 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4014 atoms have been selected out of 4088 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 696 232 232 0.00 3 C003 has 84 28 28 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 513 171 171 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1761 587 587 0.00 12 C012 has 120 40 40 0.00 13 C013 has 489 163 163 0.00 14 C014 has 102 34 34 0.00 Total of13651 atoms and 4542 groups and 4537 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4088 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1351 Number of atoms = 4088 Number of groups = 1356 Number of bonds = 4081 Number of angles = 1455 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1353 Number of HB donors = 2684 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1351 Number of atoms = 4088 Number of groups = 1356 Number of bonds = 4081 Number of angles = 1455 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1353 Number of HB donors = 2684 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.448" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1351" Evaluating: 1351-7 Parameter: NUMWAT <- "1344" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1344" Comparing "1081" and "1344". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.448" Parameter: BOX -> "34.448" Parameter: BOX -> "34.448" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.44800 B = 34.44800 C = 34.44800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0960 2 1 -1 0 -1 6.3201 3 1 -1 1 -1 4.9465 4 1 0 -1 -1 2.9127 5 1 0 0 -1 1.9394 6 1 0 1 -1 3.4172 7 1 -1 -1 0 5.0875 8 1 -1 0 0 2.4922 9 1 -1 1 0 4.4024 10 1 0 -1 0 1.3083 11 1 0 1 0 1.3083 12 1 -1 -1 1 4.2238 13 1 -1 0 1 4.1499 14 1 -1 1 1 4.8655 15 1 0 -1 1 3.4172 16 1 0 0 1 1.9394 17 1 0 1 1 2.9127 18 1 1 1 1 5.0960 19 1 1 0 1 6.3201 20 1 1 -1 1 4.9465 21 1 1 1 0 5.0875 22 1 1 0 0 2.4922 23 1 1 -1 0 4.4024 24 1 1 1 -1 4.2238 25 1 1 0 -1 4.1499 26 1 1 -1 -1 4.8655 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4014 atoms have been selected out of 4088 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 696 232 232 0.00 3 C003 has 84 28 28 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 513 171 171 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1761 587 587 0.00 12 C012 has 120 40 40 0.00 13 C013 has 489 163 163 0.00 14 C014 has 102 34 34 0.00 Total of13654 atoms and 4543 groups and 4538 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4088 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1351 Number of atoms = 4088 Number of groups = 1356 Number of bonds = 4081 Number of angles = 1455 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1353 Number of HB donors = 2684 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1351 Number of atoms = 4088 Number of groups = 1356 Number of bonds = 4081 Number of angles = 1455 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1353 Number of HB donors = 2684 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.446" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1351" Evaluating: 1351-7 Parameter: NUMWAT <- "1344" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1344" Comparing "1081" and "1344". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.446" Parameter: BOX -> "34.446" Parameter: BOX -> "34.446" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.44600 B = 34.44600 C = 34.44600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.0984 2 1 -1 0 -1 6.3178 3 1 -1 1 -1 4.9430 4 1 0 -1 -1 2.9109 5 1 0 0 -1 1.9374 6 1 0 1 -1 3.4145 7 1 -1 -1 0 5.0856 8 1 -1 0 0 2.4916 9 1 -1 1 0 4.4002 10 1 0 -1 0 1.3075 11 1 0 1 0 1.3075 12 1 -1 -1 1 4.2203 13 1 -1 0 1 4.1471 14 1 -1 1 1 4.8624 15 1 0 -1 1 3.4145 16 1 0 0 1 1.9374 17 1 0 1 1 2.9109 18 1 1 1 1 5.0984 19 1 1 0 1 6.3178 20 1 1 -1 1 4.9430 21 1 1 1 0 5.0856 22 1 1 0 0 2.4916 23 1 1 -1 0 4.4002 24 1 1 1 -1 4.2203 25 1 1 0 -1 4.1471 26 1 1 -1 -1 4.8624 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4014 atoms have been selected out of 4088 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 699 233 233 0.00 3 C003 has 84 28 28 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 513 171 171 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1761 587 587 0.00 12 C012 has 120 40 40 0.00 13 C013 has 489 163 163 0.00 14 C014 has 102 34 34 0.00 Total of13657 atoms and 4544 groups and 4539 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4088 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1351 Number of atoms = 4088 Number of groups = 1356 Number of bonds = 4081 Number of angles = 1455 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1353 Number of HB donors = 2684 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1351 Number of atoms = 4088 Number of groups = 1356 Number of bonds = 4081 Number of angles = 1455 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1353 Number of HB donors = 2684 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.444" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1351" Evaluating: 1351-7 Parameter: NUMWAT <- "1344" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1344" Comparing "1081" and "1344". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.444" Parameter: BOX -> "34.444" Parameter: BOX -> "34.444" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.44400 B = 34.44400 C = 34.44400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.1007 2 1 -1 0 -1 6.3155 3 1 -1 1 -1 4.9396 4 1 0 -1 -1 2.9092 5 1 0 0 -1 1.9355 6 1 0 1 -1 3.4117 7 1 -1 -1 0 5.0837 8 1 -1 0 0 2.4910 9 1 -1 1 0 4.3980 10 1 0 -1 0 1.3067 11 1 0 1 0 1.3067 12 1 -1 -1 1 4.2169 13 1 -1 0 1 4.1443 14 1 -1 1 1 4.8594 15 1 0 -1 1 3.4117 16 1 0 0 1 1.9355 17 1 0 1 1 2.9092 18 1 1 1 1 5.1007 19 1 1 0 1 6.3155 20 1 1 -1 1 4.9396 21 1 1 1 0 5.0837 22 1 1 0 0 2.4910 23 1 1 -1 0 4.3980 24 1 1 1 -1 4.2169 25 1 1 0 -1 4.1443 26 1 1 -1 -1 4.8594 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4014 atoms have been selected out of 4088 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1264 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 696 232 232 0.00 3 C003 has 84 28 28 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 513 171 171 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1761 587 587 0.00 12 C012 has 120 40 40 0.00 13 C013 has 489 163 163 0.00 14 C014 has 102 34 34 0.00 Total of13648 atoms and 4541 groups and 4536 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4088 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1350 Number of atoms = 4085 Number of groups = 1355 Number of bonds = 4078 Number of angles = 1454 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1352 Number of HB donors = 2682 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1350 Number of atoms = 4085 Number of groups = 1355 Number of bonds = 4078 Number of angles = 1454 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1352 Number of HB donors = 2682 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.442" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1350" Evaluating: 1350-7 Parameter: NUMWAT <- "1343" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1343" Comparing "1081" and "1343". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.442" Parameter: BOX -> "34.442" Parameter: BOX -> "34.442" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.44200 B = 34.44200 C = 34.44200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.1030 2 1 -1 0 -1 6.3132 3 1 -1 1 -1 4.9362 4 1 0 -1 -1 2.9074 5 1 0 0 -1 1.9336 6 1 0 1 -1 3.4089 7 1 -1 -1 0 5.0818 8 1 -1 0 0 2.4904 9 1 -1 1 0 4.3958 10 1 0 -1 0 1.3058 11 1 0 1 0 1.3058 12 1 -1 -1 1 4.2134 13 1 -1 0 1 4.1416 14 1 -1 1 1 4.8564 15 1 0 -1 1 3.4089 16 1 0 0 1 1.9336 17 1 0 1 1 2.9074 18 1 1 1 1 5.1030 19 1 1 0 1 6.3132 20 1 1 -1 1 4.9362 21 1 1 1 0 5.0818 22 1 1 0 0 2.4904 23 1 1 -1 0 4.3958 24 1 1 1 -1 4.2134 25 1 1 0 -1 4.1416 26 1 1 -1 -1 4.8564 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4011 atoms have been selected out of 4085 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 696 232 232 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1677 559 559 0.00 6 C006 has 513 171 171 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 120 40 40 0.00 13 C013 has 489 163 163 0.00 14 C014 has 102 34 34 0.00 Total of13633 atoms and 4536 groups and 4531 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4085 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1350 Number of atoms = 4085 Number of groups = 1355 Number of bonds = 4078 Number of angles = 1454 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1352 Number of HB donors = 2682 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1350 Number of atoms = 4085 Number of groups = 1355 Number of bonds = 4078 Number of angles = 1454 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1352 Number of HB donors = 2682 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.44" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1350" Evaluating: 1350-7 Parameter: NUMWAT <- "1343" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1343" Comparing "1081" and "1343". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.44" Parameter: BOX -> "34.44" Parameter: BOX -> "34.44" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.44000 B = 34.44000 C = 34.44000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.1054 2 1 -1 0 -1 6.3108 3 1 -1 1 -1 4.9327 4 1 0 -1 -1 2.9057 5 1 0 0 -1 1.9317 6 1 0 1 -1 3.4062 7 1 -1 -1 0 5.0799 8 1 -1 0 0 2.4898 9 1 -1 1 0 4.3935 10 1 0 -1 0 1.3050 11 1 0 1 0 1.3050 12 1 -1 -1 1 4.2100 13 1 -1 0 1 4.1388 14 1 -1 1 1 4.8534 15 1 0 -1 1 3.4062 16 1 0 0 1 1.9317 17 1 0 1 1 2.9057 18 1 1 1 1 5.1054 19 1 1 0 1 6.3108 20 1 1 -1 1 4.9327 21 1 1 1 0 5.0799 22 1 1 0 0 2.4898 23 1 1 -1 0 4.3935 24 1 1 1 -1 4.2100 25 1 1 0 -1 4.1388 26 1 1 -1 -1 4.8534 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4011 atoms have been selected out of 4085 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 696 232 232 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1677 559 559 0.00 6 C006 has 513 171 171 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 120 40 40 0.00 13 C013 has 489 163 163 0.00 14 C014 has 102 34 34 0.00 Total of13639 atoms and 4538 groups and 4533 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4085 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1350 Number of atoms = 4085 Number of groups = 1355 Number of bonds = 4078 Number of angles = 1454 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1352 Number of HB donors = 2682 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1350 Number of atoms = 4085 Number of groups = 1355 Number of bonds = 4078 Number of angles = 1454 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1352 Number of HB donors = 2682 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.438" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1350" Evaluating: 1350-7 Parameter: NUMWAT <- "1343" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1343" Comparing "1081" and "1343". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.438" Parameter: BOX -> "34.438" Parameter: BOX -> "34.438" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.43800 B = 34.43800 C = 34.43800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.1077 2 1 -1 0 -1 6.3085 3 1 -1 1 -1 4.9293 4 1 0 -1 -1 2.9039 5 1 0 0 -1 1.9297 6 1 0 1 -1 3.4034 7 1 -1 -1 0 5.0780 8 1 -1 0 0 2.4892 9 1 -1 1 0 4.3913 10 1 0 -1 0 1.3042 11 1 0 1 0 1.3042 12 1 -1 -1 1 4.2065 13 1 -1 0 1 4.1360 14 1 -1 1 1 4.8504 15 1 0 -1 1 3.4034 16 1 0 0 1 1.9297 17 1 0 1 1 2.9039 18 1 1 1 1 5.1077 19 1 1 0 1 6.3085 20 1 1 -1 1 4.9293 21 1 1 1 0 5.0780 22 1 1 0 0 2.4892 23 1 1 -1 0 4.3913 24 1 1 1 -1 4.2065 25 1 1 0 -1 4.1360 26 1 1 -1 -1 4.8504 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4011 atoms have been selected out of 4085 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 696 232 232 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1677 559 559 0.00 6 C006 has 513 171 171 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 120 40 40 0.00 13 C013 has 492 164 164 0.00 14 C014 has 102 34 34 0.00 Total of13642 atoms and 4539 groups and 4534 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4085 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1350 Number of atoms = 4085 Number of groups = 1355 Number of bonds = 4078 Number of angles = 1454 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1352 Number of HB donors = 2682 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1350 Number of atoms = 4085 Number of groups = 1355 Number of bonds = 4078 Number of angles = 1454 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1352 Number of HB donors = 2682 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.436" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1350" Evaluating: 1350-7 Parameter: NUMWAT <- "1343" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1343" Comparing "1081" and "1343". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.436" Parameter: BOX -> "34.436" Parameter: BOX -> "34.436" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.43600 B = 34.43600 C = 34.43600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.1100 2 1 -1 0 -1 6.3062 3 1 -1 1 -1 4.9258 4 1 0 -1 -1 2.9022 5 1 0 0 -1 1.9278 6 1 0 1 -1 3.4007 7 1 -1 -1 0 5.0761 8 1 -1 0 0 2.4886 9 1 -1 1 0 4.3891 10 1 0 -1 0 1.3034 11 1 0 1 0 1.3034 12 1 -1 -1 1 4.2031 13 1 -1 0 1 4.1332 14 1 -1 1 1 4.8474 15 1 0 -1 1 3.4007 16 1 0 0 1 1.9278 17 1 0 1 1 2.9022 18 1 1 1 1 5.1100 19 1 1 0 1 6.3062 20 1 1 -1 1 4.9258 21 1 1 1 0 5.0761 22 1 1 0 0 2.4886 23 1 1 -1 0 4.3891 24 1 1 1 -1 4.2031 25 1 1 0 -1 4.1332 26 1 1 -1 -1 4.8474 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4011 atoms have been selected out of 4085 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 696 232 232 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1677 559 559 0.00 6 C006 has 513 171 171 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 120 40 40 0.00 13 C013 has 492 164 164 0.00 14 C014 has 102 34 34 0.00 Total of13642 atoms and 4539 groups and 4534 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4085 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1350 Number of atoms = 4085 Number of groups = 1355 Number of bonds = 4078 Number of angles = 1454 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1352 Number of HB donors = 2682 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1350 Number of atoms = 4085 Number of groups = 1355 Number of bonds = 4078 Number of angles = 1454 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1352 Number of HB donors = 2682 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.434" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1350" Evaluating: 1350-7 Parameter: NUMWAT <- "1343" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1343" Comparing "1081" and "1343". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.434" Parameter: BOX -> "34.434" Parameter: BOX -> "34.434" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.43400 B = 34.43400 C = 34.43400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.1124 2 1 -1 0 -1 6.3039 3 1 -1 1 -1 4.9224 4 1 0 -1 -1 2.9004 5 1 0 0 -1 1.9259 6 1 0 1 -1 3.3979 7 1 -1 -1 0 5.0742 8 1 -1 0 0 2.4881 9 1 -1 1 0 4.3869 10 1 0 -1 0 1.3026 11 1 0 1 0 1.3026 12 1 -1 -1 1 4.1996 13 1 -1 0 1 4.1305 14 1 -1 1 1 4.8444 15 1 0 -1 1 3.3979 16 1 0 0 1 1.9259 17 1 0 1 1 2.9004 18 1 1 1 1 5.1124 19 1 1 0 1 6.3039 20 1 1 -1 1 4.9224 21 1 1 1 0 5.0742 22 1 1 0 0 2.4881 23 1 1 -1 0 4.3869 24 1 1 1 -1 4.1996 25 1 1 0 -1 4.1305 26 1 1 -1 -1 4.8444 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4011 atoms have been selected out of 4085 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 696 232 232 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1677 559 559 0.00 6 C006 has 513 171 171 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 120 40 40 0.00 13 C013 has 492 164 164 0.00 14 C014 has 102 34 34 0.00 Total of13642 atoms and 4539 groups and 4534 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4085 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1350 Number of atoms = 4085 Number of groups = 1355 Number of bonds = 4078 Number of angles = 1454 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1352 Number of HB donors = 2682 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1350 Number of atoms = 4085 Number of groups = 1355 Number of bonds = 4078 Number of angles = 1454 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1352 Number of HB donors = 2682 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.432" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1350" Evaluating: 1350-7 Parameter: NUMWAT <- "1343" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1343" Comparing "1081" and "1343". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.432" Parameter: BOX -> "34.432" Parameter: BOX -> "34.432" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.43200 B = 34.43200 C = 34.43200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.1147 2 1 -1 0 -1 6.3015 3 1 -1 1 -1 4.9190 4 1 0 -1 -1 2.8987 5 1 0 0 -1 1.9240 6 1 0 1 -1 3.3952 7 1 -1 -1 0 5.0723 8 1 -1 0 0 2.4875 9 1 -1 1 0 4.3847 10 1 0 -1 0 1.3017 11 1 0 1 0 1.3017 12 1 -1 -1 1 4.1962 13 1 -1 0 1 4.1277 14 1 -1 1 1 4.8414 15 1 0 -1 1 3.3952 16 1 0 0 1 1.9240 17 1 0 1 1 2.8987 18 1 1 1 1 5.1147 19 1 1 0 1 6.3015 20 1 1 -1 1 4.9190 21 1 1 1 0 5.0723 22 1 1 0 0 2.4875 23 1 1 -1 0 4.3847 24 1 1 1 -1 4.1962 25 1 1 0 -1 4.1277 26 1 1 -1 -1 4.8414 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4011 atoms have been selected out of 4085 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 696 232 232 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1677 559 559 0.00 6 C006 has 513 171 171 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 120 40 40 0.00 13 C013 has 492 164 164 0.00 14 C014 has 102 34 34 0.00 Total of13645 atoms and 4540 groups and 4535 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4085 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1350 Number of atoms = 4085 Number of groups = 1355 Number of bonds = 4078 Number of angles = 1454 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1352 Number of HB donors = 2682 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1350 Number of atoms = 4085 Number of groups = 1355 Number of bonds = 4078 Number of angles = 1454 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1352 Number of HB donors = 2682 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.43" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1350" Evaluating: 1350-7 Parameter: NUMWAT <- "1343" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1343" Comparing "1081" and "1343". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.43" Parameter: BOX -> "34.43" Parameter: BOX -> "34.43" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.43000 B = 34.43000 C = 34.43000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.1171 2 1 -1 0 -1 6.2992 3 1 -1 1 -1 4.9155 4 1 0 -1 -1 2.8970 5 1 0 0 -1 1.9221 6 1 0 1 -1 3.3924 7 1 -1 -1 0 5.0704 8 1 -1 0 0 2.4869 9 1 -1 1 0 4.3825 10 1 0 -1 0 1.3009 11 1 0 1 0 1.3009 12 1 -1 -1 1 4.1927 13 1 -1 0 1 4.1249 14 1 -1 1 1 4.8384 15 1 0 -1 1 3.3924 16 1 0 0 1 1.9221 17 1 0 1 1 2.8970 18 1 1 1 1 5.1171 19 1 1 0 1 6.2992 20 1 1 -1 1 4.9155 21 1 1 1 0 5.0704 22 1 1 0 0 2.4869 23 1 1 -1 0 4.3825 24 1 1 1 -1 4.1927 25 1 1 0 -1 4.1249 26 1 1 -1 -1 4.8384 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4011 atoms have been selected out of 4085 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 699 233 233 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1677 559 559 0.00 6 C006 has 513 171 171 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1761 587 587 0.00 12 C012 has 120 40 40 0.00 13 C013 has 492 164 164 0.00 14 C014 has 102 34 34 0.00 Total of13651 atoms and 4542 groups and 4537 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4085 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1350 Number of atoms = 4085 Number of groups = 1355 Number of bonds = 4078 Number of angles = 1454 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1352 Number of HB donors = 2682 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1350 Number of atoms = 4085 Number of groups = 1355 Number of bonds = 4078 Number of angles = 1454 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1352 Number of HB donors = 2682 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.428" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1350" Evaluating: 1350-7 Parameter: NUMWAT <- "1343" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1343" Comparing "1081" and "1343". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.428" Parameter: BOX -> "34.428" Parameter: BOX -> "34.428" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.42800 B = 34.42800 C = 34.42800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.1194 2 1 -1 0 -1 6.2969 3 1 -1 1 -1 4.9121 4 1 0 -1 -1 2.8952 5 1 0 0 -1 1.9201 6 1 0 1 -1 3.3896 7 1 -1 -1 0 5.0685 8 1 -1 0 0 2.4863 9 1 -1 1 0 4.3803 10 1 0 -1 0 1.3001 11 1 0 1 0 1.3001 12 1 -1 -1 1 4.1893 13 1 -1 0 1 4.1221 14 1 -1 1 1 4.8354 15 1 0 -1 1 3.3896 16 1 0 0 1 1.9201 17 1 0 1 1 2.8952 18 1 1 1 1 5.1194 19 1 1 0 1 6.2969 20 1 1 -1 1 4.9121 21 1 1 1 0 5.0685 22 1 1 0 0 2.4863 23 1 1 -1 0 4.3803 24 1 1 1 -1 4.1893 25 1 1 0 -1 4.1221 26 1 1 -1 -1 4.8354 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4011 atoms have been selected out of 4085 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 175 OPERATED ON BY TRANSFORMATION C011 RESIDUE 342 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 699 233 233 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1677 559 559 0.00 6 C006 has 513 171 171 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1847 614 614 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1767 589 589 0.00 12 C012 has 126 42 42 0.00 13 C013 has 492 164 164 0.00 14 C014 has 99 33 33 0.00 Total of13660 atoms and 4545 groups and 4540 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 4085 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1348 Number of atoms = 4079 Number of groups = 1353 Number of bonds = 4072 Number of angles = 1452 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1350 Number of HB donors = 2678 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1348 Number of atoms = 4079 Number of groups = 1353 Number of bonds = 4072 Number of angles = 1452 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1350 Number of HB donors = 2678 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.426" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1348" Evaluating: 1348-7 Parameter: NUMWAT <- "1341" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1341" Comparing "1081" and "1341". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.426" Parameter: BOX -> "34.426" Parameter: BOX -> "34.426" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.42600 B = 34.42600 C = 34.42600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.1218 2 1 -1 0 -1 6.2946 3 1 -1 1 -1 4.9086 4 1 0 -1 -1 2.8935 5 1 0 0 -1 1.9182 6 1 0 1 -1 3.3869 7 1 -1 -1 0 5.0666 8 1 -1 0 0 2.4857 9 1 -1 1 0 1.7863 10 1 0 -1 0 1.2993 11 1 0 1 0 1.2993 12 1 -1 -1 1 4.1858 13 1 -1 0 1 4.1193 14 1 -1 1 1 4.8324 15 1 0 -1 1 3.3869 16 1 0 0 1 1.9182 17 1 0 1 1 2.8935 18 1 1 1 1 5.1218 19 1 1 0 1 6.2946 20 1 1 -1 1 4.9086 21 1 1 1 0 5.0666 22 1 1 0 0 2.4857 23 1 1 -1 0 1.7863 24 1 1 1 -1 4.1858 25 1 1 0 -1 4.1193 26 1 1 -1 -1 4.8324 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4005 atoms have been selected out of 4079 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 699 233 233 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1677 559 559 0.00 6 C006 has 513 171 171 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1761 587 587 0.00 12 C012 has 123 41 41 0.00 13 C013 has 492 164 164 0.00 14 C014 has 99 33 33 0.00 Total of13639 atoms and 4538 groups and 4533 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4079 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1348 Number of atoms = 4079 Number of groups = 1353 Number of bonds = 4072 Number of angles = 1452 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1350 Number of HB donors = 2678 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1348 Number of atoms = 4079 Number of groups = 1353 Number of bonds = 4072 Number of angles = 1452 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1350 Number of HB donors = 2678 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.424" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1348" Evaluating: 1348-7 Parameter: NUMWAT <- "1341" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1341" Comparing "1081" and "1341". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.424" Parameter: BOX -> "34.424" Parameter: BOX -> "34.424" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.42400 B = 34.42400 C = 34.42400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.1241 2 1 -1 0 -1 6.2922 3 1 -1 1 -1 4.9052 4 1 0 -1 -1 2.8917 5 1 0 0 -1 1.9163 6 1 0 1 -1 3.3841 7 1 -1 -1 0 5.0647 8 1 -1 0 0 2.4851 9 1 -1 1 0 1.7845 10 1 0 -1 0 1.2985 11 1 0 1 0 1.2985 12 1 -1 -1 1 4.1824 13 1 -1 0 1 4.1166 14 1 -1 1 1 4.8294 15 1 0 -1 1 3.3841 16 1 0 0 1 1.9163 17 1 0 1 1 2.8917 18 1 1 1 1 5.1241 19 1 1 0 1 6.2922 20 1 1 -1 1 4.9052 21 1 1 1 0 5.0647 22 1 1 0 0 2.4851 23 1 1 -1 0 1.7845 24 1 1 1 -1 4.1824 25 1 1 0 -1 4.1166 26 1 1 -1 -1 4.8294 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4005 atoms have been selected out of 4079 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 471 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 699 233 233 0.00 3 C003 has 84 28 28 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1680 560 560 0.00 6 C006 has 513 171 171 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 123 41 41 0.00 13 C013 has 495 165 165 0.00 14 C014 has 99 33 33 0.00 Total of13648 atoms and 4541 groups and 4536 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4079 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1347 Number of atoms = 4076 Number of groups = 1352 Number of bonds = 4069 Number of angles = 1451 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1349 Number of HB donors = 2676 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1347 Number of atoms = 4076 Number of groups = 1352 Number of bonds = 4069 Number of angles = 1451 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1349 Number of HB donors = 2676 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.422" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1347" Evaluating: 1347-7 Parameter: NUMWAT <- "1340" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1340" Comparing "1081" and "1340". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.422" Parameter: BOX -> "34.422" Parameter: BOX -> "34.422" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.42200 B = 34.42200 C = 34.42200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.1264 2 1 -1 0 -1 6.2899 3 1 -1 1 -1 4.9018 4 1 0 -1 -1 2.8900 5 1 0 0 -1 1.9144 6 1 0 1 -1 3.3814 7 1 -1 -1 0 5.0628 8 1 -1 0 0 2.4846 9 1 -1 1 0 1.7828 10 1 0 -1 0 1.2977 11 1 0 1 0 1.2977 12 1 -1 -1 1 4.1789 13 1 -1 0 1 4.1138 14 1 -1 1 1 4.8264 15 1 0 -1 1 3.3814 16 1 0 0 1 1.9144 17 1 0 1 1 2.8900 18 1 1 1 1 5.1264 19 1 1 0 1 6.2899 20 1 1 -1 1 4.9018 21 1 1 1 0 5.0628 22 1 1 0 0 2.4846 23 1 1 -1 0 1.7828 24 1 1 1 -1 4.1789 25 1 1 0 -1 4.1138 26 1 1 -1 -1 4.8264 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4002 atoms have been selected out of 4076 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 699 233 233 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1677 559 559 0.00 6 C006 has 513 171 171 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 123 41 41 0.00 13 C013 has 495 165 165 0.00 14 C014 has 99 33 33 0.00 Total of13639 atoms and 4538 groups and 4533 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4076 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1347 Number of atoms = 4076 Number of groups = 1352 Number of bonds = 4069 Number of angles = 1451 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1349 Number of HB donors = 2676 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1347 Number of atoms = 4076 Number of groups = 1352 Number of bonds = 4069 Number of angles = 1451 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1349 Number of HB donors = 2676 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.42" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1347" Evaluating: 1347-7 Parameter: NUMWAT <- "1340" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1340" Comparing "1081" and "1340". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.42" Parameter: BOX -> "34.42" Parameter: BOX -> "34.42" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.42000 B = 34.42000 C = 34.42000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.1288 2 1 -1 0 -1 6.2876 3 1 -1 1 -1 4.8983 4 1 0 -1 -1 2.8883 5 1 0 0 -1 1.9125 6 1 0 1 -1 3.3786 7 1 -1 -1 0 5.0609 8 1 -1 0 0 2.4840 9 1 -1 1 0 1.7811 10 1 0 -1 0 1.2969 11 1 0 1 0 1.2969 12 1 -1 -1 1 4.1755 13 1 -1 0 1 4.1110 14 1 -1 1 1 4.8234 15 1 0 -1 1 3.3786 16 1 0 0 1 1.9125 17 1 0 1 1 2.8883 18 1 1 1 1 5.1288 19 1 1 0 1 6.2876 20 1 1 -1 1 4.8983 21 1 1 1 0 5.0609 22 1 1 0 0 2.4840 23 1 1 -1 0 1.7811 24 1 1 1 -1 4.1755 25 1 1 0 -1 4.1110 26 1 1 -1 -1 4.8234 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4002 atoms have been selected out of 4076 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 699 233 233 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1677 559 559 0.00 6 C006 has 513 171 171 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 123 41 41 0.00 13 C013 has 495 165 165 0.00 14 C014 has 99 33 33 0.00 Total of13639 atoms and 4538 groups and 4533 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4076 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1347 Number of atoms = 4076 Number of groups = 1352 Number of bonds = 4069 Number of angles = 1451 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1349 Number of HB donors = 2676 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1347 Number of atoms = 4076 Number of groups = 1352 Number of bonds = 4069 Number of angles = 1451 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1349 Number of HB donors = 2676 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.418" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1347" Evaluating: 1347-7 Parameter: NUMWAT <- "1340" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1340" Comparing "1081" and "1340". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.418" Parameter: BOX -> "34.418" Parameter: BOX -> "34.418" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.41800 B = 34.41800 C = 34.41800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.1311 2 1 -1 0 -1 6.2853 3 1 -1 1 -1 4.8949 4 1 0 -1 -1 2.8865 5 1 0 0 -1 1.9105 6 1 0 1 -1 3.3759 7 1 -1 -1 0 5.0590 8 1 -1 0 0 2.4834 9 1 -1 1 0 1.7794 10 1 0 -1 0 1.2961 11 1 0 1 0 1.2961 12 1 -1 -1 1 4.1720 13 1 -1 0 1 4.1082 14 1 -1 1 1 4.8204 15 1 0 -1 1 3.3759 16 1 0 0 1 1.9105 17 1 0 1 1 2.8865 18 1 1 1 1 5.1311 19 1 1 0 1 6.2853 20 1 1 -1 1 4.8949 21 1 1 1 0 5.0590 22 1 1 0 0 2.4834 23 1 1 -1 0 1.7794 24 1 1 1 -1 4.1720 25 1 1 0 -1 4.1082 26 1 1 -1 -1 4.8204 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4002 atoms have been selected out of 4076 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 699 233 233 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1677 559 559 0.00 6 C006 has 513 171 171 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 123 41 41 0.00 13 C013 has 495 165 165 0.00 14 C014 has 99 33 33 0.00 Total of13639 atoms and 4538 groups and 4533 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4076 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1347 Number of atoms = 4076 Number of groups = 1352 Number of bonds = 4069 Number of angles = 1451 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1349 Number of HB donors = 2676 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1347 Number of atoms = 4076 Number of groups = 1352 Number of bonds = 4069 Number of angles = 1451 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1349 Number of HB donors = 2676 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.416" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1347" Evaluating: 1347-7 Parameter: NUMWAT <- "1340" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1340" Comparing "1081" and "1340". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.416" Parameter: BOX -> "34.416" Parameter: BOX -> "34.416" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.41600 B = 34.41600 C = 34.41600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.1335 2 1 -1 0 -1 6.2830 3 1 -1 1 -1 4.8914 4 1 0 -1 -1 2.8848 5 1 0 0 -1 1.9086 6 1 0 1 -1 3.3731 7 1 -1 -1 0 5.0571 8 1 -1 0 0 2.4828 9 1 -1 1 0 1.7777 10 1 0 -1 0 1.2953 11 1 0 1 0 1.2953 12 1 -1 -1 1 4.1686 13 1 -1 0 1 4.1054 14 1 -1 1 1 4.8174 15 1 0 -1 1 3.3731 16 1 0 0 1 1.9086 17 1 0 1 1 2.8848 18 1 1 1 1 5.1335 19 1 1 0 1 6.2830 20 1 1 -1 1 4.8914 21 1 1 1 0 5.0571 22 1 1 0 0 2.4828 23 1 1 -1 0 1.7777 24 1 1 1 -1 4.1686 25 1 1 0 -1 4.1054 26 1 1 -1 -1 4.8174 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4002 atoms have been selected out of 4076 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 699 233 233 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1677 559 559 0.00 6 C006 has 513 171 171 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 123 41 41 0.00 13 C013 has 495 165 165 0.00 14 C014 has 99 33 33 0.00 Total of13639 atoms and 4538 groups and 4533 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4076 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1347 Number of atoms = 4076 Number of groups = 1352 Number of bonds = 4069 Number of angles = 1451 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1349 Number of HB donors = 2676 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1347 Number of atoms = 4076 Number of groups = 1352 Number of bonds = 4069 Number of angles = 1451 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1349 Number of HB donors = 2676 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.414" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1347" Evaluating: 1347-7 Parameter: NUMWAT <- "1340" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1340" Comparing "1081" and "1340". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.414" Parameter: BOX -> "34.414" Parameter: BOX -> "34.414" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.41400 B = 34.41400 C = 34.41400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.1358 2 1 -1 0 -1 6.2806 3 1 -1 1 -1 4.8880 4 1 0 -1 -1 2.8831 5 1 0 0 -1 1.9067 6 1 0 1 -1 3.3704 7 1 -1 -1 0 5.0552 8 1 -1 0 0 2.4823 9 1 -1 1 0 1.7759 10 1 0 -1 0 1.2945 11 1 0 1 0 1.2945 12 1 -1 -1 1 4.1651 13 1 -1 0 1 4.1027 14 1 -1 1 1 4.8144 15 1 0 -1 1 3.3704 16 1 0 0 1 1.9067 17 1 0 1 1 2.8831 18 1 1 1 1 5.1358 19 1 1 0 1 6.2806 20 1 1 -1 1 4.8880 21 1 1 1 0 5.0552 22 1 1 0 0 2.4823 23 1 1 -1 0 1.7759 24 1 1 1 -1 4.1651 25 1 1 0 -1 4.1027 26 1 1 -1 -1 4.8144 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4002 atoms have been selected out of 4076 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 699 233 233 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1677 559 559 0.00 6 C006 has 513 171 171 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 123 41 41 0.00 13 C013 has 495 165 165 0.00 14 C014 has 99 33 33 0.00 Total of13639 atoms and 4538 groups and 4533 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4076 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1347 Number of atoms = 4076 Number of groups = 1352 Number of bonds = 4069 Number of angles = 1451 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1349 Number of HB donors = 2676 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1347 Number of atoms = 4076 Number of groups = 1352 Number of bonds = 4069 Number of angles = 1451 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1349 Number of HB donors = 2676 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.412" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1347" Evaluating: 1347-7 Parameter: NUMWAT <- "1340" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1340" Comparing "1081" and "1340". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.412" Parameter: BOX -> "34.412" Parameter: BOX -> "34.412" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.41200 B = 34.41200 C = 34.41200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.1382 2 1 -1 0 -1 6.2783 3 1 -1 1 -1 4.8846 4 1 0 -1 -1 2.8814 5 1 0 0 -1 1.9048 6 1 0 1 -1 3.3676 7 1 -1 -1 0 5.0534 8 1 -1 0 0 2.4817 9 1 -1 1 0 1.7742 10 1 0 -1 0 1.2937 11 1 0 1 0 1.2937 12 1 -1 -1 1 4.1616 13 1 -1 0 1 4.0999 14 1 -1 1 1 4.8115 15 1 0 -1 1 3.3676 16 1 0 0 1 1.9048 17 1 0 1 1 2.8814 18 1 1 1 1 5.1382 19 1 1 0 1 6.2783 20 1 1 -1 1 4.8846 21 1 1 1 0 5.0534 22 1 1 0 0 2.4817 23 1 1 -1 0 1.7742 24 1 1 1 -1 4.1616 25 1 1 0 -1 4.0999 26 1 1 -1 -1 4.8115 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 4002 atoms have been selected out of 4076 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 376 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 384 128 128 0.00 2 C002 has 699 233 233 0.00 3 C003 has 84 28 28 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1671 557 557 0.00 6 C006 has 513 171 171 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1758 586 586 0.00 12 C012 has 123 41 41 0.00 13 C013 has 495 165 165 0.00 14 C014 has 99 33 33 0.00 Total of13639 atoms and 4538 groups and 4533 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4076 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1346 Number of atoms = 4073 Number of groups = 1351 Number of bonds = 4066 Number of angles = 1450 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1348 Number of HB donors = 2674 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1346 Number of atoms = 4073 Number of groups = 1351 Number of bonds = 4066 Number of angles = 1450 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1348 Number of HB donors = 2674 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.41" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1346" Evaluating: 1346-7 Parameter: NUMWAT <- "1339" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1339" Comparing "1081" and "1339". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.41" Parameter: BOX -> "34.41" Parameter: BOX -> "34.41" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.41000 B = 34.41000 C = 34.41000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.1406 2 1 -1 0 -1 6.2760 3 1 -1 1 -1 4.8811 4 1 0 -1 -1 2.8796 5 1 0 0 -1 1.9029 6 1 0 1 -1 3.3648 7 1 -1 -1 0 5.0515 8 1 -1 0 0 2.4811 9 1 -1 1 0 1.7725 10 1 0 -1 0 1.2929 11 1 0 1 0 1.2929 12 1 -1 -1 1 4.1582 13 1 -1 0 1 4.0971 14 1 -1 1 1 4.8085 15 1 0 -1 1 3.3648 16 1 0 0 1 1.9029 17 1 0 1 1 2.8796 18 1 1 1 1 5.1406 19 1 1 0 1 6.2760 20 1 1 -1 1 4.8811 21 1 1 1 0 5.0515 22 1 1 0 0 2.4811 23 1 1 -1 0 1.7725 24 1 1 1 -1 4.1582 25 1 1 0 -1 4.0971 26 1 1 -1 -1 4.8085 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3999 atoms have been selected out of 4073 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 384 128 128 0.00 2 C002 has 699 233 233 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1668 556 556 0.00 6 C006 has 513 171 171 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 123 41 41 0.00 13 C013 has 495 165 165 0.00 14 C014 has 99 33 33 0.00 Total of13627 atoms and 4534 groups and 4529 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4073 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1346 Number of atoms = 4073 Number of groups = 1351 Number of bonds = 4066 Number of angles = 1450 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1348 Number of HB donors = 2674 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1346 Number of atoms = 4073 Number of groups = 1351 Number of bonds = 4066 Number of angles = 1450 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1348 Number of HB donors = 2674 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.408" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1346" Evaluating: 1346-7 Parameter: NUMWAT <- "1339" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1339" Comparing "1081" and "1339". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.408" Parameter: BOX -> "34.408" Parameter: BOX -> "34.408" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.40800 B = 34.40800 C = 34.40800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.1429 2 1 -1 0 -1 6.2737 3 1 -1 1 -1 4.8777 4 1 0 -1 -1 2.8779 5 1 0 0 -1 1.9009 6 1 0 1 -1 3.3621 7 1 -1 -1 0 5.0496 8 1 -1 0 0 2.4806 9 1 -1 1 0 1.7708 10 1 0 -1 0 1.2922 11 1 0 1 0 1.2922 12 1 -1 -1 1 4.1547 13 1 -1 0 1 4.0943 14 1 -1 1 1 4.8055 15 1 0 -1 1 3.3621 16 1 0 0 1 1.9009 17 1 0 1 1 2.8779 18 1 1 1 1 5.1429 19 1 1 0 1 6.2737 20 1 1 -1 1 4.8777 21 1 1 1 0 5.0496 22 1 1 0 0 2.4806 23 1 1 -1 0 1.7708 24 1 1 1 -1 4.1547 25 1 1 0 -1 4.0943 26 1 1 -1 -1 4.8055 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3999 atoms have been selected out of 4073 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 384 128 128 0.00 2 C002 has 699 233 233 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1668 556 556 0.00 6 C006 has 513 171 171 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 123 41 41 0.00 13 C013 has 495 165 165 0.00 14 C014 has 99 33 33 0.00 Total of13630 atoms and 4535 groups and 4530 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4073 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1346 Number of atoms = 4073 Number of groups = 1351 Number of bonds = 4066 Number of angles = 1450 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1348 Number of HB donors = 2674 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1346 Number of atoms = 4073 Number of groups = 1351 Number of bonds = 4066 Number of angles = 1450 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1348 Number of HB donors = 2674 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.406" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1346" Evaluating: 1346-7 Parameter: NUMWAT <- "1339" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1339" Comparing "1081" and "1339". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.406" Parameter: BOX -> "34.406" Parameter: BOX -> "34.406" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.40600 B = 34.40600 C = 34.40600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.1453 2 1 -1 0 -1 6.2714 3 1 -1 1 -1 4.8742 4 1 0 -1 -1 2.8762 5 1 0 0 -1 1.8990 6 1 0 1 -1 3.3593 7 1 -1 -1 0 5.0477 8 1 -1 0 0 2.4800 9 1 -1 1 0 1.7691 10 1 0 -1 0 1.2914 11 1 0 1 0 1.2914 12 1 -1 -1 1 4.1513 13 1 -1 0 1 4.0916 14 1 -1 1 1 4.8025 15 1 0 -1 1 3.3593 16 1 0 0 1 1.8990 17 1 0 1 1 2.8762 18 1 1 1 1 5.1453 19 1 1 0 1 6.2714 20 1 1 -1 1 4.8742 21 1 1 1 0 5.0477 22 1 1 0 0 2.4800 23 1 1 -1 0 1.7691 24 1 1 1 -1 4.1513 25 1 1 0 -1 4.0916 26 1 1 -1 -1 4.8025 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3999 atoms have been selected out of 4073 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 384 128 128 0.00 2 C002 has 699 233 233 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1668 556 556 0.00 6 C006 has 513 171 171 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 123 41 41 0.00 13 C013 has 495 165 165 0.00 14 C014 has 99 33 33 0.00 Total of13633 atoms and 4536 groups and 4531 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4073 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1346 Number of atoms = 4073 Number of groups = 1351 Number of bonds = 4066 Number of angles = 1450 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1348 Number of HB donors = 2674 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1346 Number of atoms = 4073 Number of groups = 1351 Number of bonds = 4066 Number of angles = 1450 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1348 Number of HB donors = 2674 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.404" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1346" Evaluating: 1346-7 Parameter: NUMWAT <- "1339" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1339" Comparing "1081" and "1339". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.404" Parameter: BOX -> "34.404" Parameter: BOX -> "34.404" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.40400 B = 34.40400 C = 34.40400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.1476 2 1 -1 0 -1 6.2691 3 1 -1 1 -1 4.8708 4 1 0 -1 -1 2.8745 5 1 0 0 -1 1.8971 6 1 0 1 -1 3.3566 7 1 -1 -1 0 5.0458 8 1 -1 0 0 2.4794 9 1 -1 1 0 1.7674 10 1 0 -1 0 1.2906 11 1 0 1 0 1.2906 12 1 -1 -1 1 4.1478 13 1 -1 0 1 4.0888 14 1 -1 1 1 4.7995 15 1 0 -1 1 3.3566 16 1 0 0 1 1.8971 17 1 0 1 1 2.8745 18 1 1 1 1 5.1476 19 1 1 0 1 6.2691 20 1 1 -1 1 4.8708 21 1 1 1 0 5.0458 22 1 1 0 0 2.4794 23 1 1 -1 0 1.7674 24 1 1 1 -1 4.1478 25 1 1 0 -1 4.0888 26 1 1 -1 -1 4.7995 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3999 atoms have been selected out of 4073 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 384 128 128 0.00 2 C002 has 699 233 233 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1668 556 556 0.00 6 C006 has 513 171 171 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 123 41 41 0.00 13 C013 has 495 165 165 0.00 14 C014 has 99 33 33 0.00 Total of13633 atoms and 4536 groups and 4531 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4073 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1346 Number of atoms = 4073 Number of groups = 1351 Number of bonds = 4066 Number of angles = 1450 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1348 Number of HB donors = 2674 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1346 Number of atoms = 4073 Number of groups = 1351 Number of bonds = 4066 Number of angles = 1450 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1348 Number of HB donors = 2674 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.402" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1346" Evaluating: 1346-7 Parameter: NUMWAT <- "1339" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1339" Comparing "1081" and "1339". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.402" Parameter: BOX -> "34.402" Parameter: BOX -> "34.402" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.40200 B = 34.40200 C = 34.40200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.1500 2 1 -1 0 -1 6.2667 3 1 -1 1 -1 4.8674 4 1 0 -1 -1 2.8727 5 1 0 0 -1 1.8952 6 1 0 1 -1 3.3538 7 1 -1 -1 0 5.0439 8 1 -1 0 0 2.4789 9 1 -1 1 0 1.7657 10 1 0 -1 0 1.2898 11 1 0 1 0 1.2898 12 1 -1 -1 1 4.1444 13 1 -1 0 1 4.0860 14 1 -1 1 1 4.7965 15 1 0 -1 1 3.3538 16 1 0 0 1 1.8952 17 1 0 1 1 2.8727 18 1 1 1 1 5.1500 19 1 1 0 1 6.2667 20 1 1 -1 1 4.8674 21 1 1 1 0 5.0439 22 1 1 0 0 2.4789 23 1 1 -1 0 1.7657 24 1 1 1 -1 4.1444 25 1 1 0 -1 4.0860 26 1 1 -1 -1 4.7965 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3999 atoms have been selected out of 4073 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 384 128 128 0.00 2 C002 has 699 233 233 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1668 556 556 0.00 6 C006 has 513 171 171 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 123 41 41 0.00 13 C013 has 495 165 165 0.00 14 C014 has 99 33 33 0.00 Total of13633 atoms and 4536 groups and 4531 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4073 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1346 Number of atoms = 4073 Number of groups = 1351 Number of bonds = 4066 Number of angles = 1450 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1348 Number of HB donors = 2674 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1346 Number of atoms = 4073 Number of groups = 1351 Number of bonds = 4066 Number of angles = 1450 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1348 Number of HB donors = 2674 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.4" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1346" Evaluating: 1346-7 Parameter: NUMWAT <- "1339" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1339" Comparing "1081" and "1339". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.4" Parameter: BOX -> "34.4" Parameter: BOX -> "34.4" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.40000 B = 34.40000 C = 34.40000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.1523 2 1 -1 0 -1 6.2644 3 1 -1 1 -1 4.8639 4 1 0 -1 -1 2.8710 5 1 0 0 -1 1.8933 6 1 0 1 -1 3.3511 7 1 -1 -1 0 5.0420 8 1 -1 0 0 2.4783 9 1 -1 1 0 1.7641 10 1 0 -1 0 1.2890 11 1 0 1 0 1.2890 12 1 -1 -1 1 4.1409 13 1 -1 0 1 4.0832 14 1 -1 1 1 4.7935 15 1 0 -1 1 3.3511 16 1 0 0 1 1.8933 17 1 0 1 1 2.8710 18 1 1 1 1 5.1523 19 1 1 0 1 6.2644 20 1 1 -1 1 4.8639 21 1 1 1 0 5.0420 22 1 1 0 0 2.4783 23 1 1 -1 0 1.7641 24 1 1 1 -1 4.1409 25 1 1 0 -1 4.0832 26 1 1 -1 -1 4.7935 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3999 atoms have been selected out of 4073 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 384 128 128 0.00 2 C002 has 699 233 233 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1668 556 556 0.00 6 C006 has 513 171 171 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 123 41 41 0.00 13 C013 has 495 165 165 0.00 14 C014 has 99 33 33 0.00 Total of13633 atoms and 4536 groups and 4531 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4073 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1346 Number of atoms = 4073 Number of groups = 1351 Number of bonds = 4066 Number of angles = 1450 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1348 Number of HB donors = 2674 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1346 Number of atoms = 4073 Number of groups = 1351 Number of bonds = 4066 Number of angles = 1450 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1348 Number of HB donors = 2674 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.398" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1346" Evaluating: 1346-7 Parameter: NUMWAT <- "1339" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1339" Comparing "1081" and "1339". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.398" Parameter: BOX -> "34.398" Parameter: BOX -> "34.398" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.39800 B = 34.39800 C = 34.39800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.1547 2 1 -1 0 -1 6.2621 3 1 -1 1 -1 4.8605 4 1 0 -1 -1 2.8693 5 1 0 0 -1 1.8913 6 1 0 1 -1 3.3483 7 1 -1 -1 0 5.0402 8 1 -1 0 0 2.4778 9 1 -1 1 0 1.7624 10 1 0 -1 0 1.2883 11 1 0 1 0 1.2883 12 1 -1 -1 1 4.1375 13 1 -1 0 1 4.0805 14 1 -1 1 1 4.7905 15 1 0 -1 1 3.3483 16 1 0 0 1 1.8913 17 1 0 1 1 2.8693 18 1 1 1 1 5.1547 19 1 1 0 1 6.2621 20 1 1 -1 1 4.8605 21 1 1 1 0 5.0402 22 1 1 0 0 2.4778 23 1 1 -1 0 1.7624 24 1 1 1 -1 4.1375 25 1 1 0 -1 4.0805 26 1 1 -1 -1 4.7905 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3999 atoms have been selected out of 4073 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 384 128 128 0.00 2 C002 has 699 233 233 0.00 3 C003 has 84 28 28 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1668 556 556 0.00 6 C006 has 513 171 171 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 123 41 41 0.00 13 C013 has 498 166 166 0.00 14 C014 has 99 33 33 0.00 Total of13639 atoms and 4538 groups and 4533 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4073 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1346 Number of atoms = 4073 Number of groups = 1351 Number of bonds = 4066 Number of angles = 1450 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1348 Number of HB donors = 2674 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1346 Number of atoms = 4073 Number of groups = 1351 Number of bonds = 4066 Number of angles = 1450 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1348 Number of HB donors = 2674 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.396" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1346" Evaluating: 1346-7 Parameter: NUMWAT <- "1339" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1339" Comparing "1081" and "1339". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.396" Parameter: BOX -> "34.396" Parameter: BOX -> "34.396" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.39600 B = 34.39600 C = 34.39600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.1571 2 1 -1 0 -1 6.2598 3 1 -1 1 -1 4.8570 4 1 0 -1 -1 2.8676 5 1 0 0 -1 1.8894 6 1 0 1 -1 3.3456 7 1 -1 -1 0 5.0383 8 1 -1 0 0 2.4772 9 1 -1 1 0 1.7607 10 1 0 -1 0 1.2875 11 1 0 1 0 1.2875 12 1 -1 -1 1 4.1340 13 1 -1 0 1 4.0777 14 1 -1 1 1 4.7875 15 1 0 -1 1 3.3456 16 1 0 0 1 1.8894 17 1 0 1 1 2.8676 18 1 1 1 1 5.1571 19 1 1 0 1 6.2598 20 1 1 -1 1 4.8570 21 1 1 1 0 5.0383 22 1 1 0 0 2.4772 23 1 1 -1 0 1.7607 24 1 1 1 -1 4.1340 25 1 1 0 -1 4.0777 26 1 1 -1 -1 4.7875 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3999 atoms have been selected out of 4073 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 384 128 128 0.00 2 C002 has 699 233 233 0.00 3 C003 has 84 28 28 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1668 556 556 0.00 6 C006 has 513 171 171 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1755 585 585 0.00 12 C012 has 123 41 41 0.00 13 C013 has 498 166 166 0.00 14 C014 has 99 33 33 0.00 Total of13645 atoms and 4540 groups and 4535 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4073 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1346 Number of atoms = 4073 Number of groups = 1351 Number of bonds = 4066 Number of angles = 1450 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1348 Number of HB donors = 2674 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1346 Number of atoms = 4073 Number of groups = 1351 Number of bonds = 4066 Number of angles = 1450 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1348 Number of HB donors = 2674 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.394" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1346" Evaluating: 1346-7 Parameter: NUMWAT <- "1339" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1339" Comparing "1081" and "1339". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.394" Parameter: BOX -> "34.394" Parameter: BOX -> "34.394" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.39400 B = 34.39400 C = 34.39400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.1594 2 1 -1 0 -1 6.2575 3 1 -1 1 -1 4.8536 4 1 0 -1 -1 2.8659 5 1 0 0 -1 1.8875 6 1 0 1 -1 3.3428 7 1 -1 -1 0 5.0364 8 1 -1 0 0 2.4766 9 1 -1 1 0 1.7590 10 1 0 -1 0 1.2867 11 1 0 1 0 1.2867 12 1 -1 -1 1 4.1306 13 1 -1 0 1 4.0749 14 1 -1 1 1 4.7845 15 1 0 -1 1 3.3428 16 1 0 0 1 1.8875 17 1 0 1 1 2.8659 18 1 1 1 1 5.1594 19 1 1 0 1 6.2575 20 1 1 -1 1 4.8536 21 1 1 1 0 5.0364 22 1 1 0 0 2.4766 23 1 1 -1 0 1.7590 24 1 1 1 -1 4.1306 25 1 1 0 -1 4.0749 26 1 1 -1 -1 4.7845 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3999 atoms have been selected out of 4073 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 633 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1306 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 699 233 233 0.00 3 C003 has 87 29 29 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1668 556 556 0.00 6 C006 has 513 171 171 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1844 613 613 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1749 583 583 0.00 12 C012 has 120 40 40 0.00 13 C013 has 498 166 166 0.00 14 C014 has 102 34 34 0.00 Total of13636 atoms and 4537 groups and 4532 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 4073 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1344 Number of atoms = 4067 Number of groups = 1349 Number of bonds = 4060 Number of angles = 1448 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1346 Number of HB donors = 2670 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1344 Number of atoms = 4067 Number of groups = 1349 Number of bonds = 4060 Number of angles = 1448 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1346 Number of HB donors = 2670 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.392" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1344" Evaluating: 1344-7 Parameter: NUMWAT <- "1337" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1337" Comparing "1081" and "1337". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.392" Parameter: BOX -> "34.392" Parameter: BOX -> "34.392" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.39200 B = 34.39200 C = 34.39200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5869 2 1 -1 0 -1 4.0616 3 1 -1 1 -1 4.8502 4 1 0 -1 -1 3.9736 5 1 0 0 -1 1.8856 6 1 0 1 -1 3.3400 7 1 -1 -1 0 3.3583 8 1 -1 0 0 2.4761 9 1 -1 1 0 1.7573 10 1 0 -1 0 1.2860 11 1 0 1 0 1.2860 12 1 -1 -1 1 4.1271 13 1 -1 0 1 4.0721 14 1 -1 1 1 4.7815 15 1 0 -1 1 3.3400 16 1 0 0 1 1.8856 17 1 0 1 1 3.9736 18 1 1 1 1 6.5869 19 1 1 0 1 4.0616 20 1 1 -1 1 4.8502 21 1 1 1 0 3.3583 22 1 1 0 0 2.4761 23 1 1 -1 0 1.7573 24 1 1 1 -1 4.1271 25 1 1 0 -1 4.0721 26 1 1 -1 -1 4.7815 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3993 atoms have been selected out of 4067 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 696 232 232 0.00 3 C003 has 84 28 28 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1665 555 555 0.00 6 C006 has 510 170 170 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1838 611 611 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1749 583 583 0.00 12 C012 has 120 40 40 0.00 13 C013 has 495 165 165 0.00 14 C014 has 99 33 33 0.00 Total of13600 atoms and 4525 groups and 4520 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4067 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1344 Number of atoms = 4067 Number of groups = 1349 Number of bonds = 4060 Number of angles = 1448 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1346 Number of HB donors = 2670 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1344 Number of atoms = 4067 Number of groups = 1349 Number of bonds = 4060 Number of angles = 1448 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1346 Number of HB donors = 2670 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.39" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1344" Evaluating: 1344-7 Parameter: NUMWAT <- "1337" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1337" Comparing "1081" and "1337". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.39" Parameter: BOX -> "34.39" Parameter: BOX -> "34.39" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.39000 B = 34.39000 C = 34.39000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5885 2 1 -1 0 -1 4.0588 3 1 -1 1 -1 4.8467 4 1 0 -1 -1 3.9743 5 1 0 0 -1 1.8837 6 1 0 1 -1 3.3373 7 1 -1 -1 0 3.3556 8 1 -1 0 0 2.4755 9 1 -1 1 0 1.7556 10 1 0 -1 0 1.2852 11 1 0 1 0 1.2852 12 1 -1 -1 1 4.1237 13 1 -1 0 1 4.0693 14 1 -1 1 1 4.7786 15 1 0 -1 1 3.3373 16 1 0 0 1 1.8837 17 1 0 1 1 3.9743 18 1 1 1 1 6.5885 19 1 1 0 1 4.0588 20 1 1 -1 1 4.8467 21 1 1 1 0 3.3556 22 1 1 0 0 2.4755 23 1 1 -1 0 1.7556 24 1 1 1 -1 4.1237 25 1 1 0 -1 4.0693 26 1 1 -1 -1 4.7786 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3993 atoms have been selected out of 4067 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 696 232 232 0.00 3 C003 has 84 28 28 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1668 556 556 0.00 6 C006 has 510 170 170 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1838 611 611 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1749 583 583 0.00 12 C012 has 120 40 40 0.00 13 C013 has 495 165 165 0.00 14 C014 has 99 33 33 0.00 Total of13603 atoms and 4526 groups and 4521 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4067 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1344 Number of atoms = 4067 Number of groups = 1349 Number of bonds = 4060 Number of angles = 1448 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1346 Number of HB donors = 2670 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1344 Number of atoms = 4067 Number of groups = 1349 Number of bonds = 4060 Number of angles = 1448 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1346 Number of HB donors = 2670 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.388" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1344" Evaluating: 1344-7 Parameter: NUMWAT <- "1337" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1337" Comparing "1081" and "1337". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.388" Parameter: BOX -> "34.388" Parameter: BOX -> "34.388" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.38800 B = 34.38800 C = 34.38800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5901 2 1 -1 0 -1 4.0560 3 1 -1 1 -1 4.8433 4 1 0 -1 -1 3.9751 5 1 0 0 -1 1.8817 6 1 0 1 -1 3.3345 7 1 -1 -1 0 3.3528 8 1 -1 0 0 2.4750 9 1 -1 1 0 1.7540 10 1 0 -1 0 1.2845 11 1 0 1 0 1.2845 12 1 -1 -1 1 4.1202 13 1 -1 0 1 4.0666 14 1 -1 1 1 4.7756 15 1 0 -1 1 3.3345 16 1 0 0 1 1.8817 17 1 0 1 1 3.9751 18 1 1 1 1 6.5901 19 1 1 0 1 4.0560 20 1 1 -1 1 4.8433 21 1 1 1 0 3.3528 22 1 1 0 0 2.4750 23 1 1 -1 0 1.7540 24 1 1 1 -1 4.1202 25 1 1 0 -1 4.0666 26 1 1 -1 -1 4.7756 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3993 atoms have been selected out of 4067 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 954 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1668 556 556 0.00 6 C006 has 507 169 169 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1841 612 612 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1749 583 583 0.00 12 C012 has 120 40 40 0.00 13 C013 has 495 165 165 0.00 14 C014 has 99 33 33 0.00 Total of13600 atoms and 4525 groups and 4520 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4067 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1343 Number of atoms = 4064 Number of groups = 1348 Number of bonds = 4057 Number of angles = 1447 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1345 Number of HB donors = 2668 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1343 Number of atoms = 4064 Number of groups = 1348 Number of bonds = 4057 Number of angles = 1447 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1345 Number of HB donors = 2668 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.386" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1343" Evaluating: 1343-7 Parameter: NUMWAT <- "1336" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1336" Comparing "1081" and "1336". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.386" Parameter: BOX -> "34.386" Parameter: BOX -> "34.386" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.38600 B = 34.38600 C = 34.38600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5917 2 1 -1 0 -1 4.0533 3 1 -1 1 -1 4.8398 4 1 0 -1 -1 3.9758 5 1 0 0 -1 1.8798 6 1 0 1 -1 3.3318 7 1 -1 -1 0 3.3501 8 1 -1 0 0 2.4744 9 1 -1 1 0 1.7523 10 1 0 -1 0 1.2837 11 1 0 1 0 1.2837 12 1 -1 -1 1 4.1168 13 1 -1 0 1 4.0638 14 1 -1 1 1 4.7726 15 1 0 -1 1 3.3318 16 1 0 0 1 1.8798 17 1 0 1 1 3.9758 18 1 1 1 1 6.5917 19 1 1 0 1 4.0533 20 1 1 -1 1 4.8398 21 1 1 1 0 3.3501 22 1 1 0 0 2.4744 23 1 1 -1 0 1.7523 24 1 1 1 -1 4.1168 25 1 1 0 -1 4.0638 26 1 1 -1 -1 4.7726 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3990 atoms have been selected out of 4064 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 555 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1665 555 555 0.00 6 C006 has 507 169 169 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1838 611 611 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1752 584 584 0.00 12 C012 has 120 40 40 0.00 13 C013 has 495 165 165 0.00 14 C014 has 102 34 34 0.00 Total of13597 atoms and 4524 groups and 4519 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4064 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1342 Number of atoms = 4061 Number of groups = 1347 Number of bonds = 4054 Number of angles = 1446 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1344 Number of HB donors = 2666 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1342 Number of atoms = 4061 Number of groups = 1347 Number of bonds = 4054 Number of angles = 1446 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1344 Number of HB donors = 2666 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.384" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1342" Evaluating: 1342-7 Parameter: NUMWAT <- "1335" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1335" Comparing "1081" and "1335". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.384" Parameter: BOX -> "34.384" Parameter: BOX -> "34.384" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.38400 B = 34.38400 C = 34.38400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5934 2 1 -1 0 -1 4.0505 3 1 -1 1 -1 4.8364 4 1 0 -1 -1 3.9766 5 1 0 0 -1 1.8779 6 1 0 1 -1 3.3290 7 1 -1 -1 0 3.3473 8 1 -1 0 0 2.4739 9 1 -1 1 0 1.7506 10 1 0 -1 0 1.2830 11 1 0 1 0 1.2830 12 1 -1 -1 1 4.1133 13 1 -1 0 1 4.0610 14 1 -1 1 1 4.7696 15 1 0 -1 1 3.3290 16 1 0 0 1 1.8779 17 1 0 1 1 3.9766 18 1 1 1 1 6.5934 19 1 1 0 1 4.0505 20 1 1 -1 1 4.8364 21 1 1 1 0 3.3473 22 1 1 0 0 2.4739 23 1 1 -1 0 1.7506 24 1 1 1 -1 4.1133 25 1 1 0 -1 4.0610 26 1 1 -1 -1 4.7696 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3987 atoms have been selected out of 4061 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1665 555 555 0.00 6 C006 has 507 169 169 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1835 610 610 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1746 582 582 0.00 12 C012 has 120 40 40 0.00 13 C013 has 492 164 164 0.00 14 C014 has 99 33 33 0.00 Total of13576 atoms and 4517 groups and 4512 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4061 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1342 Number of atoms = 4061 Number of groups = 1347 Number of bonds = 4054 Number of angles = 1446 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1344 Number of HB donors = 2666 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1342 Number of atoms = 4061 Number of groups = 1347 Number of bonds = 4054 Number of angles = 1446 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1344 Number of HB donors = 2666 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.382" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1342" Evaluating: 1342-7 Parameter: NUMWAT <- "1335" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1335" Comparing "1081" and "1335". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.382" Parameter: BOX -> "34.382" Parameter: BOX -> "34.382" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.38200 B = 34.38200 C = 34.38200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5950 2 1 -1 0 -1 4.0477 3 1 -1 1 -1 4.8330 4 1 0 -1 -1 3.9773 5 1 0 0 -1 1.8760 6 1 0 1 -1 3.3263 7 1 -1 -1 0 3.3446 8 1 -1 0 0 2.4733 9 1 -1 1 0 1.7490 10 1 0 -1 0 1.2822 11 1 0 1 0 1.2822 12 1 -1 -1 1 4.1099 13 1 -1 0 1 4.0582 14 1 -1 1 1 4.7666 15 1 0 -1 1 3.3263 16 1 0 0 1 1.8760 17 1 0 1 1 3.9773 18 1 1 1 1 6.5950 19 1 1 0 1 4.0477 20 1 1 -1 1 4.8330 21 1 1 1 0 3.3446 22 1 1 0 0 2.4733 23 1 1 -1 0 1.7490 24 1 1 1 -1 4.1099 25 1 1 0 -1 4.0582 26 1 1 -1 -1 4.7666 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3987 atoms have been selected out of 4061 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1665 555 555 0.00 6 C006 has 507 169 169 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1835 610 610 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1746 582 582 0.00 12 C012 has 120 40 40 0.00 13 C013 has 492 164 164 0.00 14 C014 has 99 33 33 0.00 Total of13576 atoms and 4517 groups and 4512 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4061 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1342 Number of atoms = 4061 Number of groups = 1347 Number of bonds = 4054 Number of angles = 1446 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1344 Number of HB donors = 2666 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1342 Number of atoms = 4061 Number of groups = 1347 Number of bonds = 4054 Number of angles = 1446 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1344 Number of HB donors = 2666 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.38" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1342" Evaluating: 1342-7 Parameter: NUMWAT <- "1335" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1335" Comparing "1081" and "1335". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.38" Parameter: BOX -> "34.38" Parameter: BOX -> "34.38" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.38000 B = 34.38000 C = 34.38000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5966 2 1 -1 0 -1 4.0449 3 1 -1 1 -1 4.8295 4 1 0 -1 -1 3.9781 5 1 0 0 -1 1.8741 6 1 0 1 -1 3.3235 7 1 -1 -1 0 3.3418 8 1 -1 0 0 2.4728 9 1 -1 1 0 1.7473 10 1 0 -1 0 1.2815 11 1 0 1 0 1.2815 12 1 -1 -1 1 4.1064 13 1 -1 0 1 4.0555 14 1 -1 1 1 4.7636 15 1 0 -1 1 3.3235 16 1 0 0 1 1.8741 17 1 0 1 1 3.9781 18 1 1 1 1 6.5966 19 1 1 0 1 4.0449 20 1 1 -1 1 4.8295 21 1 1 1 0 3.3418 22 1 1 0 0 2.4728 23 1 1 -1 0 1.7473 24 1 1 1 -1 4.1064 25 1 1 0 -1 4.0555 26 1 1 -1 -1 4.7636 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3987 atoms have been selected out of 4061 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 440 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1665 555 555 0.00 6 C006 has 507 169 169 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1835 610 610 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1746 582 582 0.00 12 C012 has 120 40 40 0.00 13 C013 has 492 164 164 0.00 14 C014 has 99 33 33 0.00 Total of13582 atoms and 4519 groups and 4514 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4061 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1341 Number of atoms = 4058 Number of groups = 1346 Number of bonds = 4051 Number of angles = 1445 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1343 Number of HB donors = 2664 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1341 Number of atoms = 4058 Number of groups = 1346 Number of bonds = 4051 Number of angles = 1445 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1343 Number of HB donors = 2664 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.378" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1341" Evaluating: 1341-7 Parameter: NUMWAT <- "1334" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1334" Comparing "1081" and "1334". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.378" Parameter: BOX -> "34.378" Parameter: BOX -> "34.378" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.37800 B = 34.37800 C = 34.37800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5982 2 1 -1 0 -1 4.0421 3 1 -1 1 -1 4.8261 4 1 0 -1 -1 3.9788 5 1 0 0 -1 1.8721 6 1 0 1 -1 3.3208 7 1 -1 -1 0 3.3391 8 1 -1 0 0 2.4722 9 1 -1 1 0 1.7457 10 1 0 -1 0 1.2807 11 1 0 1 0 1.2807 12 1 -1 -1 1 4.1030 13 1 -1 0 1 4.0527 14 1 -1 1 1 4.7606 15 1 0 -1 1 3.3208 16 1 0 0 1 1.8721 17 1 0 1 1 3.9788 18 1 1 1 1 6.5982 19 1 1 0 1 4.0421 20 1 1 -1 1 4.8261 21 1 1 1 0 3.3391 22 1 1 0 0 2.4722 23 1 1 -1 0 1.7457 24 1 1 1 -1 4.1030 25 1 1 0 -1 4.0527 26 1 1 -1 -1 4.7606 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3984 atoms have been selected out of 4058 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1665 555 555 0.00 6 C006 has 507 169 169 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1743 581 581 0.00 12 C012 has 120 40 40 0.00 13 C013 has 492 164 164 0.00 14 C014 has 99 33 33 0.00 Total of13570 atoms and 4515 groups and 4510 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4058 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1341 Number of atoms = 4058 Number of groups = 1346 Number of bonds = 4051 Number of angles = 1445 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1343 Number of HB donors = 2664 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1341 Number of atoms = 4058 Number of groups = 1346 Number of bonds = 4051 Number of angles = 1445 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1343 Number of HB donors = 2664 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.376" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1341" Evaluating: 1341-7 Parameter: NUMWAT <- "1334" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1334" Comparing "1081" and "1334". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.376" Parameter: BOX -> "34.376" Parameter: BOX -> "34.376" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.37600 B = 34.37600 C = 34.37600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5998 2 1 -1 0 -1 4.0394 3 1 -1 1 -1 4.8226 4 1 0 -1 -1 3.9796 5 1 0 0 -1 1.8702 6 1 0 1 -1 3.3180 7 1 -1 -1 0 3.3363 8 1 -1 0 0 2.4717 9 1 -1 1 0 1.7440 10 1 0 -1 0 1.2800 11 1 0 1 0 1.2800 12 1 -1 -1 1 4.0995 13 1 -1 0 1 4.0499 14 1 -1 1 1 4.7577 15 1 0 -1 1 3.3180 16 1 0 0 1 1.8702 17 1 0 1 1 3.9796 18 1 1 1 1 6.5998 19 1 1 0 1 4.0394 20 1 1 -1 1 4.8226 21 1 1 1 0 3.3363 22 1 1 0 0 2.4717 23 1 1 -1 0 1.7440 24 1 1 1 -1 4.0995 25 1 1 0 -1 4.0499 26 1 1 -1 -1 4.7577 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3984 atoms have been selected out of 4058 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1665 555 555 0.00 6 C006 has 507 169 169 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1743 581 581 0.00 12 C012 has 123 41 41 0.00 13 C013 has 492 164 164 0.00 14 C014 has 99 33 33 0.00 Total of13573 atoms and 4516 groups and 4511 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4058 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1341 Number of atoms = 4058 Number of groups = 1346 Number of bonds = 4051 Number of angles = 1445 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1343 Number of HB donors = 2664 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1341 Number of atoms = 4058 Number of groups = 1346 Number of bonds = 4051 Number of angles = 1445 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1343 Number of HB donors = 2664 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.374" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1341" Evaluating: 1341-7 Parameter: NUMWAT <- "1334" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1334" Comparing "1081" and "1334". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.374" Parameter: BOX -> "34.374" Parameter: BOX -> "34.374" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.37400 B = 34.37400 C = 34.37400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6015 2 1 -1 0 -1 4.0366 3 1 -1 1 -1 4.8192 4 1 0 -1 -1 3.9803 5 1 0 0 -1 1.8683 6 1 0 1 -1 3.3153 7 1 -1 -1 0 3.3336 8 1 -1 0 0 2.4712 9 1 -1 1 0 1.7423 10 1 0 -1 0 1.2792 11 1 0 1 0 1.2792 12 1 -1 -1 1 4.0961 13 1 -1 0 1 4.0471 14 1 -1 1 1 4.7547 15 1 0 -1 1 3.3153 16 1 0 0 1 1.8683 17 1 0 1 1 3.9803 18 1 1 1 1 6.6015 19 1 1 0 1 4.0366 20 1 1 -1 1 4.8192 21 1 1 1 0 3.3336 22 1 1 0 0 2.4712 23 1 1 -1 0 1.7423 24 1 1 1 -1 4.0961 25 1 1 0 -1 4.0471 26 1 1 -1 -1 4.7547 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3984 atoms have been selected out of 4058 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1665 555 555 0.00 6 C006 has 507 169 169 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1743 581 581 0.00 12 C012 has 123 41 41 0.00 13 C013 has 492 164 164 0.00 14 C014 has 99 33 33 0.00 Total of13576 atoms and 4517 groups and 4512 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4058 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1341 Number of atoms = 4058 Number of groups = 1346 Number of bonds = 4051 Number of angles = 1445 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1343 Number of HB donors = 2664 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1341 Number of atoms = 4058 Number of groups = 1346 Number of bonds = 4051 Number of angles = 1445 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1343 Number of HB donors = 2664 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.372" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1341" Evaluating: 1341-7 Parameter: NUMWAT <- "1334" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1334" Comparing "1081" and "1334". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.372" Parameter: BOX -> "34.372" Parameter: BOX -> "34.372" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.37200 B = 34.37200 C = 34.37200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6031 2 1 -1 0 -1 4.0338 3 1 -1 1 -1 4.8158 4 1 0 -1 -1 3.9811 5 1 0 0 -1 1.8664 6 1 0 1 -1 3.3125 7 1 -1 -1 0 3.3308 8 1 -1 0 0 2.4706 9 1 -1 1 0 1.7407 10 1 0 -1 0 1.2785 11 1 0 1 0 1.2785 12 1 -1 -1 1 4.0926 13 1 -1 0 1 4.0444 14 1 -1 1 1 4.7517 15 1 0 -1 1 3.3125 16 1 0 0 1 1.8664 17 1 0 1 1 3.9811 18 1 1 1 1 6.6031 19 1 1 0 1 4.0338 20 1 1 -1 1 4.8158 21 1 1 1 0 3.3308 22 1 1 0 0 2.4706 23 1 1 -1 0 1.7407 24 1 1 1 -1 4.0926 25 1 1 0 -1 4.0444 26 1 1 -1 -1 4.7517 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3984 atoms have been selected out of 4058 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 696 232 232 0.00 3 C003 has 84 28 28 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1665 555 555 0.00 6 C006 has 507 169 169 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1743 581 581 0.00 12 C012 has 123 41 41 0.00 13 C013 has 492 164 164 0.00 14 C014 has 99 33 33 0.00 Total of13579 atoms and 4518 groups and 4513 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4058 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1341 Number of atoms = 4058 Number of groups = 1346 Number of bonds = 4051 Number of angles = 1445 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1343 Number of HB donors = 2664 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1341 Number of atoms = 4058 Number of groups = 1346 Number of bonds = 4051 Number of angles = 1445 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1343 Number of HB donors = 2664 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.37" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1341" Evaluating: 1341-7 Parameter: NUMWAT <- "1334" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1334" Comparing "1081" and "1334". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.37" Parameter: BOX -> "34.37" Parameter: BOX -> "34.37" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.37000 B = 34.37000 C = 34.37000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6047 2 1 -1 0 -1 4.0310 3 1 -1 1 -1 4.8123 4 1 0 -1 -1 3.9818 5 1 0 0 -1 1.8645 6 1 0 1 -1 3.3098 7 1 -1 -1 0 3.3281 8 1 -1 0 0 2.4701 9 1 -1 1 0 1.7390 10 1 0 -1 0 1.2778 11 1 0 1 0 1.2778 12 1 -1 -1 1 4.0892 13 1 -1 0 1 4.0416 14 1 -1 1 1 4.7487 15 1 0 -1 1 3.3098 16 1 0 0 1 1.8645 17 1 0 1 1 3.9818 18 1 1 1 1 6.6047 19 1 1 0 1 4.0310 20 1 1 -1 1 4.8123 21 1 1 1 0 3.3281 22 1 1 0 0 2.4701 23 1 1 -1 0 1.7390 24 1 1 1 -1 4.0892 25 1 1 0 -1 4.0416 26 1 1 -1 -1 4.7487 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3984 atoms have been selected out of 4058 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 696 232 232 0.00 3 C003 has 84 28 28 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1665 555 555 0.00 6 C006 has 507 169 169 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1743 581 581 0.00 12 C012 has 123 41 41 0.00 13 C013 has 492 164 164 0.00 14 C014 has 99 33 33 0.00 Total of13579 atoms and 4518 groups and 4513 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4058 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1341 Number of atoms = 4058 Number of groups = 1346 Number of bonds = 4051 Number of angles = 1445 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1343 Number of HB donors = 2664 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1341 Number of atoms = 4058 Number of groups = 1346 Number of bonds = 4051 Number of angles = 1445 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1343 Number of HB donors = 2664 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.368" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1341" Evaluating: 1341-7 Parameter: NUMWAT <- "1334" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1334" Comparing "1081" and "1334". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.368" Parameter: BOX -> "34.368" Parameter: BOX -> "34.368" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.36800 B = 34.36800 C = 34.36800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6064 2 1 -1 0 -1 4.0283 3 1 -1 1 -1 4.8089 4 1 0 -1 -1 3.9826 5 1 0 0 -1 1.8626 6 1 0 1 -1 3.3070 7 1 -1 -1 0 3.3253 8 1 -1 0 0 2.4695 9 1 -1 1 0 1.7374 10 1 0 -1 0 1.2770 11 1 0 1 0 1.2770 12 1 -1 -1 1 4.0857 13 1 -1 0 1 4.0388 14 1 -1 1 1 4.7457 15 1 0 -1 1 3.3070 16 1 0 0 1 1.8626 17 1 0 1 1 3.9826 18 1 1 1 1 6.6064 19 1 1 0 1 4.0283 20 1 1 -1 1 4.8089 21 1 1 1 0 3.3253 22 1 1 0 0 2.4695 23 1 1 -1 0 1.7374 24 1 1 1 -1 4.0857 25 1 1 0 -1 4.0388 26 1 1 -1 -1 4.7457 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3984 atoms have been selected out of 4058 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 533 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1207 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 699 233 233 0.00 3 C003 has 84 28 28 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1665 555 555 0.00 6 C006 has 507 169 169 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1832 609 609 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1743 581 581 0.00 12 C012 has 120 40 40 0.00 13 C013 has 492 164 164 0.00 14 C014 has 99 33 33 0.00 Total of13573 atoms and 4516 groups and 4511 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 4058 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1339 Number of atoms = 4052 Number of groups = 1344 Number of bonds = 4045 Number of angles = 1443 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1341 Number of HB donors = 2660 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1339 Number of atoms = 4052 Number of groups = 1344 Number of bonds = 4045 Number of angles = 1443 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1341 Number of HB donors = 2660 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.366" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1339" Evaluating: 1339-7 Parameter: NUMWAT <- "1332" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1332" Comparing "1081" and "1332". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.366" Parameter: BOX -> "34.366" Parameter: BOX -> "34.366" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.36600 B = 34.36600 C = 34.36600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6080 2 1 -1 0 -1 4.0255 3 1 -1 1 -1 4.8054 4 1 0 -1 -1 3.9833 5 1 0 0 -1 1.8606 6 1 0 1 -1 3.3043 7 1 -1 -1 0 3.3226 8 1 -1 0 0 2.4690 9 1 -1 1 0 1.7358 10 1 0 -1 0 1.2763 11 1 0 1 0 1.2763 12 1 -1 -1 1 4.0822 13 1 -1 0 1 4.0360 14 1 -1 1 1 4.7428 15 1 0 -1 1 3.3043 16 1 0 0 1 1.8606 17 1 0 1 1 3.9833 18 1 1 1 1 6.6080 19 1 1 0 1 4.0255 20 1 1 -1 1 4.8054 21 1 1 1 0 3.3226 22 1 1 0 0 2.4690 23 1 1 -1 0 1.7358 24 1 1 1 -1 4.0822 25 1 1 0 -1 4.0360 26 1 1 -1 -1 4.7428 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3978 atoms have been selected out of 4052 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1662 554 554 0.00 6 C006 has 507 169 169 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1826 607 607 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1737 579 579 0.00 12 C012 has 120 40 40 0.00 13 C013 has 489 163 163 0.00 14 C014 has 99 33 33 0.00 Total of13543 atoms and 4506 groups and 4501 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4052 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1339 Number of atoms = 4052 Number of groups = 1344 Number of bonds = 4045 Number of angles = 1443 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1341 Number of HB donors = 2660 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1339 Number of atoms = 4052 Number of groups = 1344 Number of bonds = 4045 Number of angles = 1443 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1341 Number of HB donors = 2660 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.364" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1339" Evaluating: 1339-7 Parameter: NUMWAT <- "1332" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1332" Comparing "1081" and "1332". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.364" Parameter: BOX -> "34.364" Parameter: BOX -> "34.364" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.36400 B = 34.36400 C = 34.36400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6096 2 1 -1 0 -1 4.0227 3 1 -1 1 -1 4.8020 4 1 0 -1 -1 3.9841 5 1 0 0 -1 1.8587 6 1 0 1 -1 3.3015 7 1 -1 -1 0 3.3199 8 1 -1 0 0 2.4685 9 1 -1 1 0 1.7341 10 1 0 -1 0 1.2756 11 1 0 1 0 1.2756 12 1 -1 -1 1 4.0788 13 1 -1 0 1 4.0333 14 1 -1 1 1 4.7398 15 1 0 -1 1 3.3015 16 1 0 0 1 1.8587 17 1 0 1 1 3.9841 18 1 1 1 1 6.6096 19 1 1 0 1 4.0227 20 1 1 -1 1 4.8020 21 1 1 1 0 3.3199 22 1 1 0 0 2.4685 23 1 1 -1 0 1.7341 24 1 1 1 -1 4.0788 25 1 1 0 -1 4.0333 26 1 1 -1 -1 4.7398 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3978 atoms have been selected out of 4052 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1662 554 554 0.00 6 C006 has 507 169 169 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1826 607 607 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1737 579 579 0.00 12 C012 has 120 40 40 0.00 13 C013 has 489 163 163 0.00 14 C014 has 99 33 33 0.00 Total of13543 atoms and 4506 groups and 4501 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4052 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1339 Number of atoms = 4052 Number of groups = 1344 Number of bonds = 4045 Number of angles = 1443 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1341 Number of HB donors = 2660 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1339 Number of atoms = 4052 Number of groups = 1344 Number of bonds = 4045 Number of angles = 1443 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1341 Number of HB donors = 2660 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.362" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1339" Evaluating: 1339-7 Parameter: NUMWAT <- "1332" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1332" Comparing "1081" and "1332". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.362" Parameter: BOX -> "34.362" Parameter: BOX -> "34.362" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.36200 B = 34.36200 C = 34.36200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6113 2 1 -1 0 -1 4.0199 3 1 -1 1 -1 4.7986 4 1 0 -1 -1 3.9849 5 1 0 0 -1 1.8568 6 1 0 1 -1 3.2987 7 1 -1 -1 0 3.3171 8 1 -1 0 0 2.4679 9 1 -1 1 0 1.7325 10 1 0 -1 0 1.2748 11 1 0 1 0 1.2748 12 1 -1 -1 1 4.0753 13 1 -1 0 1 4.0305 14 1 -1 1 1 4.7368 15 1 0 -1 1 3.2987 16 1 0 0 1 1.8568 17 1 0 1 1 3.9849 18 1 1 1 1 6.6113 19 1 1 0 1 4.0199 20 1 1 -1 1 4.7986 21 1 1 1 0 3.3171 22 1 1 0 0 2.4679 23 1 1 -1 0 1.7325 24 1 1 1 -1 4.0753 25 1 1 0 -1 4.0305 26 1 1 -1 -1 4.7368 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3978 atoms have been selected out of 4052 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1662 554 554 0.00 6 C006 has 507 169 169 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1826 607 607 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1737 579 579 0.00 12 C012 has 120 40 40 0.00 13 C013 has 489 163 163 0.00 14 C014 has 99 33 33 0.00 Total of13546 atoms and 4507 groups and 4502 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4052 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1339 Number of atoms = 4052 Number of groups = 1344 Number of bonds = 4045 Number of angles = 1443 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1341 Number of HB donors = 2660 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1339 Number of atoms = 4052 Number of groups = 1344 Number of bonds = 4045 Number of angles = 1443 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1341 Number of HB donors = 2660 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.36" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1339" Evaluating: 1339-7 Parameter: NUMWAT <- "1332" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1332" Comparing "1081" and "1332". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.36" Parameter: BOX -> "34.36" Parameter: BOX -> "34.36" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.36000 B = 34.36000 C = 34.36000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6129 2 1 -1 0 -1 4.0172 3 1 -1 1 -1 4.7951 4 1 0 -1 -1 3.9856 5 1 0 0 -1 1.8549 6 1 0 1 -1 3.2960 7 1 -1 -1 0 3.3144 8 1 -1 0 0 2.4674 9 1 -1 1 0 1.7309 10 1 0 -1 0 1.2741 11 1 0 1 0 1.2741 12 1 -1 -1 1 4.0719 13 1 -1 0 1 4.0277 14 1 -1 1 1 4.7338 15 1 0 -1 1 3.2960 16 1 0 0 1 1.8549 17 1 0 1 1 3.9856 18 1 1 1 1 6.6129 19 1 1 0 1 4.0172 20 1 1 -1 1 4.7951 21 1 1 1 0 3.3144 22 1 1 0 0 2.4674 23 1 1 -1 0 1.7309 24 1 1 1 -1 4.0719 25 1 1 0 -1 4.0277 26 1 1 -1 -1 4.7338 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3978 atoms have been selected out of 4052 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1662 554 554 0.00 6 C006 has 507 169 169 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1826 607 607 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1737 579 579 0.00 12 C012 has 120 40 40 0.00 13 C013 has 489 163 163 0.00 14 C014 has 99 33 33 0.00 Total of13549 atoms and 4508 groups and 4503 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4052 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1339 Number of atoms = 4052 Number of groups = 1344 Number of bonds = 4045 Number of angles = 1443 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1341 Number of HB donors = 2660 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1339 Number of atoms = 4052 Number of groups = 1344 Number of bonds = 4045 Number of angles = 1443 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1341 Number of HB donors = 2660 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.358" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1339" Evaluating: 1339-7 Parameter: NUMWAT <- "1332" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1332" Comparing "1081" and "1332". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.358" Parameter: BOX -> "34.358" Parameter: BOX -> "34.358" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.35800 B = 34.35800 C = 34.35800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6145 2 1 -1 0 -1 4.0144 3 1 -1 1 -1 4.7917 4 1 0 -1 -1 3.9864 5 1 0 0 -1 1.8530 6 1 0 1 -1 3.2932 7 1 -1 -1 0 3.3116 8 1 -1 0 0 2.4669 9 1 -1 1 0 1.7292 10 1 0 -1 0 1.2734 11 1 0 1 0 1.2734 12 1 -1 -1 1 4.0684 13 1 -1 0 1 4.0249 14 1 -1 1 1 4.7308 15 1 0 -1 1 3.2932 16 1 0 0 1 1.8530 17 1 0 1 1 3.9864 18 1 1 1 1 6.6145 19 1 1 0 1 4.0144 20 1 1 -1 1 4.7917 21 1 1 1 0 3.3116 22 1 1 0 0 2.4669 23 1 1 -1 0 1.7292 24 1 1 1 -1 4.0684 25 1 1 0 -1 4.0249 26 1 1 -1 -1 4.7308 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3978 atoms have been selected out of 4052 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 786 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1662 554 554 0.00 6 C006 has 504 168 168 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1826 607 607 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1737 579 579 0.00 12 C012 has 120 40 40 0.00 13 C013 has 489 163 163 0.00 14 C014 has 99 33 33 0.00 Total of13549 atoms and 4508 groups and 4503 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4052 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1338 Number of atoms = 4049 Number of groups = 1343 Number of bonds = 4042 Number of angles = 1442 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1340 Number of HB donors = 2658 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1338 Number of atoms = 4049 Number of groups = 1343 Number of bonds = 4042 Number of angles = 1442 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1340 Number of HB donors = 2658 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.356" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1338" Evaluating: 1338-7 Parameter: NUMWAT <- "1331" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1331" Comparing "1081" and "1331". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.356" Parameter: BOX -> "34.356" Parameter: BOX -> "34.356" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.35600 B = 34.35600 C = 34.35600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6162 2 1 -1 0 -1 4.0116 3 1 -1 1 -1 4.7882 4 1 0 -1 -1 3.9872 5 1 0 0 -1 1.8511 6 1 0 1 -1 3.2905 7 1 -1 -1 0 3.3089 8 1 -1 0 0 2.4664 9 1 -1 1 0 1.7276 10 1 0 -1 0 1.2727 11 1 0 1 0 1.2727 12 1 -1 -1 1 4.0650 13 1 -1 0 1 4.0221 14 1 -1 1 1 4.7279 15 1 0 -1 1 3.2905 16 1 0 0 1 1.8511 17 1 0 1 1 3.9872 18 1 1 1 1 6.6162 19 1 1 0 1 4.0116 20 1 1 -1 1 4.7882 21 1 1 1 0 3.3089 22 1 1 0 0 2.4664 23 1 1 -1 0 1.7276 24 1 1 1 -1 4.0650 25 1 1 0 -1 4.0221 26 1 1 -1 -1 4.7279 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3975 atoms have been selected out of 4049 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1659 553 553 0.00 6 C006 has 504 168 168 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1826 607 607 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1737 579 579 0.00 12 C012 has 120 40 40 0.00 13 C013 has 489 163 163 0.00 14 C014 has 99 33 33 0.00 Total of13540 atoms and 4505 groups and 4500 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4049 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1338 Number of atoms = 4049 Number of groups = 1343 Number of bonds = 4042 Number of angles = 1442 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1340 Number of HB donors = 2658 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1338 Number of atoms = 4049 Number of groups = 1343 Number of bonds = 4042 Number of angles = 1442 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1340 Number of HB donors = 2658 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.354" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1338" Evaluating: 1338-7 Parameter: NUMWAT <- "1331" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1331" Comparing "1081" and "1331". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.354" Parameter: BOX -> "34.354" Parameter: BOX -> "34.354" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.35400 B = 34.35400 C = 34.35400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6178 2 1 -1 0 -1 4.0088 3 1 -1 1 -1 4.7848 4 1 0 -1 -1 3.9879 5 1 0 0 -1 1.8492 6 1 0 1 -1 3.2877 7 1 -1 -1 0 3.3061 8 1 -1 0 0 2.4658 9 1 -1 1 0 1.7260 10 1 0 -1 0 1.2720 11 1 0 1 0 1.2720 12 1 -1 -1 1 4.0615 13 1 -1 0 1 4.0194 14 1 -1 1 1 4.7249 15 1 0 -1 1 3.2877 16 1 0 0 1 1.8492 17 1 0 1 1 3.9879 18 1 1 1 1 6.6178 19 1 1 0 1 4.0088 20 1 1 -1 1 4.7848 21 1 1 1 0 3.3061 22 1 1 0 0 2.4658 23 1 1 -1 0 1.7260 24 1 1 1 -1 4.0615 25 1 1 0 -1 4.0194 26 1 1 -1 -1 4.7249 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3975 atoms have been selected out of 4049 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1659 553 553 0.00 6 C006 has 504 168 168 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1826 607 607 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1737 579 579 0.00 12 C012 has 120 40 40 0.00 13 C013 has 489 163 163 0.00 14 C014 has 99 33 33 0.00 Total of13540 atoms and 4505 groups and 4500 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4049 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1338 Number of atoms = 4049 Number of groups = 1343 Number of bonds = 4042 Number of angles = 1442 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1340 Number of HB donors = 2658 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1338 Number of atoms = 4049 Number of groups = 1343 Number of bonds = 4042 Number of angles = 1442 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1340 Number of HB donors = 2658 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.352" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1338" Evaluating: 1338-7 Parameter: NUMWAT <- "1331" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1331" Comparing "1081" and "1331". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.352" Parameter: BOX -> "34.352" Parameter: BOX -> "34.352" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.35200 B = 34.35200 C = 34.35200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6195 2 1 -1 0 -1 4.0060 3 1 -1 1 -1 4.7814 4 1 0 -1 -1 3.9887 5 1 0 0 -1 1.8472 6 1 0 1 -1 3.2850 7 1 -1 -1 0 3.3034 8 1 -1 0 0 2.4653 9 1 -1 1 0 1.7244 10 1 0 -1 0 1.2713 11 1 0 1 0 1.2713 12 1 -1 -1 1 4.0581 13 1 -1 0 1 4.0166 14 1 -1 1 1 4.7219 15 1 0 -1 1 3.2850 16 1 0 0 1 1.8472 17 1 0 1 1 3.9887 18 1 1 1 1 6.6195 19 1 1 0 1 4.0060 20 1 1 -1 1 4.7814 21 1 1 1 0 3.3034 22 1 1 0 0 2.4653 23 1 1 -1 0 1.7244 24 1 1 1 -1 4.0581 25 1 1 0 -1 4.0166 26 1 1 -1 -1 4.7219 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3975 atoms have been selected out of 4049 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1659 553 553 0.00 6 C006 has 504 168 168 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1826 607 607 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1737 579 579 0.00 12 C012 has 120 40 40 0.00 13 C013 has 489 163 163 0.00 14 C014 has 99 33 33 0.00 Total of13540 atoms and 4505 groups and 4500 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4049 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1338 Number of atoms = 4049 Number of groups = 1343 Number of bonds = 4042 Number of angles = 1442 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1340 Number of HB donors = 2658 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1338 Number of atoms = 4049 Number of groups = 1343 Number of bonds = 4042 Number of angles = 1442 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1340 Number of HB donors = 2658 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.35" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1338" Evaluating: 1338-7 Parameter: NUMWAT <- "1331" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1331" Comparing "1081" and "1331". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.35" Parameter: BOX -> "34.35" Parameter: BOX -> "34.35" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.35000 B = 34.35000 C = 34.35000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6211 2 1 -1 0 -1 4.0033 3 1 -1 1 -1 4.7779 4 1 0 -1 -1 3.9895 5 1 0 0 -1 1.8453 6 1 0 1 -1 3.2822 7 1 -1 -1 0 3.3006 8 1 -1 0 0 2.4648 9 1 -1 1 0 1.7228 10 1 0 -1 0 1.2706 11 1 0 1 0 1.2706 12 1 -1 -1 1 4.0546 13 1 -1 0 1 4.0138 14 1 -1 1 1 4.7189 15 1 0 -1 1 3.2822 16 1 0 0 1 1.8453 17 1 0 1 1 3.9895 18 1 1 1 1 6.6211 19 1 1 0 1 4.0033 20 1 1 -1 1 4.7779 21 1 1 1 0 3.3006 22 1 1 0 0 2.4648 23 1 1 -1 0 1.7228 24 1 1 1 -1 4.0546 25 1 1 0 -1 4.0138 26 1 1 -1 -1 4.7189 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3975 atoms have been selected out of 4049 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1662 554 554 0.00 6 C006 has 504 168 168 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1829 608 608 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1737 579 579 0.00 12 C012 has 120 40 40 0.00 13 C013 has 489 163 163 0.00 14 C014 has 99 33 33 0.00 Total of13546 atoms and 4507 groups and 4502 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4049 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1338 Number of atoms = 4049 Number of groups = 1343 Number of bonds = 4042 Number of angles = 1442 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1340 Number of HB donors = 2658 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1338 Number of atoms = 4049 Number of groups = 1343 Number of bonds = 4042 Number of angles = 1442 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1340 Number of HB donors = 2658 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.348" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1338" Evaluating: 1338-7 Parameter: NUMWAT <- "1331" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1331" Comparing "1081" and "1331". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.348" Parameter: BOX -> "34.348" Parameter: BOX -> "34.348" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.34800 B = 34.34800 C = 34.34800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6228 2 1 -1 0 -1 4.0005 3 1 -1 1 -1 4.7745 4 1 0 -1 -1 3.9903 5 1 0 0 -1 1.8434 6 1 0 1 -1 3.2795 7 1 -1 -1 0 3.2979 8 1 -1 0 0 2.4643 9 1 -1 1 0 1.7211 10 1 0 -1 0 1.2699 11 1 0 1 0 1.2699 12 1 -1 -1 1 4.0512 13 1 -1 0 1 4.0110 14 1 -1 1 1 4.7160 15 1 0 -1 1 3.2795 16 1 0 0 1 1.8434 17 1 0 1 1 3.9903 18 1 1 1 1 6.6228 19 1 1 0 1 4.0005 20 1 1 -1 1 4.7745 21 1 1 1 0 3.2979 22 1 1 0 0 2.4643 23 1 1 -1 0 1.7211 24 1 1 1 -1 4.0512 25 1 1 0 -1 4.0110 26 1 1 -1 -1 4.7160 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3975 atoms have been selected out of 4049 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1662 554 554 0.00 6 C006 has 504 168 168 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1829 608 608 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1737 579 579 0.00 12 C012 has 120 40 40 0.00 13 C013 has 489 163 163 0.00 14 C014 has 99 33 33 0.00 Total of13546 atoms and 4507 groups and 4502 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4049 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1338 Number of atoms = 4049 Number of groups = 1343 Number of bonds = 4042 Number of angles = 1442 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1340 Number of HB donors = 2658 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1338 Number of atoms = 4049 Number of groups = 1343 Number of bonds = 4042 Number of angles = 1442 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1340 Number of HB donors = 2658 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.346" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1338" Evaluating: 1338-7 Parameter: NUMWAT <- "1331" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1331" Comparing "1081" and "1331". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.346" Parameter: BOX -> "34.346" Parameter: BOX -> "34.346" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.34600 B = 34.34600 C = 34.34600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6244 2 1 -1 0 -1 3.9977 3 1 -1 1 -1 4.7710 4 1 0 -1 -1 3.9911 5 1 0 0 -1 1.8415 6 1 0 1 -1 3.2767 7 1 -1 -1 0 3.2951 8 1 -1 0 0 2.4637 9 1 -1 1 0 1.7195 10 1 0 -1 0 1.2692 11 1 0 1 0 1.2692 12 1 -1 -1 1 4.0477 13 1 -1 0 1 4.0083 14 1 -1 1 1 4.7130 15 1 0 -1 1 3.2767 16 1 0 0 1 1.8415 17 1 0 1 1 3.9911 18 1 1 1 1 6.6244 19 1 1 0 1 3.9977 20 1 1 -1 1 4.7710 21 1 1 1 0 3.2951 22 1 1 0 0 2.4637 23 1 1 -1 0 1.7195 24 1 1 1 -1 4.0477 25 1 1 0 -1 4.0083 26 1 1 -1 -1 4.7130 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3975 atoms have been selected out of 4049 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1662 554 554 0.00 6 C006 has 504 168 168 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1829 608 608 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1737 579 579 0.00 12 C012 has 120 40 40 0.00 13 C013 has 489 163 163 0.00 14 C014 has 99 33 33 0.00 Total of13546 atoms and 4507 groups and 4502 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4049 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1338 Number of atoms = 4049 Number of groups = 1343 Number of bonds = 4042 Number of angles = 1442 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1340 Number of HB donors = 2658 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1338 Number of atoms = 4049 Number of groups = 1343 Number of bonds = 4042 Number of angles = 1442 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1340 Number of HB donors = 2658 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.344" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1338" Evaluating: 1338-7 Parameter: NUMWAT <- "1331" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1331" Comparing "1081" and "1331". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.344" Parameter: BOX -> "34.344" Parameter: BOX -> "34.344" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.34400 B = 34.34400 C = 34.34400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6261 2 1 -1 0 -1 3.9949 3 1 -1 1 -1 4.7676 4 1 0 -1 -1 3.9918 5 1 0 0 -1 1.8396 6 1 0 1 -1 3.2740 7 1 -1 -1 0 3.2924 8 1 -1 0 0 2.4632 9 1 -1 1 0 1.7179 10 1 0 -1 0 1.2685 11 1 0 1 0 1.2685 12 1 -1 -1 1 4.0443 13 1 -1 0 1 4.0055 14 1 -1 1 1 4.7100 15 1 0 -1 1 3.2740 16 1 0 0 1 1.8396 17 1 0 1 1 3.9918 18 1 1 1 1 6.6261 19 1 1 0 1 3.9949 20 1 1 -1 1 4.7676 21 1 1 1 0 3.2924 22 1 1 0 0 2.4632 23 1 1 -1 0 1.7179 24 1 1 1 -1 4.0443 25 1 1 0 -1 4.0055 26 1 1 -1 -1 4.7100 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3975 atoms have been selected out of 4049 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1662 554 554 0.00 6 C006 has 504 168 168 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1829 608 608 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1737 579 579 0.00 12 C012 has 123 41 41 0.00 13 C013 has 489 163 163 0.00 14 C014 has 99 33 33 0.00 Total of13549 atoms and 4508 groups and 4503 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4049 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1338 Number of atoms = 4049 Number of groups = 1343 Number of bonds = 4042 Number of angles = 1442 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1340 Number of HB donors = 2658 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1338 Number of atoms = 4049 Number of groups = 1343 Number of bonds = 4042 Number of angles = 1442 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1340 Number of HB donors = 2658 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.342" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1338" Evaluating: 1338-7 Parameter: NUMWAT <- "1331" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1331" Comparing "1081" and "1331". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.342" Parameter: BOX -> "34.342" Parameter: BOX -> "34.342" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.34200 B = 34.34200 C = 34.34200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6277 2 1 -1 0 -1 3.9922 3 1 -1 1 -1 4.7642 4 1 0 -1 -1 3.9926 5 1 0 0 -1 1.8377 6 1 0 1 -1 3.2712 7 1 -1 -1 0 3.2896 8 1 -1 0 0 2.4627 9 1 -1 1 0 1.7163 10 1 0 -1 0 1.2678 11 1 0 1 0 1.2678 12 1 -1 -1 1 4.0408 13 1 -1 0 1 4.0027 14 1 -1 1 1 4.7070 15 1 0 -1 1 3.2712 16 1 0 0 1 1.8377 17 1 0 1 1 3.9926 18 1 1 1 1 6.6277 19 1 1 0 1 3.9922 20 1 1 -1 1 4.7642 21 1 1 1 0 3.2896 22 1 1 0 0 2.4627 23 1 1 -1 0 1.7163 24 1 1 1 -1 4.0408 25 1 1 0 -1 4.0027 26 1 1 -1 -1 4.7070 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3975 atoms have been selected out of 4049 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1256 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1668 556 556 0.00 6 C006 has 504 168 168 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1829 608 608 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1740 580 580 0.00 12 C012 has 123 41 41 0.00 13 C013 has 489 163 163 0.00 14 C014 has 99 33 33 0.00 Total of13555 atoms and 4510 groups and 4505 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4049 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1337 Number of atoms = 4046 Number of groups = 1342 Number of bonds = 4039 Number of angles = 1441 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1339 Number of HB donors = 2656 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1337 Number of atoms = 4046 Number of groups = 1342 Number of bonds = 4039 Number of angles = 1441 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1339 Number of HB donors = 2656 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.34" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1337" Evaluating: 1337-7 Parameter: NUMWAT <- "1330" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1330" Comparing "1081" and "1330". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.34" Parameter: BOX -> "34.34" Parameter: BOX -> "34.34" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.34000 B = 34.34000 C = 34.34000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6294 2 1 -1 0 -1 3.9894 3 1 -1 1 -1 4.7607 4 1 0 -1 -1 3.9934 5 1 0 0 -1 1.8357 6 1 0 1 -1 3.2685 7 1 -1 -1 0 3.2869 8 1 -1 0 0 2.4622 9 1 -1 1 0 1.7147 10 1 0 -1 0 1.2671 11 1 0 1 0 1.2671 12 1 -1 -1 1 4.0374 13 1 -1 0 1 3.9999 14 1 -1 1 1 4.7041 15 1 0 -1 1 3.2685 16 1 0 0 1 1.8357 17 1 0 1 1 3.9934 18 1 1 1 1 6.6294 19 1 1 0 1 3.9894 20 1 1 -1 1 4.7607 21 1 1 1 0 3.2869 22 1 1 0 0 2.4622 23 1 1 -1 0 1.7147 24 1 1 1 -1 4.0374 25 1 1 0 -1 3.9999 26 1 1 -1 -1 4.7041 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3972 atoms have been selected out of 4046 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1081 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1659 553 553 0.00 6 C006 has 504 168 168 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1829 608 608 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1734 578 578 0.00 12 C012 has 123 41 41 0.00 13 C013 has 489 163 163 0.00 14 C014 has 99 33 33 0.00 Total of13534 atoms and 4503 groups and 4498 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4046 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1336 Number of atoms = 4043 Number of groups = 1341 Number of bonds = 4036 Number of angles = 1440 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1338 Number of HB donors = 2654 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1336 Number of atoms = 4043 Number of groups = 1341 Number of bonds = 4036 Number of angles = 1440 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1338 Number of HB donors = 2654 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.338" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1336" Evaluating: 1336-7 Parameter: NUMWAT <- "1329" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1329" Comparing "1081" and "1329". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.338" Parameter: BOX -> "34.338" Parameter: BOX -> "34.338" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.33800 B = 34.33800 C = 34.33800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6310 2 1 -1 0 -1 3.9866 3 1 -1 1 -1 4.7573 4 1 0 -1 -1 3.9942 5 1 0 0 -1 1.8338 6 1 0 1 -1 3.2657 7 1 -1 -1 0 3.2841 8 1 -1 0 0 2.4617 9 1 -1 1 0 1.7131 10 1 0 -1 0 1.2664 11 1 0 1 0 1.2664 12 1 -1 -1 1 4.0339 13 1 -1 0 1 3.9972 14 1 -1 1 1 4.7011 15 1 0 -1 1 3.2657 16 1 0 0 1 1.8338 17 1 0 1 1 3.9942 18 1 1 1 1 6.6310 19 1 1 0 1 3.9866 20 1 1 -1 1 4.7573 21 1 1 1 0 3.2841 22 1 1 0 0 2.4617 23 1 1 -1 0 1.7131 24 1 1 1 -1 4.0339 25 1 1 0 -1 3.9972 26 1 1 -1 -1 4.7011 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3969 atoms have been selected out of 4043 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 693 231 231 0.00 3 C003 has 84 28 28 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1659 553 553 0.00 6 C006 has 504 168 168 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1829 608 608 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1734 578 578 0.00 12 C012 has 123 41 41 0.00 13 C013 has 489 163 163 0.00 14 C014 has 99 33 33 0.00 Total of13531 atoms and 4502 groups and 4497 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4043 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1336 Number of atoms = 4043 Number of groups = 1341 Number of bonds = 4036 Number of angles = 1440 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1338 Number of HB donors = 2654 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1336 Number of atoms = 4043 Number of groups = 1341 Number of bonds = 4036 Number of angles = 1440 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1338 Number of HB donors = 2654 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.336" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1336" Evaluating: 1336-7 Parameter: NUMWAT <- "1329" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1329" Comparing "1081" and "1329". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.336" Parameter: BOX -> "34.336" Parameter: BOX -> "34.336" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.33600 B = 34.33600 C = 34.33600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6327 2 1 -1 0 -1 3.9838 3 1 -1 1 -1 4.7538 4 1 0 -1 -1 3.9950 5 1 0 0 -1 1.8319 6 1 0 1 -1 3.2630 7 1 -1 -1 0 3.2814 8 1 -1 0 0 2.4612 9 1 -1 1 0 1.7115 10 1 0 -1 0 1.2657 11 1 0 1 0 1.2657 12 1 -1 -1 1 4.0305 13 1 -1 0 1 3.9944 14 1 -1 1 1 4.6981 15 1 0 -1 1 3.2630 16 1 0 0 1 1.8319 17 1 0 1 1 3.9950 18 1 1 1 1 6.6327 19 1 1 0 1 3.9838 20 1 1 -1 1 4.7538 21 1 1 1 0 3.2814 22 1 1 0 0 2.4612 23 1 1 -1 0 1.7115 24 1 1 1 -1 4.0305 25 1 1 0 -1 3.9944 26 1 1 -1 -1 4.6981 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3969 atoms have been selected out of 4043 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 693 231 231 0.00 3 C003 has 87 29 29 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1659 553 553 0.00 6 C006 has 504 168 168 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1829 608 608 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1734 578 578 0.00 12 C012 has 123 41 41 0.00 13 C013 has 489 163 163 0.00 14 C014 has 99 33 33 0.00 Total of13534 atoms and 4503 groups and 4498 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4043 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1336 Number of atoms = 4043 Number of groups = 1341 Number of bonds = 4036 Number of angles = 1440 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1338 Number of HB donors = 2654 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1336 Number of atoms = 4043 Number of groups = 1341 Number of bonds = 4036 Number of angles = 1440 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1338 Number of HB donors = 2654 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.334" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1336" Evaluating: 1336-7 Parameter: NUMWAT <- "1329" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1329" Comparing "1081" and "1329". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.334" Parameter: BOX -> "34.334" Parameter: BOX -> "34.334" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.33400 B = 34.33400 C = 34.33400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6343 2 1 -1 0 -1 3.9811 3 1 -1 1 -1 4.7504 4 1 0 -1 -1 3.9958 5 1 0 0 -1 1.8300 6 1 0 1 -1 3.2602 7 1 -1 -1 0 3.2786 8 1 -1 0 0 2.4607 9 1 -1 1 0 1.7100 10 1 0 -1 0 1.2650 11 1 0 1 0 1.2650 12 1 -1 -1 1 4.0270 13 1 -1 0 1 3.9916 14 1 -1 1 1 4.6952 15 1 0 -1 1 3.2602 16 1 0 0 1 1.8300 17 1 0 1 1 3.9958 18 1 1 1 1 6.6343 19 1 1 0 1 3.9811 20 1 1 -1 1 4.7504 21 1 1 1 0 3.2786 22 1 1 0 0 2.4607 23 1 1 -1 0 1.7100 24 1 1 1 -1 4.0270 25 1 1 0 -1 3.9916 26 1 1 -1 -1 4.6952 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3969 atoms have been selected out of 4043 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 693 231 231 0.00 3 C003 has 90 30 30 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1659 553 553 0.00 6 C006 has 504 168 168 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1829 608 608 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1734 578 578 0.00 12 C012 has 123 41 41 0.00 13 C013 has 489 163 163 0.00 14 C014 has 99 33 33 0.00 Total of13537 atoms and 4504 groups and 4499 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4043 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1336 Number of atoms = 4043 Number of groups = 1341 Number of bonds = 4036 Number of angles = 1440 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1338 Number of HB donors = 2654 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1336 Number of atoms = 4043 Number of groups = 1341 Number of bonds = 4036 Number of angles = 1440 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1338 Number of HB donors = 2654 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.332" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1336" Evaluating: 1336-7 Parameter: NUMWAT <- "1329" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1329" Comparing "1081" and "1329". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.332" Parameter: BOX -> "34.332" Parameter: BOX -> "34.332" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.33200 B = 34.33200 C = 34.33200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6360 2 1 -1 0 -1 3.9783 3 1 -1 1 -1 4.7470 4 1 0 -1 -1 3.9966 5 1 0 0 -1 1.8281 6 1 0 1 -1 3.2575 7 1 -1 -1 0 3.2759 8 1 -1 0 0 2.4601 9 1 -1 1 0 1.7084 10 1 0 -1 0 1.2643 11 1 0 1 0 1.2643 12 1 -1 -1 1 4.0236 13 1 -1 0 1 3.9888 14 1 -1 1 1 4.6922 15 1 0 -1 1 3.2575 16 1 0 0 1 1.8281 17 1 0 1 1 3.9966 18 1 1 1 1 6.6360 19 1 1 0 1 3.9783 20 1 1 -1 1 4.7470 21 1 1 1 0 3.2759 22 1 1 0 0 2.4601 23 1 1 -1 0 1.7084 24 1 1 1 -1 4.0236 25 1 1 0 -1 3.9888 26 1 1 -1 -1 4.6922 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3969 atoms have been selected out of 4043 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 693 231 231 0.00 3 C003 has 90 30 30 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1662 554 554 0.00 6 C006 has 504 168 168 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1829 608 608 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1734 578 578 0.00 12 C012 has 123 41 41 0.00 13 C013 has 489 163 163 0.00 14 C014 has 99 33 33 0.00 Total of13540 atoms and 4505 groups and 4500 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4043 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1336 Number of atoms = 4043 Number of groups = 1341 Number of bonds = 4036 Number of angles = 1440 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1338 Number of HB donors = 2654 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1336 Number of atoms = 4043 Number of groups = 1341 Number of bonds = 4036 Number of angles = 1440 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1338 Number of HB donors = 2654 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.33" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1336" Evaluating: 1336-7 Parameter: NUMWAT <- "1329" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1329" Comparing "1081" and "1329". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.33" Parameter: BOX -> "34.33" Parameter: BOX -> "34.33" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.33000 B = 34.33000 C = 34.33000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6376 2 1 -1 0 -1 3.9755 3 1 -1 1 -1 4.7435 4 1 0 -1 -1 3.9974 5 1 0 0 -1 1.8262 6 1 0 1 -1 3.2547 7 1 -1 -1 0 3.2731 8 1 -1 0 0 2.4596 9 1 -1 1 0 1.7068 10 1 0 -1 0 1.2637 11 1 0 1 0 1.2637 12 1 -1 -1 1 4.0201 13 1 -1 0 1 3.9861 14 1 -1 1 1 4.6892 15 1 0 -1 1 3.2547 16 1 0 0 1 1.8262 17 1 0 1 1 3.9974 18 1 1 1 1 6.6376 19 1 1 0 1 3.9755 20 1 1 -1 1 4.7435 21 1 1 1 0 3.2731 22 1 1 0 0 2.4596 23 1 1 -1 0 1.7068 24 1 1 1 -1 4.0201 25 1 1 0 -1 3.9861 26 1 1 -1 -1 4.6892 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3969 atoms have been selected out of 4043 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 693 231 231 0.00 3 C003 has 90 30 30 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1662 554 554 0.00 6 C006 has 504 168 168 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1829 608 608 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1734 578 578 0.00 12 C012 has 123 41 41 0.00 13 C013 has 489 163 163 0.00 14 C014 has 99 33 33 0.00 Total of13543 atoms and 4506 groups and 4501 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4043 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1336 Number of atoms = 4043 Number of groups = 1341 Number of bonds = 4036 Number of angles = 1440 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1338 Number of HB donors = 2654 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1336 Number of atoms = 4043 Number of groups = 1341 Number of bonds = 4036 Number of angles = 1440 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1338 Number of HB donors = 2654 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.328" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1336" Evaluating: 1336-7 Parameter: NUMWAT <- "1329" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1329" Comparing "1081" and "1329". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.328" Parameter: BOX -> "34.328" Parameter: BOX -> "34.328" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.32800 B = 34.32800 C = 34.32800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6393 2 1 -1 0 -1 3.9727 3 1 -1 1 -1 4.7401 4 1 0 -1 -1 3.9982 5 1 0 0 -1 1.8243 6 1 0 1 -1 3.2520 7 1 -1 -1 0 3.2704 8 1 -1 0 0 2.4591 9 1 -1 1 0 1.7052 10 1 0 -1 0 1.2630 11 1 0 1 0 1.2630 12 1 -1 -1 1 4.0167 13 1 -1 0 1 3.9833 14 1 -1 1 1 4.6863 15 1 0 -1 1 3.2520 16 1 0 0 1 1.8243 17 1 0 1 1 3.9982 18 1 1 1 1 6.6393 19 1 1 0 1 3.9727 20 1 1 -1 1 4.7401 21 1 1 1 0 3.2704 22 1 1 0 0 2.4591 23 1 1 -1 0 1.7052 24 1 1 1 -1 4.0167 25 1 1 0 -1 3.9833 26 1 1 -1 -1 4.6863 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3969 atoms have been selected out of 4043 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 447 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 693 231 231 0.00 3 C003 has 90 30 30 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1662 554 554 0.00 6 C006 has 504 168 168 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1829 608 608 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1731 577 577 0.00 12 C012 has 123 41 41 0.00 13 C013 has 489 163 163 0.00 14 C014 has 99 33 33 0.00 Total of13543 atoms and 4506 groups and 4501 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4043 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1335 Number of atoms = 4040 Number of groups = 1340 Number of bonds = 4033 Number of angles = 1439 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1337 Number of HB donors = 2652 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1335 Number of atoms = 4040 Number of groups = 1340 Number of bonds = 4033 Number of angles = 1439 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1337 Number of HB donors = 2652 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.326" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1335" Evaluating: 1335-7 Parameter: NUMWAT <- "1328" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1328" Comparing "1081" and "1328". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.326" Parameter: BOX -> "34.326" Parameter: BOX -> "34.326" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.32600 B = 34.32600 C = 34.32600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6410 2 1 -1 0 -1 3.9700 3 1 -1 1 -1 4.7366 4 1 0 -1 -1 3.9990 5 1 0 0 -1 1.8224 6 1 0 1 -1 3.2492 7 1 -1 -1 0 3.2676 8 1 -1 0 0 2.4586 9 1 -1 1 0 1.7036 10 1 0 -1 0 1.2623 11 1 0 1 0 1.2623 12 1 -1 -1 1 4.0132 13 1 -1 0 1 3.9805 14 1 -1 1 1 4.6833 15 1 0 -1 1 3.2492 16 1 0 0 1 1.8224 17 1 0 1 1 3.9990 18 1 1 1 1 6.6410 19 1 1 0 1 3.9700 20 1 1 -1 1 4.7366 21 1 1 1 0 3.2676 22 1 1 0 0 2.4586 23 1 1 -1 0 1.7036 24 1 1 1 -1 4.0132 25 1 1 0 -1 3.9805 26 1 1 -1 -1 4.6833 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3966 atoms have been selected out of 4040 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 298 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 693 231 231 0.00 3 C003 has 90 30 30 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1662 554 554 0.00 6 C006 has 504 168 168 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1829 608 608 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1734 578 578 0.00 12 C012 has 126 42 42 0.00 13 C013 has 489 163 163 0.00 14 C014 has 96 32 32 0.00 Total of13543 atoms and 4506 groups and 4501 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4040 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1334 Number of atoms = 4037 Number of groups = 1339 Number of bonds = 4030 Number of angles = 1438 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1336 Number of HB donors = 2650 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1334 Number of atoms = 4037 Number of groups = 1339 Number of bonds = 4030 Number of angles = 1438 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1336 Number of HB donors = 2650 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.324" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1334" Evaluating: 1334-7 Parameter: NUMWAT <- "1327" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1327" Comparing "1081" and "1327". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.324" Parameter: BOX -> "34.324" Parameter: BOX -> "34.324" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.32400 B = 34.32400 C = 34.32400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6426 2 1 -1 0 -1 3.9672 3 1 -1 1 -1 4.7332 4 1 0 -1 -1 3.9998 5 1 0 0 -1 1.8204 6 1 0 1 -1 3.2465 7 1 -1 -1 0 3.2649 8 1 -1 0 0 2.4581 9 1 -1 1 0 1.7021 10 1 0 -1 0 1.2616 11 1 0 1 0 1.2616 12 1 -1 -1 1 4.0098 13 1 -1 0 1 3.9778 14 1 -1 1 1 4.6803 15 1 0 -1 1 3.2465 16 1 0 0 1 1.8204 17 1 0 1 1 3.9998 18 1 1 1 1 6.6426 19 1 1 0 1 3.9672 20 1 1 -1 1 4.7332 21 1 1 1 0 3.2649 22 1 1 0 0 2.4581 23 1 1 -1 0 1.7021 24 1 1 1 -1 4.0098 25 1 1 0 -1 3.9778 26 1 1 -1 -1 4.6803 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3963 atoms have been selected out of 4037 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 437 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1275 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 690 230 230 0.00 3 C003 has 90 30 30 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1659 553 553 0.00 6 C006 has 504 168 168 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1829 608 608 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1731 577 577 0.00 12 C012 has 126 42 42 0.00 13 C013 has 492 164 164 0.00 14 C014 has 96 32 32 0.00 Total of13534 atoms and 4503 groups and 4498 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 4037 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1332 Number of atoms = 4031 Number of groups = 1337 Number of bonds = 4024 Number of angles = 1436 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1334 Number of HB donors = 2646 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1332 Number of atoms = 4031 Number of groups = 1337 Number of bonds = 4024 Number of angles = 1436 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1334 Number of HB donors = 2646 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.322" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1332" Evaluating: 1332-7 Parameter: NUMWAT <- "1325" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1325" Comparing "1081" and "1325". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.322" Parameter: BOX -> "34.322" Parameter: BOX -> "34.322" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.32200 B = 34.32200 C = 34.32200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6443 2 1 -1 0 -1 3.9644 3 1 -1 1 -1 4.7298 4 1 0 -1 -1 4.0006 5 1 0 0 -1 1.8185 6 1 0 1 -1 3.2437 7 1 -1 -1 0 3.2622 8 1 -1 0 0 2.4576 9 1 -1 1 0 1.7005 10 1 0 -1 0 1.2610 11 1 0 1 0 1.2610 12 1 -1 -1 1 4.0063 13 1 -1 0 1 3.9750 14 1 -1 1 1 4.6774 15 1 0 -1 1 3.2437 16 1 0 0 1 1.8185 17 1 0 1 1 4.0006 18 1 1 1 1 6.6443 19 1 1 0 1 3.9644 20 1 1 -1 1 4.7298 21 1 1 1 0 3.2622 22 1 1 0 0 2.4576 23 1 1 -1 0 1.7005 24 1 1 1 -1 4.0063 25 1 1 0 -1 3.9750 26 1 1 -1 -1 4.6774 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3957 atoms have been selected out of 4031 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 690 230 230 0.00 3 C003 has 90 30 30 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1659 553 553 0.00 6 C006 has 504 168 168 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1823 606 606 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1728 576 576 0.00 12 C012 has 123 41 41 0.00 13 C013 has 486 162 162 0.00 14 C014 has 96 32 32 0.00 Total of13504 atoms and 4493 groups and 4488 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4031 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1332 Number of atoms = 4031 Number of groups = 1337 Number of bonds = 4024 Number of angles = 1436 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1334 Number of HB donors = 2646 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1332 Number of atoms = 4031 Number of groups = 1337 Number of bonds = 4024 Number of angles = 1436 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1334 Number of HB donors = 2646 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.32" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1332" Evaluating: 1332-7 Parameter: NUMWAT <- "1325" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1325" Comparing "1081" and "1325". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.32" Parameter: BOX -> "34.32" Parameter: BOX -> "34.32" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.32000 B = 34.32000 C = 34.32000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6459 2 1 -1 0 -1 3.9616 3 1 -1 1 -1 4.7263 4 1 0 -1 -1 4.0014 5 1 0 0 -1 1.8166 6 1 0 1 -1 3.2410 7 1 -1 -1 0 3.2594 8 1 -1 0 0 2.4571 9 1 -1 1 0 1.6989 10 1 0 -1 0 1.2603 11 1 0 1 0 1.2603 12 1 -1 -1 1 4.0029 13 1 -1 0 1 3.9722 14 1 -1 1 1 4.6744 15 1 0 -1 1 3.2410 16 1 0 0 1 1.8166 17 1 0 1 1 4.0014 18 1 1 1 1 6.6459 19 1 1 0 1 3.9616 20 1 1 -1 1 4.7263 21 1 1 1 0 3.2594 22 1 1 0 0 2.4571 23 1 1 -1 0 1.6989 24 1 1 1 -1 4.0029 25 1 1 0 -1 3.9722 26 1 1 -1 -1 4.6744 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3957 atoms have been selected out of 4031 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 989 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1316 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 684 228 228 0.00 3 C003 has 87 29 29 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1653 551 551 0.00 6 C006 has 501 167 167 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1823 606 606 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1728 576 576 0.00 12 C012 has 126 42 42 0.00 13 C013 has 492 164 164 0.00 14 C014 has 99 33 33 0.00 Total of13498 atoms and 4491 groups and 4486 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 4031 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1330 Number of atoms = 4025 Number of groups = 1335 Number of bonds = 4018 Number of angles = 1434 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1332 Number of HB donors = 2642 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1330 Number of atoms = 4025 Number of groups = 1335 Number of bonds = 4018 Number of angles = 1434 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1332 Number of HB donors = 2642 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.318" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1330" Evaluating: 1330-7 Parameter: NUMWAT <- "1323" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1323" Comparing "1081" and "1323". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.318" Parameter: BOX -> "34.318" Parameter: BOX -> "34.318" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.31800 B = 34.31800 C = 34.31800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6476 2 1 -1 0 -1 3.9589 3 1 -1 1 -1 4.7229 4 1 0 -1 -1 4.0022 5 1 0 0 -1 1.8147 6 1 0 1 -1 3.2382 7 1 -1 -1 0 3.2567 8 1 -1 0 0 2.4566 9 1 -1 1 0 1.6974 10 1 0 -1 0 1.2596 11 1 0 1 0 1.2596 12 1 -1 -1 1 3.9994 13 1 -1 0 1 3.9694 14 1 -1 1 1 4.6714 15 1 0 -1 1 3.2382 16 1 0 0 1 1.8147 17 1 0 1 1 4.0022 18 1 1 1 1 6.6476 19 1 1 0 1 3.9589 20 1 1 -1 1 4.7229 21 1 1 1 0 3.2567 22 1 1 0 0 2.4566 23 1 1 -1 0 1.6974 24 1 1 1 -1 3.9994 25 1 1 0 -1 3.9694 26 1 1 -1 -1 4.6714 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3951 atoms have been selected out of 4025 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 684 228 228 0.00 3 C003 has 87 29 29 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1653 551 551 0.00 6 C006 has 501 167 167 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1817 604 604 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1725 575 575 0.00 12 C012 has 123 41 41 0.00 13 C013 has 486 162 162 0.00 14 C014 has 96 32 32 0.00 Total of13459 atoms and 4478 groups and 4473 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4025 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1330 Number of atoms = 4025 Number of groups = 1335 Number of bonds = 4018 Number of angles = 1434 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1332 Number of HB donors = 2642 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1330 Number of atoms = 4025 Number of groups = 1335 Number of bonds = 4018 Number of angles = 1434 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1332 Number of HB donors = 2642 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.316" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1330" Evaluating: 1330-7 Parameter: NUMWAT <- "1323" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1323" Comparing "1081" and "1323". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.316" Parameter: BOX -> "34.316" Parameter: BOX -> "34.316" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.31600 B = 34.31600 C = 34.31600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6493 2 1 -1 0 -1 3.9561 3 1 -1 1 -1 4.7195 4 1 0 -1 -1 4.0030 5 1 0 0 -1 1.8128 6 1 0 1 -1 3.2355 7 1 -1 -1 0 3.2539 8 1 -1 0 0 2.4561 9 1 -1 1 0 1.6958 10 1 0 -1 0 1.2590 11 1 0 1 0 1.2590 12 1 -1 -1 1 3.9960 13 1 -1 0 1 3.9667 14 1 -1 1 1 4.6685 15 1 0 -1 1 3.2355 16 1 0 0 1 1.8128 17 1 0 1 1 4.0030 18 1 1 1 1 6.6493 19 1 1 0 1 3.9561 20 1 1 -1 1 4.7195 21 1 1 1 0 3.2539 22 1 1 0 0 2.4561 23 1 1 -1 0 1.6958 24 1 1 1 -1 3.9960 25 1 1 0 -1 3.9667 26 1 1 -1 -1 4.6685 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3951 atoms have been selected out of 4025 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 834 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 684 228 228 0.00 3 C003 has 87 29 29 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1653 551 551 0.00 6 C006 has 498 166 166 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1817 604 604 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1725 575 575 0.00 12 C012 has 123 41 41 0.00 13 C013 has 486 162 162 0.00 14 C014 has 96 32 32 0.00 Total of13459 atoms and 4478 groups and 4473 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4025 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1329 Number of atoms = 4022 Number of groups = 1334 Number of bonds = 4015 Number of angles = 1433 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1331 Number of HB donors = 2640 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1329 Number of atoms = 4022 Number of groups = 1334 Number of bonds = 4015 Number of angles = 1433 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1331 Number of HB donors = 2640 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.314" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1329" Evaluating: 1329-7 Parameter: NUMWAT <- "1322" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1322" Comparing "1081" and "1322". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.314" Parameter: BOX -> "34.314" Parameter: BOX -> "34.314" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.31400 B = 34.31400 C = 34.31400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6509 2 1 -1 0 -1 3.9533 3 1 -1 1 -1 4.7160 4 1 0 -1 -1 4.0038 5 1 0 0 -1 1.8109 6 1 0 1 -1 3.2327 7 1 -1 -1 0 3.2512 8 1 -1 0 0 2.4556 9 1 -1 1 0 1.6942 10 1 0 -1 0 1.2583 11 1 0 1 0 1.2583 12 1 -1 -1 1 3.9925 13 1 -1 0 1 3.9639 14 1 -1 1 1 4.6655 15 1 0 -1 1 3.2327 16 1 0 0 1 1.8109 17 1 0 1 1 4.0038 18 1 1 1 1 6.6509 19 1 1 0 1 3.9533 20 1 1 -1 1 4.7160 21 1 1 1 0 3.2512 22 1 1 0 0 2.4556 23 1 1 -1 0 1.6942 24 1 1 1 -1 3.9925 25 1 1 0 -1 3.9639 26 1 1 -1 -1 4.6655 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3948 atoms have been selected out of 4022 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 115 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 690 230 230 0.00 3 C003 has 87 29 29 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 501 167 167 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1722 574 574 0.00 12 C012 has 123 41 41 0.00 13 C013 has 486 162 162 0.00 14 C014 has 96 32 32 0.00 Total of13444 atoms and 4473 groups and 4468 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4022 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1328 Number of atoms = 4019 Number of groups = 1333 Number of bonds = 4012 Number of angles = 1432 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1330 Number of HB donors = 2638 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1328 Number of atoms = 4019 Number of groups = 1333 Number of bonds = 4012 Number of angles = 1432 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1330 Number of HB donors = 2638 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.312" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1328" Evaluating: 1328-7 Parameter: NUMWAT <- "1321" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1321" Comparing "1081" and "1321". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.312" Parameter: BOX -> "34.312" Parameter: BOX -> "34.312" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.31200 B = 34.31200 C = 34.31200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6526 2 1 -1 0 -1 3.9505 3 1 -1 1 -1 4.7126 4 1 0 -1 -1 4.0046 5 1 0 0 -1 1.8090 6 1 0 1 -1 3.2300 7 1 -1 -1 0 3.2484 8 1 -1 0 0 2.4551 9 1 -1 1 0 1.6927 10 1 0 -1 0 1.2577 11 1 0 1 0 1.2577 12 1 -1 -1 1 3.9891 13 1 -1 0 1 3.9611 14 1 -1 1 1 4.6625 15 1 0 -1 1 3.2300 16 1 0 0 1 1.8090 17 1 0 1 1 4.0046 18 1 1 1 1 6.6526 19 1 1 0 1 3.9505 20 1 1 -1 1 4.7126 21 1 1 1 0 3.2484 22 1 1 0 0 2.4551 23 1 1 -1 0 1.6927 24 1 1 1 -1 3.9891 25 1 1 0 -1 3.9611 26 1 1 -1 -1 4.6625 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3945 atoms have been selected out of 4019 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 687 229 229 0.00 3 C003 has 87 29 29 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 498 166 166 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1722 574 574 0.00 12 C012 has 126 42 42 0.00 13 C013 has 486 162 162 0.00 14 C014 has 96 32 32 0.00 Total of13438 atoms and 4471 groups and 4466 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4019 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1328 Number of atoms = 4019 Number of groups = 1333 Number of bonds = 4012 Number of angles = 1432 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1330 Number of HB donors = 2638 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1328 Number of atoms = 4019 Number of groups = 1333 Number of bonds = 4012 Number of angles = 1432 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1330 Number of HB donors = 2638 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.31" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1328" Evaluating: 1328-7 Parameter: NUMWAT <- "1321" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1321" Comparing "1081" and "1321". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.31" Parameter: BOX -> "34.31" Parameter: BOX -> "34.31" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.31000 B = 34.31000 C = 34.31000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6543 2 1 -1 0 -1 3.9478 3 1 -1 1 -1 4.7091 4 1 0 -1 -1 4.0054 5 1 0 0 -1 1.8071 6 1 0 1 -1 3.2272 7 1 -1 -1 0 3.2457 8 1 -1 0 0 2.4546 9 1 -1 1 0 1.6911 10 1 0 -1 0 1.2570 11 1 0 1 0 1.2570 12 1 -1 -1 1 3.9856 13 1 -1 0 1 3.9583 14 1 -1 1 1 4.6596 15 1 0 -1 1 3.2272 16 1 0 0 1 1.8071 17 1 0 1 1 4.0054 18 1 1 1 1 6.6543 19 1 1 0 1 3.9478 20 1 1 -1 1 4.7091 21 1 1 1 0 3.2457 22 1 1 0 0 2.4546 23 1 1 -1 0 1.6911 24 1 1 1 -1 3.9856 25 1 1 0 -1 3.9583 26 1 1 -1 -1 4.6596 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3945 atoms have been selected out of 4019 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 687 229 229 0.00 3 C003 has 87 29 29 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 498 166 166 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1725 575 575 0.00 12 C012 has 126 42 42 0.00 13 C013 has 486 162 162 0.00 14 C014 has 96 32 32 0.00 Total of13441 atoms and 4472 groups and 4467 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4019 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1328 Number of atoms = 4019 Number of groups = 1333 Number of bonds = 4012 Number of angles = 1432 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1330 Number of HB donors = 2638 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1328 Number of atoms = 4019 Number of groups = 1333 Number of bonds = 4012 Number of angles = 1432 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1330 Number of HB donors = 2638 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.308" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1328" Evaluating: 1328-7 Parameter: NUMWAT <- "1321" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1321" Comparing "1081" and "1321". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.308" Parameter: BOX -> "34.308" Parameter: BOX -> "34.308" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.30800 B = 34.30800 C = 34.30800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6560 2 1 -1 0 -1 3.9450 3 1 -1 1 -1 4.7057 4 1 0 -1 -1 4.0062 5 1 0 0 -1 1.8051 6 1 0 1 -1 3.2245 7 1 -1 -1 0 3.2429 8 1 -1 0 0 2.4541 9 1 -1 1 0 1.6896 10 1 0 -1 0 1.2564 11 1 0 1 0 1.2564 12 1 -1 -1 1 3.9822 13 1 -1 0 1 3.9556 14 1 -1 1 1 4.6566 15 1 0 -1 1 3.2245 16 1 0 0 1 1.8051 17 1 0 1 1 4.0062 18 1 1 1 1 6.6560 19 1 1 0 1 3.9450 20 1 1 -1 1 4.7057 21 1 1 1 0 3.2429 22 1 1 0 0 2.4541 23 1 1 -1 0 1.6896 24 1 1 1 -1 3.9822 25 1 1 0 -1 3.9556 26 1 1 -1 -1 4.6566 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3945 atoms have been selected out of 4019 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 687 229 229 0.00 3 C003 has 87 29 29 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 498 166 166 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1725 575 575 0.00 12 C012 has 126 42 42 0.00 13 C013 has 486 162 162 0.00 14 C014 has 96 32 32 0.00 Total of13441 atoms and 4472 groups and 4467 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4019 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1328 Number of atoms = 4019 Number of groups = 1333 Number of bonds = 4012 Number of angles = 1432 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1330 Number of HB donors = 2638 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1328 Number of atoms = 4019 Number of groups = 1333 Number of bonds = 4012 Number of angles = 1432 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1330 Number of HB donors = 2638 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.306" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1328" Evaluating: 1328-7 Parameter: NUMWAT <- "1321" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1321" Comparing "1081" and "1321". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.306" Parameter: BOX -> "34.306" Parameter: BOX -> "34.306" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.30600 B = 34.30600 C = 34.30600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6576 2 1 -1 0 -1 3.9422 3 1 -1 1 -1 4.7023 4 1 0 -1 -1 4.0070 5 1 0 0 -1 1.8032 6 1 0 1 -1 3.2217 7 1 -1 -1 0 3.2402 8 1 -1 0 0 2.4537 9 1 -1 1 0 1.6880 10 1 0 -1 0 1.2557 11 1 0 1 0 1.2557 12 1 -1 -1 1 3.9787 13 1 -1 0 1 3.9528 14 1 -1 1 1 4.6537 15 1 0 -1 1 3.2217 16 1 0 0 1 1.8032 17 1 0 1 1 4.0070 18 1 1 1 1 6.6576 19 1 1 0 1 3.9422 20 1 1 -1 1 4.7023 21 1 1 1 0 3.2402 22 1 1 0 0 2.4537 23 1 1 -1 0 1.6880 24 1 1 1 -1 3.9787 25 1 1 0 -1 3.9528 26 1 1 -1 -1 4.6537 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3945 atoms have been selected out of 4019 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1193 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 684 228 228 0.00 3 C003 has 87 29 29 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 498 166 166 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1811 602 602 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1725 575 575 0.00 12 C012 has 126 42 42 0.00 13 C013 has 486 162 162 0.00 14 C014 has 96 32 32 0.00 Total of13438 atoms and 4471 groups and 4466 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4019 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1327 Number of atoms = 4016 Number of groups = 1332 Number of bonds = 4009 Number of angles = 1431 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1329 Number of HB donors = 2636 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1327 Number of atoms = 4016 Number of groups = 1332 Number of bonds = 4009 Number of angles = 1431 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1329 Number of HB donors = 2636 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.304" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1327" Evaluating: 1327-7 Parameter: NUMWAT <- "1320" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1320" Comparing "1081" and "1320". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.304" Parameter: BOX -> "34.304" Parameter: BOX -> "34.304" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.30400 B = 34.30400 C = 34.30400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6593 2 1 -1 0 -1 3.9394 3 1 -1 1 -1 4.6988 4 1 0 -1 -1 4.0078 5 1 0 0 -1 1.8013 6 1 0 1 -1 3.2190 7 1 -1 -1 0 3.2374 8 1 -1 0 0 2.4532 9 1 -1 1 0 1.6865 10 1 0 -1 0 1.2551 11 1 0 1 0 1.2551 12 1 -1 -1 1 3.9753 13 1 -1 0 1 3.9500 14 1 -1 1 1 4.6507 15 1 0 -1 1 3.2190 16 1 0 0 1 1.8013 17 1 0 1 1 4.0078 18 1 1 1 1 6.6593 19 1 1 0 1 3.9394 20 1 1 -1 1 4.6988 21 1 1 1 0 3.2374 22 1 1 0 0 2.4532 23 1 1 -1 0 1.6865 24 1 1 1 -1 3.9753 25 1 1 0 -1 3.9500 26 1 1 -1 -1 4.6507 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3942 atoms have been selected out of 4016 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 684 228 228 0.00 3 C003 has 87 29 29 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 498 166 166 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1811 602 602 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1725 575 575 0.00 12 C012 has 126 42 42 0.00 13 C013 has 486 162 162 0.00 14 C014 has 96 32 32 0.00 Total of13432 atoms and 4469 groups and 4464 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4016 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1327 Number of atoms = 4016 Number of groups = 1332 Number of bonds = 4009 Number of angles = 1431 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1329 Number of HB donors = 2636 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1327 Number of atoms = 4016 Number of groups = 1332 Number of bonds = 4009 Number of angles = 1431 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1329 Number of HB donors = 2636 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.302" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1327" Evaluating: 1327-7 Parameter: NUMWAT <- "1320" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1320" Comparing "1081" and "1320". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.302" Parameter: BOX -> "34.302" Parameter: BOX -> "34.302" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.30200 B = 34.30200 C = 34.30200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6610 2 1 -1 0 -1 3.9367 3 1 -1 1 -1 4.6954 4 1 0 -1 -1 4.0087 5 1 0 0 -1 1.7994 6 1 0 1 -1 3.2162 7 1 -1 -1 0 3.2347 8 1 -1 0 0 2.4527 9 1 -1 1 0 1.6850 10 1 0 -1 0 1.2545 11 1 0 1 0 1.2545 12 1 -1 -1 1 3.9718 13 1 -1 0 1 3.9472 14 1 -1 1 1 4.6477 15 1 0 -1 1 3.2162 16 1 0 0 1 1.7994 17 1 0 1 1 4.0087 18 1 1 1 1 6.6610 19 1 1 0 1 3.9367 20 1 1 -1 1 4.6954 21 1 1 1 0 3.2347 22 1 1 0 0 2.4527 23 1 1 -1 0 1.6850 24 1 1 1 -1 3.9718 25 1 1 0 -1 3.9472 26 1 1 -1 -1 4.6477 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3942 atoms have been selected out of 4016 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 372 124 124 0.00 2 C002 has 684 228 228 0.00 3 C003 has 87 29 29 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 498 166 166 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1725 575 575 0.00 12 C012 has 126 42 42 0.00 13 C013 has 486 162 162 0.00 14 C014 has 96 32 32 0.00 Total of13435 atoms and 4470 groups and 4465 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4016 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1327 Number of atoms = 4016 Number of groups = 1332 Number of bonds = 4009 Number of angles = 1431 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1329 Number of HB donors = 2636 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1327 Number of atoms = 4016 Number of groups = 1332 Number of bonds = 4009 Number of angles = 1431 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1329 Number of HB donors = 2636 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.3" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1327" Evaluating: 1327-7 Parameter: NUMWAT <- "1320" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1320" Comparing "1081" and "1320". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.3" Parameter: BOX -> "34.3" Parameter: BOX -> "34.3" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.30000 B = 34.30000 C = 34.30000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6627 2 1 -1 0 -1 3.9339 3 1 -1 1 -1 4.6919 4 1 0 -1 -1 4.0065 5 1 0 0 -1 1.7975 6 1 0 1 -1 3.2135 7 1 -1 -1 0 3.2320 8 1 -1 0 0 2.4522 9 1 -1 1 0 1.6834 10 1 0 -1 0 1.2538 11 1 0 1 0 1.2538 12 1 -1 -1 1 3.9683 13 1 -1 0 1 3.9445 14 1 -1 1 1 4.6448 15 1 0 -1 1 3.2135 16 1 0 0 1 1.7975 17 1 0 1 1 4.0065 18 1 1 1 1 6.6627 19 1 1 0 1 3.9339 20 1 1 -1 1 4.6919 21 1 1 1 0 3.2320 22 1 1 0 0 2.4522 23 1 1 -1 0 1.6834 24 1 1 1 -1 3.9683 25 1 1 0 -1 3.9445 26 1 1 -1 -1 4.6448 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3942 atoms have been selected out of 4016 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 684 228 228 0.00 3 C003 has 87 29 29 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 498 166 166 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1725 575 575 0.00 12 C012 has 126 42 42 0.00 13 C013 has 486 162 162 0.00 14 C014 has 96 32 32 0.00 Total of13441 atoms and 4472 groups and 4467 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4016 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1327 Number of atoms = 4016 Number of groups = 1332 Number of bonds = 4009 Number of angles = 1431 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1329 Number of HB donors = 2636 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1327 Number of atoms = 4016 Number of groups = 1332 Number of bonds = 4009 Number of angles = 1431 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1329 Number of HB donors = 2636 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.298" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1327" Evaluating: 1327-7 Parameter: NUMWAT <- "1320" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1320" Comparing "1081" and "1320". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.298" Parameter: BOX -> "34.298" Parameter: BOX -> "34.298" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.29800 B = 34.29800 C = 34.29800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6643 2 1 -1 0 -1 3.9311 3 1 -1 1 -1 4.6885 4 1 0 -1 -1 4.0037 5 1 0 0 -1 1.7956 6 1 0 1 -1 3.2107 7 1 -1 -1 0 3.2292 8 1 -1 0 0 2.4517 9 1 -1 1 0 1.6819 10 1 0 -1 0 1.2532 11 1 0 1 0 1.2532 12 1 -1 -1 1 3.9649 13 1 -1 0 1 3.9417 14 1 -1 1 1 4.6418 15 1 0 -1 1 3.2107 16 1 0 0 1 1.7956 17 1 0 1 1 4.0037 18 1 1 1 1 6.6643 19 1 1 0 1 3.9311 20 1 1 -1 1 4.6885 21 1 1 1 0 3.2292 22 1 1 0 0 2.4517 23 1 1 -1 0 1.6819 24 1 1 1 -1 3.9649 25 1 1 0 -1 3.9417 26 1 1 -1 -1 4.6418 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3942 atoms have been selected out of 4016 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 684 228 228 0.00 3 C003 has 87 29 29 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 498 166 166 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1728 576 576 0.00 12 C012 has 126 42 42 0.00 13 C013 has 486 162 162 0.00 14 C014 has 96 32 32 0.00 Total of13444 atoms and 4473 groups and 4468 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4016 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1327 Number of atoms = 4016 Number of groups = 1332 Number of bonds = 4009 Number of angles = 1431 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1329 Number of HB donors = 2636 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1327 Number of atoms = 4016 Number of groups = 1332 Number of bonds = 4009 Number of angles = 1431 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1329 Number of HB donors = 2636 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.296" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1327" Evaluating: 1327-7 Parameter: NUMWAT <- "1320" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1320" Comparing "1081" and "1320". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.296" Parameter: BOX -> "34.296" Parameter: BOX -> "34.296" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.29600 B = 34.29600 C = 34.29600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6660 2 1 -1 0 -1 3.9283 3 1 -1 1 -1 4.6851 4 1 0 -1 -1 4.0010 5 1 0 0 -1 1.7937 6 1 0 1 -1 3.2080 7 1 -1 -1 0 3.2265 8 1 -1 0 0 2.4512 9 1 -1 1 0 1.6804 10 1 0 -1 0 1.2526 11 1 0 1 0 1.2526 12 1 -1 -1 1 3.9614 13 1 -1 0 1 3.9389 14 1 -1 1 1 4.6389 15 1 0 -1 1 3.2080 16 1 0 0 1 1.7937 17 1 0 1 1 4.0010 18 1 1 1 1 6.6660 19 1 1 0 1 3.9283 20 1 1 -1 1 4.6851 21 1 1 1 0 3.2265 22 1 1 0 0 2.4512 23 1 1 -1 0 1.6804 24 1 1 1 -1 3.9614 25 1 1 0 -1 3.9389 26 1 1 -1 -1 4.6389 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3942 atoms have been selected out of 4016 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 684 228 228 0.00 3 C003 has 87 29 29 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 501 167 167 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1728 576 576 0.00 12 C012 has 126 42 42 0.00 13 C013 has 486 162 162 0.00 14 C014 has 96 32 32 0.00 Total of13447 atoms and 4474 groups and 4469 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4016 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1327 Number of atoms = 4016 Number of groups = 1332 Number of bonds = 4009 Number of angles = 1431 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1329 Number of HB donors = 2636 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1327 Number of atoms = 4016 Number of groups = 1332 Number of bonds = 4009 Number of angles = 1431 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1329 Number of HB donors = 2636 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.294" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1327" Evaluating: 1327-7 Parameter: NUMWAT <- "1320" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1320" Comparing "1081" and "1320". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.294" Parameter: BOX -> "34.294" Parameter: BOX -> "34.294" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.29400 B = 34.29400 C = 34.29400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6677 2 1 -1 0 -1 3.9256 3 1 -1 1 -1 4.6816 4 1 0 -1 -1 3.9982 5 1 0 0 -1 1.7918 6 1 0 1 -1 3.2052 7 1 -1 -1 0 3.2237 8 1 -1 0 0 2.4508 9 1 -1 1 0 1.6788 10 1 0 -1 0 1.2519 11 1 0 1 0 1.2519 12 1 -1 -1 1 3.9580 13 1 -1 0 1 3.9361 14 1 -1 1 1 4.6359 15 1 0 -1 1 3.2052 16 1 0 0 1 1.7918 17 1 0 1 1 3.9982 18 1 1 1 1 6.6677 19 1 1 0 1 3.9256 20 1 1 -1 1 4.6816 21 1 1 1 0 3.2237 22 1 1 0 0 2.4508 23 1 1 -1 0 1.6788 24 1 1 1 -1 3.9580 25 1 1 0 -1 3.9361 26 1 1 -1 -1 4.6359 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3942 atoms have been selected out of 4016 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 684 228 228 0.00 3 C003 has 87 29 29 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 504 168 168 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1728 576 576 0.00 12 C012 has 126 42 42 0.00 13 C013 has 486 162 162 0.00 14 C014 has 96 32 32 0.00 Total of13453 atoms and 4476 groups and 4471 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4016 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1327 Number of atoms = 4016 Number of groups = 1332 Number of bonds = 4009 Number of angles = 1431 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1329 Number of HB donors = 2636 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1327 Number of atoms = 4016 Number of groups = 1332 Number of bonds = 4009 Number of angles = 1431 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1329 Number of HB donors = 2636 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.292" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1327" Evaluating: 1327-7 Parameter: NUMWAT <- "1320" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1320" Comparing "1081" and "1320". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.292" Parameter: BOX -> "34.292" Parameter: BOX -> "34.292" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.29200 B = 34.29200 C = 34.29200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6694 2 1 -1 0 -1 3.9228 3 1 -1 1 -1 4.6782 4 1 0 -1 -1 3.9954 5 1 0 0 -1 1.7899 6 1 0 1 -1 3.2025 7 1 -1 -1 0 3.2210 8 1 -1 0 0 2.4503 9 1 -1 1 0 1.6773 10 1 0 -1 0 1.2513 11 1 0 1 0 1.2513 12 1 -1 -1 1 3.9545 13 1 -1 0 1 3.9334 14 1 -1 1 1 4.6330 15 1 0 -1 1 3.2025 16 1 0 0 1 1.7899 17 1 0 1 1 3.9954 18 1 1 1 1 6.6694 19 1 1 0 1 3.9228 20 1 1 -1 1 4.6782 21 1 1 1 0 3.2210 22 1 1 0 0 2.4503 23 1 1 -1 0 1.6773 24 1 1 1 -1 3.9545 25 1 1 0 -1 3.9334 26 1 1 -1 -1 4.6330 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3942 atoms have been selected out of 4016 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 684 228 228 0.00 3 C003 has 87 29 29 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 504 168 168 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1817 604 604 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1728 576 576 0.00 12 C012 has 126 42 42 0.00 13 C013 has 486 162 162 0.00 14 C014 has 96 32 32 0.00 Total of13459 atoms and 4478 groups and 4473 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4016 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1327 Number of atoms = 4016 Number of groups = 1332 Number of bonds = 4009 Number of angles = 1431 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1329 Number of HB donors = 2636 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1327 Number of atoms = 4016 Number of groups = 1332 Number of bonds = 4009 Number of angles = 1431 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1329 Number of HB donors = 2636 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.29" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1327" Evaluating: 1327-7 Parameter: NUMWAT <- "1320" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1320" Comparing "1081" and "1320". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.29" Parameter: BOX -> "34.29" Parameter: BOX -> "34.29" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.29000 B = 34.29000 C = 34.29000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6711 2 1 -1 0 -1 3.9200 3 1 -1 1 -1 4.6747 4 1 0 -1 -1 3.9927 5 1 0 0 -1 1.7880 6 1 0 1 -1 3.1997 7 1 -1 -1 0 3.2182 8 1 -1 0 0 2.4498 9 1 -1 1 0 1.6758 10 1 0 -1 0 1.2507 11 1 0 1 0 1.2507 12 1 -1 -1 1 3.9511 13 1 -1 0 1 3.9306 14 1 -1 1 1 4.6300 15 1 0 -1 1 3.1997 16 1 0 0 1 1.7880 17 1 0 1 1 3.9927 18 1 1 1 1 6.6711 19 1 1 0 1 3.9200 20 1 1 -1 1 4.6747 21 1 1 1 0 3.2182 22 1 1 0 0 2.4498 23 1 1 -1 0 1.6758 24 1 1 1 -1 3.9511 25 1 1 0 -1 3.9306 26 1 1 -1 -1 4.6300 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3942 atoms have been selected out of 4016 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 684 228 228 0.00 3 C003 has 87 29 29 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 504 168 168 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1817 604 604 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1728 576 576 0.00 12 C012 has 126 42 42 0.00 13 C013 has 486 162 162 0.00 14 C014 has 99 33 33 0.00 Total of13462 atoms and 4479 groups and 4474 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4016 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1327 Number of atoms = 4016 Number of groups = 1332 Number of bonds = 4009 Number of angles = 1431 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1329 Number of HB donors = 2636 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1327 Number of atoms = 4016 Number of groups = 1332 Number of bonds = 4009 Number of angles = 1431 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1329 Number of HB donors = 2636 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.288" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1327" Evaluating: 1327-7 Parameter: NUMWAT <- "1320" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1320" Comparing "1081" and "1320". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.288" Parameter: BOX -> "34.288" Parameter: BOX -> "34.288" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.28800 B = 34.28800 C = 34.28800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6728 2 1 -1 0 -1 3.9172 3 1 -1 1 -1 4.6713 4 1 0 -1 -1 3.9899 5 1 0 0 -1 1.7860 6 1 0 1 -1 3.1970 7 1 -1 -1 0 3.2155 8 1 -1 0 0 2.4493 9 1 -1 1 0 1.6743 10 1 0 -1 0 1.2501 11 1 0 1 0 1.2501 12 1 -1 -1 1 3.9476 13 1 -1 0 1 3.9278 14 1 -1 1 1 4.6271 15 1 0 -1 1 3.1970 16 1 0 0 1 1.7860 17 1 0 1 1 3.9899 18 1 1 1 1 6.6728 19 1 1 0 1 3.9172 20 1 1 -1 1 4.6713 21 1 1 1 0 3.2155 22 1 1 0 0 2.4493 23 1 1 -1 0 1.6743 24 1 1 1 -1 3.9476 25 1 1 0 -1 3.9278 26 1 1 -1 -1 4.6271 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3942 atoms have been selected out of 4016 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 684 228 228 0.00 3 C003 has 87 29 29 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 504 168 168 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1817 604 604 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1728 576 576 0.00 12 C012 has 126 42 42 0.00 13 C013 has 486 162 162 0.00 14 C014 has 99 33 33 0.00 Total of13462 atoms and 4479 groups and 4474 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4016 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1327 Number of atoms = 4016 Number of groups = 1332 Number of bonds = 4009 Number of angles = 1431 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1329 Number of HB donors = 2636 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1327 Number of atoms = 4016 Number of groups = 1332 Number of bonds = 4009 Number of angles = 1431 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1329 Number of HB donors = 2636 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.286" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1327" Evaluating: 1327-7 Parameter: NUMWAT <- "1320" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1320" Comparing "1081" and "1320". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.286" Parameter: BOX -> "34.286" Parameter: BOX -> "34.286" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.28600 B = 34.28600 C = 34.28600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6745 2 1 -1 0 -1 3.9145 3 1 -1 1 -1 4.6679 4 1 0 -1 -1 3.9871 5 1 0 0 -1 1.7841 6 1 0 1 -1 3.1942 7 1 -1 -1 0 3.2128 8 1 -1 0 0 2.4488 9 1 -1 1 0 1.6728 10 1 0 -1 0 1.2494 11 1 0 1 0 1.2494 12 1 -1 -1 1 3.9442 13 1 -1 0 1 3.9251 14 1 -1 1 1 4.6241 15 1 0 -1 1 3.1942 16 1 0 0 1 1.7841 17 1 0 1 1 3.9871 18 1 1 1 1 6.6745 19 1 1 0 1 3.9145 20 1 1 -1 1 4.6679 21 1 1 1 0 3.2128 22 1 1 0 0 2.4488 23 1 1 -1 0 1.6728 24 1 1 1 -1 3.9442 25 1 1 0 -1 3.9251 26 1 1 -1 -1 4.6241 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3942 atoms have been selected out of 4016 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 684 228 228 0.00 3 C003 has 87 29 29 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 504 168 168 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1817 604 604 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1728 576 576 0.00 12 C012 has 126 42 42 0.00 13 C013 has 486 162 162 0.00 14 C014 has 99 33 33 0.00 Total of13462 atoms and 4479 groups and 4474 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4016 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1327 Number of atoms = 4016 Number of groups = 1332 Number of bonds = 4009 Number of angles = 1431 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1329 Number of HB donors = 2636 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1327 Number of atoms = 4016 Number of groups = 1332 Number of bonds = 4009 Number of angles = 1431 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1329 Number of HB donors = 2636 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.284" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1327" Evaluating: 1327-7 Parameter: NUMWAT <- "1320" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1320" Comparing "1081" and "1320". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.284" Parameter: BOX -> "34.284" Parameter: BOX -> "34.284" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.28400 B = 34.28400 C = 34.28400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6762 2 1 -1 0 -1 3.9117 3 1 -1 1 -1 4.6644 4 1 0 -1 -1 3.9844 5 1 0 0 -1 1.7822 6 1 0 1 -1 3.1915 7 1 -1 -1 0 3.2100 8 1 -1 0 0 2.4484 9 1 -1 1 0 1.6713 10 1 0 -1 0 1.2488 11 1 0 1 0 1.2488 12 1 -1 -1 1 3.9407 13 1 -1 0 1 3.9223 14 1 -1 1 1 4.6212 15 1 0 -1 1 3.1915 16 1 0 0 1 1.7822 17 1 0 1 1 3.9844 18 1 1 1 1 6.6762 19 1 1 0 1 3.9117 20 1 1 -1 1 4.6644 21 1 1 1 0 3.2100 22 1 1 0 0 2.4484 23 1 1 -1 0 1.6713 24 1 1 1 -1 3.9407 25 1 1 0 -1 3.9223 26 1 1 -1 -1 4.6212 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3942 atoms have been selected out of 4016 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 684 228 228 0.00 3 C003 has 90 30 30 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 504 168 168 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1817 604 604 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1728 576 576 0.00 12 C012 has 126 42 42 0.00 13 C013 has 486 162 162 0.00 14 C014 has 99 33 33 0.00 Total of13468 atoms and 4481 groups and 4476 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4016 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1327 Number of atoms = 4016 Number of groups = 1332 Number of bonds = 4009 Number of angles = 1431 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1329 Number of HB donors = 2636 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1327 Number of atoms = 4016 Number of groups = 1332 Number of bonds = 4009 Number of angles = 1431 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1329 Number of HB donors = 2636 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.282" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1327" Evaluating: 1327-7 Parameter: NUMWAT <- "1320" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1320" Comparing "1081" and "1320". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.282" Parameter: BOX -> "34.282" Parameter: BOX -> "34.282" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.28200 B = 34.28200 C = 34.28200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6778 2 1 -1 0 -1 3.9089 3 1 -1 1 -1 4.6610 4 1 0 -1 -1 3.9816 5 1 0 0 -1 1.7803 6 1 0 1 -1 3.1888 7 1 -1 -1 0 3.2073 8 1 -1 0 0 2.4479 9 1 -1 1 0 1.6698 10 1 0 -1 0 1.2482 11 1 0 1 0 1.2482 12 1 -1 -1 1 3.9373 13 1 -1 0 1 3.9195 14 1 -1 1 1 4.6182 15 1 0 -1 1 3.1888 16 1 0 0 1 1.7803 17 1 0 1 1 3.9816 18 1 1 1 1 6.6778 19 1 1 0 1 3.9089 20 1 1 -1 1 4.6610 21 1 1 1 0 3.2073 22 1 1 0 0 2.4479 23 1 1 -1 0 1.6698 24 1 1 1 -1 3.9373 25 1 1 0 -1 3.9195 26 1 1 -1 -1 4.6182 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3942 atoms have been selected out of 4016 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 525 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 684 228 228 0.00 3 C003 has 90 30 30 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 504 168 168 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1817 604 604 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1734 578 578 0.00 12 C012 has 126 42 42 0.00 13 C013 has 486 162 162 0.00 14 C014 has 99 33 33 0.00 Total of13474 atoms and 4483 groups and 4478 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 4016 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1326 Number of atoms = 4013 Number of groups = 1331 Number of bonds = 4006 Number of angles = 1430 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1328 Number of HB donors = 2634 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1326 Number of atoms = 4013 Number of groups = 1331 Number of bonds = 4006 Number of angles = 1430 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1328 Number of HB donors = 2634 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.28" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1326" Evaluating: 1326-7 Parameter: NUMWAT <- "1319" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1319" Comparing "1081" and "1319". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.28" Parameter: BOX -> "34.28" Parameter: BOX -> "34.28" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.28000 B = 34.28000 C = 34.28000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6795 2 1 -1 0 -1 3.9062 3 1 -1 1 -1 4.6576 4 1 0 -1 -1 3.9788 5 1 0 0 -1 1.7784 6 1 0 1 -1 3.1860 7 1 -1 -1 0 3.2045 8 1 -1 0 0 2.4474 9 1 -1 1 0 1.6683 10 1 0 -1 0 1.2476 11 1 0 1 0 1.2476 12 1 -1 -1 1 3.9338 13 1 -1 0 1 3.9167 14 1 -1 1 1 4.6153 15 1 0 -1 1 3.1860 16 1 0 0 1 1.7784 17 1 0 1 1 3.9788 18 1 1 1 1 6.6795 19 1 1 0 1 3.9062 20 1 1 -1 1 4.6576 21 1 1 1 0 3.2045 22 1 1 0 0 2.4474 23 1 1 -1 0 1.6683 24 1 1 1 -1 3.9338 25 1 1 0 -1 3.9167 26 1 1 -1 -1 4.6153 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3939 atoms have been selected out of 4013 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 684 228 228 0.00 3 C003 has 90 30 30 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 504 168 168 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1728 576 576 0.00 12 C012 has 126 42 42 0.00 13 C013 has 486 162 162 0.00 14 C014 has 99 33 33 0.00 Total of13462 atoms and 4479 groups and 4474 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4013 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1326 Number of atoms = 4013 Number of groups = 1331 Number of bonds = 4006 Number of angles = 1430 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1328 Number of HB donors = 2634 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1326 Number of atoms = 4013 Number of groups = 1331 Number of bonds = 4006 Number of angles = 1430 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1328 Number of HB donors = 2634 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.278" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1326" Evaluating: 1326-7 Parameter: NUMWAT <- "1319" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1319" Comparing "1081" and "1319". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.278" Parameter: BOX -> "34.278" Parameter: BOX -> "34.278" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.27800 B = 34.27800 C = 34.27800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6812 2 1 -1 0 -1 3.9034 3 1 -1 1 -1 4.6541 4 1 0 -1 -1 3.9760 5 1 0 0 -1 1.7765 6 1 0 1 -1 3.1833 7 1 -1 -1 0 3.2018 8 1 -1 0 0 2.4470 9 1 -1 1 0 1.6668 10 1 0 -1 0 1.2470 11 1 0 1 0 1.2470 12 1 -1 -1 1 3.9304 13 1 -1 0 1 3.9140 14 1 -1 1 1 4.6123 15 1 0 -1 1 3.1833 16 1 0 0 1 1.7765 17 1 0 1 1 3.9760 18 1 1 1 1 6.6812 19 1 1 0 1 3.9034 20 1 1 -1 1 4.6541 21 1 1 1 0 3.2018 22 1 1 0 0 2.4470 23 1 1 -1 0 1.6668 24 1 1 1 -1 3.9304 25 1 1 0 -1 3.9140 26 1 1 -1 -1 4.6123 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3939 atoms have been selected out of 4013 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 684 228 228 0.00 3 C003 has 90 30 30 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1647 549 549 0.00 6 C006 has 504 168 168 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1728 576 576 0.00 12 C012 has 126 42 42 0.00 13 C013 has 486 162 162 0.00 14 C014 has 99 33 33 0.00 Total of13465 atoms and 4480 groups and 4475 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4013 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1326 Number of atoms = 4013 Number of groups = 1331 Number of bonds = 4006 Number of angles = 1430 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1328 Number of HB donors = 2634 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1326 Number of atoms = 4013 Number of groups = 1331 Number of bonds = 4006 Number of angles = 1430 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1328 Number of HB donors = 2634 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.276" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1326" Evaluating: 1326-7 Parameter: NUMWAT <- "1319" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1319" Comparing "1081" and "1319". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.276" Parameter: BOX -> "34.276" Parameter: BOX -> "34.276" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.27600 B = 34.27600 C = 34.27600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6829 2 1 -1 0 -1 3.9006 3 1 -1 1 -1 4.6507 4 1 0 -1 -1 3.9733 5 1 0 0 -1 1.7746 6 1 0 1 -1 3.1805 7 1 -1 -1 0 3.1990 8 1 -1 0 0 2.4465 9 1 -1 1 0 1.6653 10 1 0 -1 0 1.2464 11 1 0 1 0 1.2464 12 1 -1 -1 1 3.9269 13 1 -1 0 1 3.9112 14 1 -1 1 1 4.6094 15 1 0 -1 1 3.1805 16 1 0 0 1 1.7746 17 1 0 1 1 3.9733 18 1 1 1 1 6.6829 19 1 1 0 1 3.9006 20 1 1 -1 1 4.6507 21 1 1 1 0 3.1990 22 1 1 0 0 2.4465 23 1 1 -1 0 1.6653 24 1 1 1 -1 3.9269 25 1 1 0 -1 3.9112 26 1 1 -1 -1 4.6094 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3939 atoms have been selected out of 4013 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 684 228 228 0.00 3 C003 has 90 30 30 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1647 549 549 0.00 6 C006 has 504 168 168 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1728 576 576 0.00 12 C012 has 126 42 42 0.00 13 C013 has 486 162 162 0.00 14 C014 has 99 33 33 0.00 Total of13465 atoms and 4480 groups and 4475 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4013 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1326 Number of atoms = 4013 Number of groups = 1331 Number of bonds = 4006 Number of angles = 1430 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1328 Number of HB donors = 2634 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1326 Number of atoms = 4013 Number of groups = 1331 Number of bonds = 4006 Number of angles = 1430 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1328 Number of HB donors = 2634 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.274" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1326" Evaluating: 1326-7 Parameter: NUMWAT <- "1319" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1319" Comparing "1081" and "1319". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.274" Parameter: BOX -> "34.274" Parameter: BOX -> "34.274" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.27400 B = 34.27400 C = 34.27400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6846 2 1 -1 0 -1 3.8978 3 1 -1 1 -1 4.6472 4 1 0 -1 -1 3.9705 5 1 0 0 -1 1.7727 6 1 0 1 -1 3.1778 7 1 -1 -1 0 3.1963 8 1 -1 0 0 2.4460 9 1 -1 1 0 1.6638 10 1 0 -1 0 1.2458 11 1 0 1 0 1.2458 12 1 -1 -1 1 3.9235 13 1 -1 0 1 3.9084 14 1 -1 1 1 4.6064 15 1 0 -1 1 3.1778 16 1 0 0 1 1.7727 17 1 0 1 1 3.9705 18 1 1 1 1 6.6846 19 1 1 0 1 3.8978 20 1 1 -1 1 4.6472 21 1 1 1 0 3.1963 22 1 1 0 0 2.4460 23 1 1 -1 0 1.6638 24 1 1 1 -1 3.9235 25 1 1 0 -1 3.9084 26 1 1 -1 -1 4.6064 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3939 atoms have been selected out of 4013 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 684 228 228 0.00 3 C003 has 90 30 30 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1647 549 549 0.00 6 C006 has 504 168 168 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1728 576 576 0.00 12 C012 has 126 42 42 0.00 13 C013 has 486 162 162 0.00 14 C014 has 99 33 33 0.00 Total of13465 atoms and 4480 groups and 4475 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4013 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1326 Number of atoms = 4013 Number of groups = 1331 Number of bonds = 4006 Number of angles = 1430 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1328 Number of HB donors = 2634 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1326 Number of atoms = 4013 Number of groups = 1331 Number of bonds = 4006 Number of angles = 1430 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1328 Number of HB donors = 2634 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.272" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1326" Evaluating: 1326-7 Parameter: NUMWAT <- "1319" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1319" Comparing "1081" and "1319". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.272" Parameter: BOX -> "34.272" Parameter: BOX -> "34.272" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.27200 B = 34.27200 C = 34.27200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6863 2 1 -1 0 -1 3.8951 3 1 -1 1 -1 4.6438 4 1 0 -1 -1 3.9677 5 1 0 0 -1 1.7708 6 1 0 1 -1 3.1750 7 1 -1 -1 0 3.1936 8 1 -1 0 0 2.4456 9 1 -1 1 0 1.6623 10 1 0 -1 0 1.2452 11 1 0 1 0 1.2452 12 1 -1 -1 1 3.9200 13 1 -1 0 1 3.9056 14 1 -1 1 1 4.6035 15 1 0 -1 1 3.1750 16 1 0 0 1 1.7708 17 1 0 1 1 3.9677 18 1 1 1 1 6.6863 19 1 1 0 1 3.8951 20 1 1 -1 1 4.6438 21 1 1 1 0 3.1936 22 1 1 0 0 2.4456 23 1 1 -1 0 1.6623 24 1 1 1 -1 3.9200 25 1 1 0 -1 3.9056 26 1 1 -1 -1 4.6035 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3939 atoms have been selected out of 4013 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 595 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1267 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 708 236 236 0.00 3 C003 has 93 31 31 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1647 549 549 0.00 6 C006 has 504 168 168 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1808 601 601 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1728 576 576 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 99 33 33 0.00 Total of13471 atoms and 4482 groups and 4477 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 4013 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1324 Number of atoms = 4007 Number of groups = 1329 Number of bonds = 4000 Number of angles = 1428 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1326 Number of HB donors = 2630 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1324 Number of atoms = 4007 Number of groups = 1329 Number of bonds = 4000 Number of angles = 1428 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1326 Number of HB donors = 2630 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.27" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1324" Evaluating: 1324-7 Parameter: NUMWAT <- "1317" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1317" Comparing "1081" and "1317". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.27" Parameter: BOX -> "34.27" Parameter: BOX -> "34.27" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.27000 B = 34.27000 C = 34.27000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6880 2 1 -1 0 -1 3.8923 3 1 -1 1 -1 4.6404 4 1 0 -1 -1 3.9650 5 1 0 0 -1 1.7689 6 1 0 1 -1 3.1723 7 1 -1 -1 0 3.1908 8 1 -1 0 0 2.4451 9 1 -1 1 0 1.6608 10 1 0 -1 0 1.2446 11 1 0 1 0 1.2446 12 1 -1 -1 1 3.9166 13 1 -1 0 1 3.9029 14 1 -1 1 1 4.6005 15 1 0 -1 1 3.1723 16 1 0 0 1 1.7689 17 1 0 1 1 3.9650 18 1 1 1 1 6.6880 19 1 1 0 1 3.8923 20 1 1 -1 1 4.6404 21 1 1 1 0 3.1908 22 1 1 0 0 2.4451 23 1 1 -1 0 1.6608 24 1 1 1 -1 3.9166 25 1 1 0 -1 3.9029 26 1 1 -1 -1 4.6005 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3933 atoms have been selected out of 4007 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 681 227 227 0.00 3 C003 has 93 31 31 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 504 168 168 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1808 601 601 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1722 574 574 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 99 33 33 0.00 Total of13426 atoms and 4467 groups and 4462 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4007 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1324 Number of atoms = 4007 Number of groups = 1329 Number of bonds = 4000 Number of angles = 1428 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1326 Number of HB donors = 2630 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1324 Number of atoms = 4007 Number of groups = 1329 Number of bonds = 4000 Number of angles = 1428 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1326 Number of HB donors = 2630 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.268" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1324" Evaluating: 1324-7 Parameter: NUMWAT <- "1317" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1317" Comparing "1081" and "1317". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.268" Parameter: BOX -> "34.268" Parameter: BOX -> "34.268" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.26800 B = 34.26800 C = 34.26800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6897 2 1 -1 0 -1 3.8895 3 1 -1 1 -1 4.6369 4 1 0 -1 -1 3.9622 5 1 0 0 -1 1.7670 6 1 0 1 -1 3.1695 7 1 -1 -1 0 3.1881 8 1 -1 0 0 2.4446 9 1 -1 1 0 1.6593 10 1 0 -1 0 1.2440 11 1 0 1 0 1.2440 12 1 -1 -1 1 3.9131 13 1 -1 0 1 3.9001 14 1 -1 1 1 4.5976 15 1 0 -1 1 3.1695 16 1 0 0 1 1.7670 17 1 0 1 1 3.9622 18 1 1 1 1 6.6897 19 1 1 0 1 3.8895 20 1 1 -1 1 4.6369 21 1 1 1 0 3.1881 22 1 1 0 0 2.4446 23 1 1 -1 0 1.6593 24 1 1 1 -1 3.9131 25 1 1 0 -1 3.9001 26 1 1 -1 -1 4.5976 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3933 atoms have been selected out of 4007 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 681 227 227 0.00 3 C003 has 93 31 31 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 504 168 168 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1808 601 601 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1722 574 574 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 99 33 33 0.00 Total of13426 atoms and 4467 groups and 4462 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4007 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1324 Number of atoms = 4007 Number of groups = 1329 Number of bonds = 4000 Number of angles = 1428 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1326 Number of HB donors = 2630 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1324 Number of atoms = 4007 Number of groups = 1329 Number of bonds = 4000 Number of angles = 1428 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1326 Number of HB donors = 2630 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.266" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1324" Evaluating: 1324-7 Parameter: NUMWAT <- "1317" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1317" Comparing "1081" and "1317". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.266" Parameter: BOX -> "34.266" Parameter: BOX -> "34.266" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.26600 B = 34.26600 C = 34.26600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6914 2 1 -1 0 -1 3.8867 3 1 -1 1 -1 4.6335 4 1 0 -1 -1 3.9594 5 1 0 0 -1 1.7651 6 1 0 1 -1 3.1668 7 1 -1 -1 0 3.1853 8 1 -1 0 0 2.4442 9 1 -1 1 0 1.6579 10 1 0 -1 0 1.2434 11 1 0 1 0 1.2434 12 1 -1 -1 1 3.9097 13 1 -1 0 1 3.8973 14 1 -1 1 1 4.5946 15 1 0 -1 1 3.1668 16 1 0 0 1 1.7651 17 1 0 1 1 3.9594 18 1 1 1 1 6.6914 19 1 1 0 1 3.8867 20 1 1 -1 1 4.6335 21 1 1 1 0 3.1853 22 1 1 0 0 2.4442 23 1 1 -1 0 1.6579 24 1 1 1 -1 3.9097 25 1 1 0 -1 3.8973 26 1 1 -1 -1 4.5946 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3933 atoms have been selected out of 4007 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 681 227 227 0.00 3 C003 has 93 31 31 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 504 168 168 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1808 601 601 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1722 574 574 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 99 33 33 0.00 Total of13426 atoms and 4467 groups and 4462 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4007 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1324 Number of atoms = 4007 Number of groups = 1329 Number of bonds = 4000 Number of angles = 1428 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1326 Number of HB donors = 2630 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1324 Number of atoms = 4007 Number of groups = 1329 Number of bonds = 4000 Number of angles = 1428 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1326 Number of HB donors = 2630 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.264" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1324" Evaluating: 1324-7 Parameter: NUMWAT <- "1317" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1317" Comparing "1081" and "1317". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.264" Parameter: BOX -> "34.264" Parameter: BOX -> "34.264" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.26400 B = 34.26400 C = 34.26400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6931 2 1 -1 0 -1 3.8840 3 1 -1 1 -1 4.6301 4 1 0 -1 -1 3.9567 5 1 0 0 -1 1.7632 6 1 0 1 -1 3.1640 7 1 -1 -1 0 3.1826 8 1 -1 0 0 2.4437 9 1 -1 1 0 1.6564 10 1 0 -1 0 1.2429 11 1 0 1 0 1.2429 12 1 -1 -1 1 3.9062 13 1 -1 0 1 3.8946 14 1 -1 1 1 4.5917 15 1 0 -1 1 3.1640 16 1 0 0 1 1.7632 17 1 0 1 1 3.9567 18 1 1 1 1 6.6931 19 1 1 0 1 3.8840 20 1 1 -1 1 4.6301 21 1 1 1 0 3.1826 22 1 1 0 0 2.4437 23 1 1 -1 0 1.6564 24 1 1 1 -1 3.9062 25 1 1 0 -1 3.8946 26 1 1 -1 -1 4.5917 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3933 atoms have been selected out of 4007 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 681 227 227 0.00 3 C003 has 93 31 31 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 507 169 169 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1811 602 602 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1722 574 574 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13438 atoms and 4471 groups and 4466 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4007 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1324 Number of atoms = 4007 Number of groups = 1329 Number of bonds = 4000 Number of angles = 1428 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1326 Number of HB donors = 2630 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1324 Number of atoms = 4007 Number of groups = 1329 Number of bonds = 4000 Number of angles = 1428 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1326 Number of HB donors = 2630 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.262" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1324" Evaluating: 1324-7 Parameter: NUMWAT <- "1317" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1317" Comparing "1081" and "1317". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.262" Parameter: BOX -> "34.262" Parameter: BOX -> "34.262" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.26200 B = 34.26200 C = 34.26200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6948 2 1 -1 0 -1 3.8812 3 1 -1 1 -1 4.6266 4 1 0 -1 -1 3.9539 5 1 0 0 -1 1.7612 6 1 0 1 -1 3.1613 7 1 -1 -1 0 3.1798 8 1 -1 0 0 2.4433 9 1 -1 1 0 1.6549 10 1 0 -1 0 1.2423 11 1 0 1 0 1.2423 12 1 -1 -1 1 3.9028 13 1 -1 0 1 3.8918 14 1 -1 1 1 4.5887 15 1 0 -1 1 3.1613 16 1 0 0 1 1.7612 17 1 0 1 1 3.9539 18 1 1 1 1 6.6948 19 1 1 0 1 3.8812 20 1 1 -1 1 4.6266 21 1 1 1 0 3.1798 22 1 1 0 0 2.4433 23 1 1 -1 0 1.6549 24 1 1 1 -1 3.9028 25 1 1 0 -1 3.8918 26 1 1 -1 -1 4.5887 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3933 atoms have been selected out of 4007 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 444 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1098 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 684 228 228 0.00 3 C003 has 93 31 31 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 495 165 165 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1719 573 573 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13420 atoms and 4465 groups and 4460 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 4007 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.26" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1322" Evaluating: 1322-7 Parameter: NUMWAT <- "1315" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1315" Comparing "1081" and "1315". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.26" Parameter: BOX -> "34.26" Parameter: BOX -> "34.26" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.26000 B = 34.26000 C = 34.26000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6965 2 1 -1 0 -1 3.8784 3 1 -1 1 -1 4.6232 4 1 0 -1 -1 3.9511 5 1 0 0 -1 1.7593 6 1 0 1 -1 3.1585 7 1 -1 -1 0 3.1771 8 1 -1 0 0 2.4428 9 1 -1 1 0 1.6535 10 1 0 -1 0 1.2417 11 1 0 1 0 1.2417 12 1 -1 -1 1 3.8993 13 1 -1 0 1 3.8890 14 1 -1 1 1 4.5858 15 1 0 -1 1 3.1585 16 1 0 0 1 1.7593 17 1 0 1 1 3.9511 18 1 1 1 1 6.6965 19 1 1 0 1 3.8784 20 1 1 -1 1 4.6232 21 1 1 1 0 3.1771 22 1 1 0 0 2.4428 23 1 1 -1 0 1.6535 24 1 1 1 -1 3.8993 25 1 1 0 -1 3.8890 26 1 1 -1 -1 4.5858 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3927 atoms have been selected out of 4001 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 681 227 227 0.00 3 C003 has 93 31 31 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 492 164 164 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1811 602 602 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1716 572 572 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13402 atoms and 4459 groups and 4454 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4001 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.258" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1322" Evaluating: 1322-7 Parameter: NUMWAT <- "1315" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1315" Comparing "1081" and "1315". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.258" Parameter: BOX -> "34.258" Parameter: BOX -> "34.258" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.25800 B = 34.25800 C = 34.25800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6982 2 1 -1 0 -1 3.8756 3 1 -1 1 -1 4.6197 4 1 0 -1 -1 3.9484 5 1 0 0 -1 1.7574 6 1 0 1 -1 3.1558 7 1 -1 -1 0 3.1744 8 1 -1 0 0 2.4424 9 1 -1 1 0 1.6520 10 1 0 -1 0 1.2411 11 1 0 1 0 1.2411 12 1 -1 -1 1 3.8959 13 1 -1 0 1 3.8862 14 1 -1 1 1 4.5828 15 1 0 -1 1 3.1558 16 1 0 0 1 1.7574 17 1 0 1 1 3.9484 18 1 1 1 1 6.6982 19 1 1 0 1 3.8756 20 1 1 -1 1 4.6197 21 1 1 1 0 3.1744 22 1 1 0 0 2.4424 23 1 1 -1 0 1.6520 24 1 1 1 -1 3.8959 25 1 1 0 -1 3.8862 26 1 1 -1 -1 4.5828 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3927 atoms have been selected out of 4001 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 681 227 227 0.00 3 C003 has 93 31 31 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 492 164 164 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1811 602 602 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1716 572 572 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13402 atoms and 4459 groups and 4454 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4001 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.256" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1322" Evaluating: 1322-7 Parameter: NUMWAT <- "1315" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1315" Comparing "1081" and "1315". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.256" Parameter: BOX -> "34.256" Parameter: BOX -> "34.256" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.25600 B = 34.25600 C = 34.25600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7000 2 1 -1 0 -1 3.8729 3 1 -1 1 -1 4.6163 4 1 0 -1 -1 3.9456 5 1 0 0 -1 1.7555 6 1 0 1 -1 3.1531 7 1 -1 -1 0 3.1716 8 1 -1 0 0 2.4419 9 1 -1 1 0 1.6505 10 1 0 -1 0 1.2406 11 1 0 1 0 1.2406 12 1 -1 -1 1 3.8924 13 1 -1 0 1 3.8835 14 1 -1 1 1 4.5799 15 1 0 -1 1 3.1531 16 1 0 0 1 1.7555 17 1 0 1 1 3.9456 18 1 1 1 1 6.7000 19 1 1 0 1 3.8729 20 1 1 -1 1 4.6163 21 1 1 1 0 3.1716 22 1 1 0 0 2.4419 23 1 1 -1 0 1.6505 24 1 1 1 -1 3.8924 25 1 1 0 -1 3.8835 26 1 1 -1 -1 4.5799 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3927 atoms have been selected out of 4001 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 681 227 227 0.00 3 C003 has 93 31 31 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 492 164 164 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1716 572 572 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 102 34 34 0.00 Total of13405 atoms and 4460 groups and 4455 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4001 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.254" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1322" Evaluating: 1322-7 Parameter: NUMWAT <- "1315" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1315" Comparing "1081" and "1315". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.254" Parameter: BOX -> "34.254" Parameter: BOX -> "34.254" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.25400 B = 34.25400 C = 34.25400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7017 2 1 -1 0 -1 3.8701 3 1 -1 1 -1 4.6129 4 1 0 -1 -1 3.9428 5 1 0 0 -1 1.7536 6 1 0 1 -1 3.1503 7 1 -1 -1 0 3.1689 8 1 -1 0 0 2.4415 9 1 -1 1 0 1.6491 10 1 0 -1 0 1.2400 11 1 0 1 0 1.2400 12 1 -1 -1 1 3.8890 13 1 -1 0 1 3.8807 14 1 -1 1 1 4.5770 15 1 0 -1 1 3.1503 16 1 0 0 1 1.7536 17 1 0 1 1 3.9428 18 1 1 1 1 6.7017 19 1 1 0 1 3.8701 20 1 1 -1 1 4.6129 21 1 1 1 0 3.1689 22 1 1 0 0 2.4415 23 1 1 -1 0 1.6491 24 1 1 1 -1 3.8890 25 1 1 0 -1 3.8807 26 1 1 -1 -1 4.5770 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3927 atoms have been selected out of 4001 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 681 227 227 0.00 3 C003 has 93 31 31 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 495 165 165 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1716 572 572 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 0.00 Total of13417 atoms and 4464 groups and 4459 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4001 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.252" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1322" Evaluating: 1322-7 Parameter: NUMWAT <- "1315" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1315" Comparing "1081" and "1315". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.252" Parameter: BOX -> "34.252" Parameter: BOX -> "34.252" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.25200 B = 34.25200 C = 34.25200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7034 2 1 -1 0 -1 3.8673 3 1 -1 1 -1 4.6094 4 1 0 -1 -1 3.9401 5 1 0 0 -1 1.7517 6 1 0 1 -1 3.1476 7 1 -1 -1 0 3.1661 8 1 -1 0 0 2.4410 9 1 -1 1 0 1.6476 10 1 0 -1 0 1.2394 11 1 0 1 0 1.2394 12 1 -1 -1 1 3.8855 13 1 -1 0 1 3.8779 14 1 -1 1 1 4.5740 15 1 0 -1 1 3.1476 16 1 0 0 1 1.7517 17 1 0 1 1 3.9401 18 1 1 1 1 6.7034 19 1 1 0 1 3.8673 20 1 1 -1 1 4.6094 21 1 1 1 0 3.1661 22 1 1 0 0 2.4410 23 1 1 -1 0 1.6476 24 1 1 1 -1 3.8855 25 1 1 0 -1 3.8779 26 1 1 -1 -1 4.5740 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3927 atoms have been selected out of 4001 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 681 227 227 0.00 3 C003 has 93 31 31 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 495 165 165 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1716 572 572 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 0.00 Total of13417 atoms and 4464 groups and 4459 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4001 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.25" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1322" Evaluating: 1322-7 Parameter: NUMWAT <- "1315" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1315" Comparing "1081" and "1315". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.25" Parameter: BOX -> "34.25" Parameter: BOX -> "34.25" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.25000 B = 34.25000 C = 34.25000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7051 2 1 -1 0 -1 3.8646 3 1 -1 1 -1 4.6060 4 1 0 -1 -1 3.9373 5 1 0 0 -1 1.7498 6 1 0 1 -1 3.1448 7 1 -1 -1 0 3.1634 8 1 -1 0 0 2.4406 9 1 -1 1 0 1.6462 10 1 0 -1 0 1.2389 11 1 0 1 0 1.2389 12 1 -1 -1 1 3.8821 13 1 -1 0 1 3.8752 14 1 -1 1 1 4.5711 15 1 0 -1 1 3.1448 16 1 0 0 1 1.7498 17 1 0 1 1 3.9373 18 1 1 1 1 6.7051 19 1 1 0 1 3.8646 20 1 1 -1 1 4.6060 21 1 1 1 0 3.1634 22 1 1 0 0 2.4406 23 1 1 -1 0 1.6462 24 1 1 1 -1 3.8821 25 1 1 0 -1 3.8752 26 1 1 -1 -1 4.5711 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3927 atoms have been selected out of 4001 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 681 227 227 0.00 3 C003 has 93 31 31 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 495 165 165 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1722 574 574 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 0.00 Total of13423 atoms and 4466 groups and 4461 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4001 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.248" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1322" Evaluating: 1322-7 Parameter: NUMWAT <- "1315" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1315" Comparing "1081" and "1315". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.248" Parameter: BOX -> "34.248" Parameter: BOX -> "34.248" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.24800 B = 34.24800 C = 34.24800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7068 2 1 -1 0 -1 3.8618 3 1 -1 1 -1 4.6026 4 1 0 -1 -1 3.9345 5 1 0 0 -1 1.7479 6 1 0 1 -1 3.1421 7 1 -1 -1 0 3.1607 8 1 -1 0 0 2.4401 9 1 -1 1 0 1.6447 10 1 0 -1 0 1.2383 11 1 0 1 0 1.2383 12 1 -1 -1 1 3.8786 13 1 -1 0 1 3.8724 14 1 -1 1 1 4.5681 15 1 0 -1 1 3.1421 16 1 0 0 1 1.7479 17 1 0 1 1 3.9345 18 1 1 1 1 6.7068 19 1 1 0 1 3.8618 20 1 1 -1 1 4.6026 21 1 1 1 0 3.1607 22 1 1 0 0 2.4401 23 1 1 -1 0 1.6447 24 1 1 1 -1 3.8786 25 1 1 0 -1 3.8724 26 1 1 -1 -1 4.5681 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3927 atoms have been selected out of 4001 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 375 125 125 0.00 2 C002 has 681 227 227 0.00 3 C003 has 93 31 31 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 498 166 166 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1722 574 574 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 0.00 Total of13435 atoms and 4470 groups and 4465 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4001 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.246" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1322" Evaluating: 1322-7 Parameter: NUMWAT <- "1315" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1315" Comparing "1081" and "1315". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.246" Parameter: BOX -> "34.246" Parameter: BOX -> "34.246" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.24600 B = 34.24600 C = 34.24600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7085 2 1 -1 0 -1 3.8590 3 1 -1 1 -1 4.5991 4 1 0 -1 -1 3.9318 5 1 0 0 -1 1.7460 6 1 0 1 -1 3.1393 7 1 -1 -1 0 3.1579 8 1 -1 0 0 2.4397 9 1 -1 1 0 1.6433 10 1 0 -1 0 1.2377 11 1 0 1 0 1.2377 12 1 -1 -1 1 3.8752 13 1 -1 0 1 3.8696 14 1 -1 1 1 4.5652 15 1 0 -1 1 3.1393 16 1 0 0 1 1.7460 17 1 0 1 1 3.9318 18 1 1 1 1 6.7085 19 1 1 0 1 3.8590 20 1 1 -1 1 4.5991 21 1 1 1 0 3.1579 22 1 1 0 0 2.4397 23 1 1 -1 0 1.6433 24 1 1 1 -1 3.8752 25 1 1 0 -1 3.8696 26 1 1 -1 -1 4.5652 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3927 atoms have been selected out of 4001 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 681 227 227 0.00 3 C003 has 93 31 31 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1722 574 574 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 0.00 Total of13441 atoms and 4472 groups and 4467 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4001 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.244" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1322" Evaluating: 1322-7 Parameter: NUMWAT <- "1315" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1315" Comparing "1081" and "1315". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.244" Parameter: BOX -> "34.244" Parameter: BOX -> "34.244" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.24400 B = 34.24400 C = 34.24400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7102 2 1 -1 0 -1 3.8562 3 1 -1 1 -1 4.5957 4 1 0 -1 -1 3.9290 5 1 0 0 -1 1.7441 6 1 0 1 -1 3.1366 7 1 -1 -1 0 3.1552 8 1 -1 0 0 2.4392 9 1 -1 1 0 1.6419 10 1 0 -1 0 1.2372 11 1 0 1 0 1.2372 12 1 -1 -1 1 3.8717 13 1 -1 0 1 3.8668 14 1 -1 1 1 4.5623 15 1 0 -1 1 3.1366 16 1 0 0 1 1.7441 17 1 0 1 1 3.9290 18 1 1 1 1 6.7102 19 1 1 0 1 3.8562 20 1 1 -1 1 4.5957 21 1 1 1 0 3.1552 22 1 1 0 0 2.4392 23 1 1 -1 0 1.6419 24 1 1 1 -1 3.8717 25 1 1 0 -1 3.8668 26 1 1 -1 -1 4.5623 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3927 atoms have been selected out of 4001 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 681 227 227 0.00 3 C003 has 93 31 31 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1722 574 574 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 0.00 Total of13441 atoms and 4472 groups and 4467 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4001 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.242" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1322" Evaluating: 1322-7 Parameter: NUMWAT <- "1315" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1315" Comparing "1081" and "1315". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.242" Parameter: BOX -> "34.242" Parameter: BOX -> "34.242" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.24200 B = 34.24200 C = 34.24200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7120 2 1 -1 0 -1 3.8535 3 1 -1 1 -1 4.5922 4 1 0 -1 -1 3.9262 5 1 0 0 -1 1.7422 6 1 0 1 -1 3.1338 7 1 -1 -1 0 3.1524 8 1 -1 0 0 2.4388 9 1 -1 1 0 1.6404 10 1 0 -1 0 1.2366 11 1 0 1 0 1.2366 12 1 -1 -1 1 3.8683 13 1 -1 0 1 3.8641 14 1 -1 1 1 4.5593 15 1 0 -1 1 3.1338 16 1 0 0 1 1.7422 17 1 0 1 1 3.9262 18 1 1 1 1 6.7120 19 1 1 0 1 3.8535 20 1 1 -1 1 4.5922 21 1 1 1 0 3.1524 22 1 1 0 0 2.4388 23 1 1 -1 0 1.6404 24 1 1 1 -1 3.8683 25 1 1 0 -1 3.8641 26 1 1 -1 -1 4.5593 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3927 atoms have been selected out of 4001 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 681 227 227 0.00 3 C003 has 93 31 31 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1722 574 574 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 0.00 Total of13444 atoms and 4473 groups and 4468 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4001 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.24" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1322" Evaluating: 1322-7 Parameter: NUMWAT <- "1315" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1315" Comparing "1081" and "1315". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.24" Parameter: BOX -> "34.24" Parameter: BOX -> "34.24" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.24000 B = 34.24000 C = 34.24000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7137 2 1 -1 0 -1 3.8507 3 1 -1 1 -1 4.5888 4 1 0 -1 -1 3.9235 5 1 0 0 -1 1.7403 6 1 0 1 -1 3.1311 7 1 -1 -1 0 3.1497 8 1 -1 0 0 2.4384 9 1 -1 1 0 1.6390 10 1 0 -1 0 1.2361 11 1 0 1 0 1.2361 12 1 -1 -1 1 3.8648 13 1 -1 0 1 3.8613 14 1 -1 1 1 4.5564 15 1 0 -1 1 3.1311 16 1 0 0 1 1.7403 17 1 0 1 1 3.9235 18 1 1 1 1 6.7137 19 1 1 0 1 3.8507 20 1 1 -1 1 4.5888 21 1 1 1 0 3.1497 22 1 1 0 0 2.4384 23 1 1 -1 0 1.6390 24 1 1 1 -1 3.8648 25 1 1 0 -1 3.8613 26 1 1 -1 -1 4.5564 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3927 atoms have been selected out of 4001 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 681 227 227 0.00 3 C003 has 93 31 31 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 504 168 168 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1722 574 574 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 0.00 Total of13447 atoms and 4474 groups and 4469 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4001 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.238" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1322" Evaluating: 1322-7 Parameter: NUMWAT <- "1315" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1315" Comparing "1081" and "1315". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.238" Parameter: BOX -> "34.238" Parameter: BOX -> "34.238" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.23800 B = 34.23800 C = 34.23800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7154 2 1 -1 0 -1 3.8479 3 1 -1 1 -1 4.5854 4 1 0 -1 -1 3.9207 5 1 0 0 -1 1.7384 6 1 0 1 -1 3.1284 7 1 -1 -1 0 3.1470 8 1 -1 0 0 2.4375 9 1 -1 1 0 1.6376 10 1 0 -1 0 1.2355 11 1 0 1 0 1.2355 12 1 -1 -1 1 3.8614 13 1 -1 0 1 3.8585 14 1 -1 1 1 4.5535 15 1 0 -1 1 3.1284 16 1 0 0 1 1.7384 17 1 0 1 1 3.9207 18 1 1 1 1 6.7154 19 1 1 0 1 3.8479 20 1 1 -1 1 4.5854 21 1 1 1 0 3.1470 22 1 1 0 0 2.4375 23 1 1 -1 0 1.6376 24 1 1 1 -1 3.8614 25 1 1 0 -1 3.8585 26 1 1 -1 -1 4.5535 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3927 atoms have been selected out of 4001 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 378 126 126 0.00 2 C002 has 681 227 227 0.00 3 C003 has 93 31 31 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1647 549 549 0.00 6 C006 has 504 168 168 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1817 604 604 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1722 574 574 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 0.00 Total of13453 atoms and 4476 groups and 4471 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4001 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.236" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1322" Evaluating: 1322-7 Parameter: NUMWAT <- "1315" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1315" Comparing "1081" and "1315". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.236" Parameter: BOX -> "34.236" Parameter: BOX -> "34.236" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.23600 B = 34.23600 C = 34.23600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7171 2 1 -1 0 -1 3.8452 3 1 -1 1 -1 4.5819 4 1 0 -1 -1 3.9179 5 1 0 0 -1 1.7365 6 1 0 1 -1 3.1256 7 1 -1 -1 0 3.1442 8 1 -1 0 0 2.4356 9 1 -1 1 0 1.6362 10 1 0 -1 0 1.2350 11 1 0 1 0 1.2350 12 1 -1 -1 1 3.8579 13 1 -1 0 1 3.8558 14 1 -1 1 1 4.5505 15 1 0 -1 1 3.1256 16 1 0 0 1 1.7365 17 1 0 1 1 3.9179 18 1 1 1 1 6.7171 19 1 1 0 1 3.8452 20 1 1 -1 1 4.5819 21 1 1 1 0 3.1442 22 1 1 0 0 2.4356 23 1 1 -1 0 1.6362 24 1 1 1 -1 3.8579 25 1 1 0 -1 3.8558 26 1 1 -1 -1 4.5505 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3927 atoms have been selected out of 4001 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 681 227 227 0.00 3 C003 has 93 31 31 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1647 549 549 0.00 6 C006 has 504 168 168 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1817 604 604 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1722 574 574 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 0.00 Total of13456 atoms and 4477 groups and 4472 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4001 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.234" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1322" Evaluating: 1322-7 Parameter: NUMWAT <- "1315" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1315" Comparing "1081" and "1315". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.234" Parameter: BOX -> "34.234" Parameter: BOX -> "34.234" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.23400 B = 34.23400 C = 34.23400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7188 2 1 -1 0 -1 3.8424 3 1 -1 1 -1 4.5785 4 1 0 -1 -1 3.9151 5 1 0 0 -1 1.7346 6 1 0 1 -1 3.1229 7 1 -1 -1 0 3.1415 8 1 -1 0 0 2.4336 9 1 -1 1 0 1.6347 10 1 0 -1 0 1.2345 11 1 0 1 0 1.2345 12 1 -1 -1 1 3.8545 13 1 -1 0 1 3.8530 14 1 -1 1 1 4.5476 15 1 0 -1 1 3.1229 16 1 0 0 1 1.7346 17 1 0 1 1 3.9151 18 1 1 1 1 6.7188 19 1 1 0 1 3.8424 20 1 1 -1 1 4.5785 21 1 1 1 0 3.1415 22 1 1 0 0 2.4336 23 1 1 -1 0 1.6347 24 1 1 1 -1 3.8545 25 1 1 0 -1 3.8530 26 1 1 -1 -1 4.5476 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3927 atoms have been selected out of 4001 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 681 227 227 0.00 3 C003 has 93 31 31 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1647 549 549 0.00 6 C006 has 504 168 168 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1817 604 604 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1722 574 574 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 0.00 Total of13456 atoms and 4477 groups and 4472 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4001 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.232" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1322" Evaluating: 1322-7 Parameter: NUMWAT <- "1315" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1315" Comparing "1081" and "1315". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.232" Parameter: BOX -> "34.232" Parameter: BOX -> "34.232" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.23200 B = 34.23200 C = 34.23200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7206 2 1 -1 0 -1 3.8396 3 1 -1 1 -1 4.5751 4 1 0 -1 -1 3.9124 5 1 0 0 -1 1.7327 6 1 0 1 -1 3.1201 7 1 -1 -1 0 3.1387 8 1 -1 0 0 2.4317 9 1 -1 1 0 1.6333 10 1 0 -1 0 1.2339 11 1 0 1 0 1.2339 12 1 -1 -1 1 3.8510 13 1 -1 0 1 3.8502 14 1 -1 1 1 4.5447 15 1 0 -1 1 3.1201 16 1 0 0 1 1.7327 17 1 0 1 1 3.9124 18 1 1 1 1 6.7206 19 1 1 0 1 3.8396 20 1 1 -1 1 4.5751 21 1 1 1 0 3.1387 22 1 1 0 0 2.4317 23 1 1 -1 0 1.6333 24 1 1 1 -1 3.8510 25 1 1 0 -1 3.8502 26 1 1 -1 -1 4.5447 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3927 atoms have been selected out of 4001 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 681 227 227 0.00 3 C003 has 93 31 31 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1647 549 549 0.00 6 C006 has 504 168 168 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1817 604 604 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1722 574 574 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 0.00 Total of13456 atoms and 4477 groups and 4472 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4001 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.23" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1322" Evaluating: 1322-7 Parameter: NUMWAT <- "1315" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1315" Comparing "1081" and "1315". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.23" Parameter: BOX -> "34.23" Parameter: BOX -> "34.23" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.23000 B = 34.23000 C = 34.23000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7223 2 1 -1 0 -1 3.8368 3 1 -1 1 -1 4.5716 4 1 0 -1 -1 3.9096 5 1 0 0 -1 1.7308 6 1 0 1 -1 3.1174 7 1 -1 -1 0 3.1360 8 1 -1 0 0 2.4298 9 1 -1 1 0 1.6319 10 1 0 -1 0 1.2334 11 1 0 1 0 1.2334 12 1 -1 -1 1 3.8476 13 1 -1 0 1 3.8474 14 1 -1 1 1 4.5417 15 1 0 -1 1 3.1174 16 1 0 0 1 1.7308 17 1 0 1 1 3.9096 18 1 1 1 1 6.7223 19 1 1 0 1 3.8368 20 1 1 -1 1 4.5716 21 1 1 1 0 3.1360 22 1 1 0 0 2.4298 23 1 1 -1 0 1.6319 24 1 1 1 -1 3.8476 25 1 1 0 -1 3.8474 26 1 1 -1 -1 4.5417 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3927 atoms have been selected out of 4001 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 681 227 227 0.00 3 C003 has 93 31 31 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1647 549 549 0.00 6 C006 has 504 168 168 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1817 604 604 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1722 574 574 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 0.00 Total of13456 atoms and 4477 groups and 4472 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4001 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.228" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1322" Evaluating: 1322-7 Parameter: NUMWAT <- "1315" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1315" Comparing "1081" and "1315". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.228" Parameter: BOX -> "34.228" Parameter: BOX -> "34.228" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.22800 B = 34.22800 C = 34.22800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7240 2 1 -1 0 -1 3.8341 3 1 -1 1 -1 4.5682 4 1 0 -1 -1 3.9068 5 1 0 0 -1 1.7289 6 1 0 1 -1 3.1146 7 1 -1 -1 0 3.1333 8 1 -1 0 0 2.4278 9 1 -1 1 0 1.6305 10 1 0 -1 0 1.2329 11 1 0 1 0 1.2329 12 1 -1 -1 1 3.8441 13 1 -1 0 1 3.8447 14 1 -1 1 1 4.5388 15 1 0 -1 1 3.1146 16 1 0 0 1 1.7289 17 1 0 1 1 3.9068 18 1 1 1 1 6.7240 19 1 1 0 1 3.8341 20 1 1 -1 1 4.5682 21 1 1 1 0 3.1333 22 1 1 0 0 2.4278 23 1 1 -1 0 1.6305 24 1 1 1 -1 3.8441 25 1 1 0 -1 3.8447 26 1 1 -1 -1 4.5388 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3927 atoms have been selected out of 4001 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 681 227 227 0.00 3 C003 has 93 31 31 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1647 549 549 0.00 6 C006 has 504 168 168 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1817 604 604 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1722 574 574 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 0.00 Total of13456 atoms and 4477 groups and 4472 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4001 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.226" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1322" Evaluating: 1322-7 Parameter: NUMWAT <- "1315" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1315" Comparing "1081" and "1315". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.226" Parameter: BOX -> "34.226" Parameter: BOX -> "34.226" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.22600 B = 34.22600 C = 34.22600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7257 2 1 -1 0 -1 3.8313 3 1 -1 1 -1 4.5647 4 1 0 -1 -1 3.9041 5 1 0 0 -1 1.7270 6 1 0 1 -1 3.1119 7 1 -1 -1 0 3.1305 8 1 -1 0 0 2.4259 9 1 -1 1 0 1.6291 10 1 0 -1 0 1.2323 11 1 0 1 0 1.2323 12 1 -1 -1 1 3.8407 13 1 -1 0 1 3.8419 14 1 -1 1 1 4.5359 15 1 0 -1 1 3.1119 16 1 0 0 1 1.7270 17 1 0 1 1 3.9041 18 1 1 1 1 6.7257 19 1 1 0 1 3.8313 20 1 1 -1 1 4.5647 21 1 1 1 0 3.1305 22 1 1 0 0 2.4259 23 1 1 -1 0 1.6291 24 1 1 1 -1 3.8407 25 1 1 0 -1 3.8419 26 1 1 -1 -1 4.5359 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3927 atoms have been selected out of 4001 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 681 227 227 0.00 3 C003 has 93 31 31 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1647 549 549 0.00 6 C006 has 504 168 168 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1817 604 604 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1725 575 575 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 0.00 Total of13462 atoms and 4479 groups and 4474 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 4001 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1322 Number of atoms = 4001 Number of groups = 1327 Number of bonds = 3994 Number of angles = 1426 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1324 Number of HB donors = 2626 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.224" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1322" Evaluating: 1322-7 Parameter: NUMWAT <- "1315" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1315" Comparing "1081" and "1315". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.224" Parameter: BOX -> "34.224" Parameter: BOX -> "34.224" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.22400 B = 34.22400 C = 34.22400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7275 2 1 -1 0 -1 3.8285 3 1 -1 1 -1 4.5613 4 1 0 -1 -1 3.9013 5 1 0 0 -1 1.7251 6 1 0 1 -1 3.1092 7 1 -1 -1 0 3.1278 8 1 -1 0 0 2.4240 9 1 -1 1 0 1.6277 10 1 0 -1 0 1.2318 11 1 0 1 0 1.2318 12 1 -1 -1 1 3.8372 13 1 -1 0 1 3.8391 14 1 -1 1 1 4.5329 15 1 0 -1 1 3.1092 16 1 0 0 1 1.7251 17 1 0 1 1 3.9013 18 1 1 1 1 6.7275 19 1 1 0 1 3.8285 20 1 1 -1 1 4.5613 21 1 1 1 0 3.1278 22 1 1 0 0 2.4240 23 1 1 -1 0 1.6277 24 1 1 1 -1 3.8372 25 1 1 0 -1 3.8391 26 1 1 -1 -1 4.5329 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3927 atoms have been selected out of 4001 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 151 OPERATED ON BY TRANSFORMATION C011 RESIDUE 806 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 384 128 128 0.00 2 C002 has 678 226 226 0.00 3 C003 has 93 31 31 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1650 550 550 0.00 6 C006 has 522 174 174 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1731 577 577 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 0.00 Total of13492 atoms and 4489 groups and 4484 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 4001 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1320 Number of atoms = 3995 Number of groups = 1325 Number of bonds = 3988 Number of angles = 1424 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1322 Number of HB donors = 2622 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1320 Number of atoms = 3995 Number of groups = 1325 Number of bonds = 3988 Number of angles = 1424 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1322 Number of HB donors = 2622 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.222" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1320" Evaluating: 1320-7 Parameter: NUMWAT <- "1313" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1313" Comparing "1081" and "1313". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.222" Parameter: BOX -> "34.222" Parameter: BOX -> "34.222" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.22200 B = 34.22200 C = 34.22200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7292 2 1 -1 0 -1 3.8258 3 1 -1 1 -1 4.5579 4 1 0 -1 -1 3.8985 5 1 0 0 -1 1.7232 6 1 0 1 -1 3.1064 7 1 -1 -1 0 3.1250 8 1 -1 0 0 2.4220 9 1 -1 1 0 1.6263 10 1 0 -1 0 1.2313 11 1 0 1 0 1.2313 12 1 -1 -1 1 3.8338 13 1 -1 0 1 3.8364 14 1 -1 1 1 4.5300 15 1 0 -1 1 3.1064 16 1 0 0 1 1.7232 17 1 0 1 1 3.8985 18 1 1 1 1 6.7292 19 1 1 0 1 3.8258 20 1 1 -1 1 4.5579 21 1 1 1 0 3.1250 22 1 1 0 0 2.4220 23 1 1 -1 0 1.6263 24 1 1 1 -1 3.8338 25 1 1 0 -1 3.8364 26 1 1 -1 -1 4.5300 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3921 atoms have been selected out of 3995 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 678 226 226 0.00 3 C003 has 93 31 31 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1725 575 575 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 0.00 Total of13450 atoms and 4475 groups and 4470 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3995 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1320 Number of atoms = 3995 Number of groups = 1325 Number of bonds = 3988 Number of angles = 1424 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1322 Number of HB donors = 2622 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1320 Number of atoms = 3995 Number of groups = 1325 Number of bonds = 3988 Number of angles = 1424 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1322 Number of HB donors = 2622 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.22" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1320" Evaluating: 1320-7 Parameter: NUMWAT <- "1313" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1313" Comparing "1081" and "1313". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.22" Parameter: BOX -> "34.22" Parameter: BOX -> "34.22" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.22000 B = 34.22000 C = 34.22000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7309 2 1 -1 0 -1 3.8230 3 1 -1 1 -1 4.5544 4 1 0 -1 -1 3.8958 5 1 0 0 -1 1.7213 6 1 0 1 -1 3.1037 7 1 -1 -1 0 3.1223 8 1 -1 0 0 2.4201 9 1 -1 1 0 1.6249 10 1 0 -1 0 1.2308 11 1 0 1 0 1.2308 12 1 -1 -1 1 3.8303 13 1 -1 0 1 3.8336 14 1 -1 1 1 4.5271 15 1 0 -1 1 3.1037 16 1 0 0 1 1.7213 17 1 0 1 1 3.8958 18 1 1 1 1 6.7309 19 1 1 0 1 3.8230 20 1 1 -1 1 4.5544 21 1 1 1 0 3.1223 22 1 1 0 0 2.4201 23 1 1 -1 0 1.6249 24 1 1 1 -1 3.8303 25 1 1 0 -1 3.8336 26 1 1 -1 -1 4.5271 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3921 atoms have been selected out of 3995 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 678 226 226 0.00 3 C003 has 93 31 31 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1725 575 575 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 0.00 Total of13450 atoms and 4475 groups and 4470 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3995 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1320 Number of atoms = 3995 Number of groups = 1325 Number of bonds = 3988 Number of angles = 1424 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1322 Number of HB donors = 2622 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1320 Number of atoms = 3995 Number of groups = 1325 Number of bonds = 3988 Number of angles = 1424 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1322 Number of HB donors = 2622 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.218" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1320" Evaluating: 1320-7 Parameter: NUMWAT <- "1313" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1313" Comparing "1081" and "1313". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.218" Parameter: BOX -> "34.218" Parameter: BOX -> "34.218" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.21800 B = 34.21800 C = 34.21800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7327 2 1 -1 0 -1 3.8202 3 1 -1 1 -1 4.5510 4 1 0 -1 -1 3.8930 5 1 0 0 -1 1.7194 6 1 0 1 -1 3.1009 7 1 -1 -1 0 3.1196 8 1 -1 0 0 2.4182 9 1 -1 1 0 1.6235 10 1 0 -1 0 1.2303 11 1 0 1 0 1.2303 12 1 -1 -1 1 3.8269 13 1 -1 0 1 3.8308 14 1 -1 1 1 4.5242 15 1 0 -1 1 3.1009 16 1 0 0 1 1.7194 17 1 0 1 1 3.8930 18 1 1 1 1 6.7327 19 1 1 0 1 3.8202 20 1 1 -1 1 4.5510 21 1 1 1 0 3.1196 22 1 1 0 0 2.4182 23 1 1 -1 0 1.6235 24 1 1 1 -1 3.8269 25 1 1 0 -1 3.8308 26 1 1 -1 -1 4.5242 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3921 atoms have been selected out of 3995 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 681 227 227 0.00 3 C003 has 93 31 31 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1728 576 576 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 0.00 Total of13456 atoms and 4477 groups and 4472 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3995 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1320 Number of atoms = 3995 Number of groups = 1325 Number of bonds = 3988 Number of angles = 1424 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1322 Number of HB donors = 2622 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1320 Number of atoms = 3995 Number of groups = 1325 Number of bonds = 3988 Number of angles = 1424 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1322 Number of HB donors = 2622 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.216" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1320" Evaluating: 1320-7 Parameter: NUMWAT <- "1313" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1313" Comparing "1081" and "1313". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.216" Parameter: BOX -> "34.216" Parameter: BOX -> "34.216" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.21600 B = 34.21600 C = 34.21600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7344 2 1 -1 0 -1 3.8174 3 1 -1 1 -1 4.5476 4 1 0 -1 -1 3.8902 5 1 0 0 -1 1.7175 6 1 0 1 -1 3.0982 7 1 -1 -1 0 3.1168 8 1 -1 0 0 2.4163 9 1 -1 1 0 1.6221 10 1 0 -1 0 1.2297 11 1 0 1 0 1.2297 12 1 -1 -1 1 3.8234 13 1 -1 0 1 3.8281 14 1 -1 1 1 4.5212 15 1 0 -1 1 3.0982 16 1 0 0 1 1.7175 17 1 0 1 1 3.8902 18 1 1 1 1 6.7344 19 1 1 0 1 3.8174 20 1 1 -1 1 4.5476 21 1 1 1 0 3.1168 22 1 1 0 0 2.4163 23 1 1 -1 0 1.6221 24 1 1 1 -1 3.8234 25 1 1 0 -1 3.8281 26 1 1 -1 -1 4.5212 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3921 atoms have been selected out of 3995 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 681 227 227 0.00 3 C003 has 93 31 31 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1728 576 576 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 0.00 Total of13456 atoms and 4477 groups and 4472 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3995 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1320 Number of atoms = 3995 Number of groups = 1325 Number of bonds = 3988 Number of angles = 1424 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1322 Number of HB donors = 2622 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1320 Number of atoms = 3995 Number of groups = 1325 Number of bonds = 3988 Number of angles = 1424 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1322 Number of HB donors = 2622 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.214" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1320" Evaluating: 1320-7 Parameter: NUMWAT <- "1313" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1313" Comparing "1081" and "1313". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.214" Parameter: BOX -> "34.214" Parameter: BOX -> "34.214" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.21400 B = 34.21400 C = 34.21400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7362 2 1 -1 0 -1 3.8147 3 1 -1 1 -1 4.5441 4 1 0 -1 -1 3.8875 5 1 0 0 -1 1.7155 6 1 0 1 -1 3.0954 7 1 -1 -1 0 3.1141 8 1 -1 0 0 2.4143 9 1 -1 1 0 1.6208 10 1 0 -1 0 1.2292 11 1 0 1 0 1.2292 12 1 -1 -1 1 3.8200 13 1 -1 0 1 3.8253 14 1 -1 1 1 4.5183 15 1 0 -1 1 3.0954 16 1 0 0 1 1.7155 17 1 0 1 1 3.8875 18 1 1 1 1 6.7362 19 1 1 0 1 3.8147 20 1 1 -1 1 4.5441 21 1 1 1 0 3.1141 22 1 1 0 0 2.4143 23 1 1 -1 0 1.6208 24 1 1 1 -1 3.8200 25 1 1 0 -1 3.8253 26 1 1 -1 -1 4.5183 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3921 atoms have been selected out of 3995 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 381 127 127 0.00 2 C002 has 681 227 227 0.00 3 C003 has 96 32 32 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1728 576 576 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 108 36 36 0.00 Total of13462 atoms and 4479 groups and 4474 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3995 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1320 Number of atoms = 3995 Number of groups = 1325 Number of bonds = 3988 Number of angles = 1424 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1322 Number of HB donors = 2622 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1320 Number of atoms = 3995 Number of groups = 1325 Number of bonds = 3988 Number of angles = 1424 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1322 Number of HB donors = 2622 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.212" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1320" Evaluating: 1320-7 Parameter: NUMWAT <- "1313" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1313" Comparing "1081" and "1313". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.212" Parameter: BOX -> "34.212" Parameter: BOX -> "34.212" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.21200 B = 34.21200 C = 34.21200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7379 2 1 -1 0 -1 3.8119 3 1 -1 1 -1 4.5407 4 1 0 -1 -1 3.8847 5 1 0 0 -1 1.7136 6 1 0 1 -1 3.0927 7 1 -1 -1 0 3.1114 8 1 -1 0 0 2.4124 9 1 -1 1 0 1.6194 10 1 0 -1 0 1.2287 11 1 0 1 0 1.2287 12 1 -1 -1 1 3.8165 13 1 -1 0 1 3.8225 14 1 -1 1 1 4.5154 15 1 0 -1 1 3.0927 16 1 0 0 1 1.7136 17 1 0 1 1 3.8847 18 1 1 1 1 6.7379 19 1 1 0 1 3.8119 20 1 1 -1 1 4.5407 21 1 1 1 0 3.1114 22 1 1 0 0 2.4124 23 1 1 -1 0 1.6194 24 1 1 1 -1 3.8165 25 1 1 0 -1 3.8225 26 1 1 -1 -1 4.5154 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3921 atoms have been selected out of 3995 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 384 128 128 0.00 2 C002 has 681 227 227 0.00 3 C003 has 96 32 32 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1728 576 576 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 108 36 36 0.00 Total of13465 atoms and 4480 groups and 4475 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3995 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1320 Number of atoms = 3995 Number of groups = 1325 Number of bonds = 3988 Number of angles = 1424 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1322 Number of HB donors = 2622 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1320 Number of atoms = 3995 Number of groups = 1325 Number of bonds = 3988 Number of angles = 1424 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1322 Number of HB donors = 2622 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.21" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1320" Evaluating: 1320-7 Parameter: NUMWAT <- "1313" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1313" Comparing "1081" and "1313". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.21" Parameter: BOX -> "34.21" Parameter: BOX -> "34.21" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.21000 B = 34.21000 C = 34.21000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7396 2 1 -1 0 -1 3.8091 3 1 -1 1 -1 4.5372 4 1 0 -1 -1 3.8820 5 1 0 0 -1 1.7117 6 1 0 1 -1 3.0900 7 1 -1 -1 0 3.1086 8 1 -1 0 0 2.4105 9 1 -1 1 0 1.6180 10 1 0 -1 0 1.2282 11 1 0 1 0 1.2282 12 1 -1 -1 1 3.8131 13 1 -1 0 1 3.8197 14 1 -1 1 1 4.5125 15 1 0 -1 1 3.0900 16 1 0 0 1 1.7117 17 1 0 1 1 3.8820 18 1 1 1 1 6.7396 19 1 1 0 1 3.8091 20 1 1 -1 1 4.5372 21 1 1 1 0 3.1086 22 1 1 0 0 2.4105 23 1 1 -1 0 1.6180 24 1 1 1 -1 3.8131 25 1 1 0 -1 3.8197 26 1 1 -1 -1 4.5125 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3921 atoms have been selected out of 3995 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 384 128 128 0.00 2 C002 has 681 227 227 0.00 3 C003 has 96 32 32 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1728 576 576 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 108 36 36 0.00 Total of13465 atoms and 4480 groups and 4475 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3995 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1320 Number of atoms = 3995 Number of groups = 1325 Number of bonds = 3988 Number of angles = 1424 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1322 Number of HB donors = 2622 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1320 Number of atoms = 3995 Number of groups = 1325 Number of bonds = 3988 Number of angles = 1424 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1322 Number of HB donors = 2622 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.208" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1320" Evaluating: 1320-7 Parameter: NUMWAT <- "1313" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1313" Comparing "1081" and "1313". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.208" Parameter: BOX -> "34.208" Parameter: BOX -> "34.208" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.20800 B = 34.20800 C = 34.20800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7414 2 1 -1 0 -1 3.8064 3 1 -1 1 -1 4.5338 4 1 0 -1 -1 3.8792 5 1 0 0 -1 1.7098 6 1 0 1 -1 3.0872 7 1 -1 -1 0 3.1059 8 1 -1 0 0 2.4085 9 1 -1 1 0 1.6166 10 1 0 -1 0 1.2277 11 1 0 1 0 1.2277 12 1 -1 -1 1 3.8096 13 1 -1 0 1 3.8170 14 1 -1 1 1 4.5095 15 1 0 -1 1 3.0872 16 1 0 0 1 1.7098 17 1 0 1 1 3.8792 18 1 1 1 1 6.7414 19 1 1 0 1 3.8064 20 1 1 -1 1 4.5338 21 1 1 1 0 3.1059 22 1 1 0 0 2.4085 23 1 1 -1 0 1.6166 24 1 1 1 -1 3.8096 25 1 1 0 -1 3.8170 26 1 1 -1 -1 4.5095 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3921 atoms have been selected out of 3995 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1103 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 384 128 128 0.00 2 C002 has 681 227 227 0.00 3 C003 has 96 32 32 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1647 549 549 0.00 6 C006 has 504 168 168 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1725 575 575 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 108 36 36 0.00 Total of13465 atoms and 4480 groups and 4475 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3995 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1319 Number of atoms = 3992 Number of groups = 1324 Number of bonds = 3985 Number of angles = 1423 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1321 Number of HB donors = 2620 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1319 Number of atoms = 3992 Number of groups = 1324 Number of bonds = 3985 Number of angles = 1423 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1321 Number of HB donors = 2620 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.206" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1319" Evaluating: 1319-7 Parameter: NUMWAT <- "1312" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1312" Comparing "1081" and "1312". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.206" Parameter: BOX -> "34.206" Parameter: BOX -> "34.206" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.20600 B = 34.20600 C = 34.20600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7431 2 1 -1 0 -1 3.8036 3 1 -1 1 -1 4.5304 4 1 0 -1 -1 3.8764 5 1 0 0 -1 1.7079 6 1 0 1 -1 3.0845 7 1 -1 -1 0 3.1031 8 1 -1 0 0 2.4066 9 1 -1 1 0 1.6153 10 1 0 -1 0 1.2272 11 1 0 1 0 1.2272 12 1 -1 -1 1 3.8062 13 1 -1 0 1 3.8142 14 1 -1 1 1 4.5066 15 1 0 -1 1 3.0845 16 1 0 0 1 1.7079 17 1 0 1 1 3.8764 18 1 1 1 1 6.7431 19 1 1 0 1 3.8036 20 1 1 -1 1 4.5304 21 1 1 1 0 3.1031 22 1 1 0 0 2.4066 23 1 1 -1 0 1.6153 24 1 1 1 -1 3.8062 25 1 1 0 -1 3.8142 26 1 1 -1 -1 4.5066 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3918 atoms have been selected out of 3992 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 387 129 129 0.00 2 C002 has 681 227 227 0.00 3 C003 has 99 33 33 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1725 575 575 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 108 36 36 0.00 Total of13462 atoms and 4479 groups and 4474 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3992 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1319 Number of atoms = 3992 Number of groups = 1324 Number of bonds = 3985 Number of angles = 1423 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1321 Number of HB donors = 2620 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1319 Number of atoms = 3992 Number of groups = 1324 Number of bonds = 3985 Number of angles = 1423 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1321 Number of HB donors = 2620 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.204" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1319" Evaluating: 1319-7 Parameter: NUMWAT <- "1312" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1312" Comparing "1081" and "1312". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.204" Parameter: BOX -> "34.204" Parameter: BOX -> "34.204" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.20400 B = 34.20400 C = 34.20400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7449 2 1 -1 0 -1 3.8008 3 1 -1 1 -1 4.5269 4 1 0 -1 -1 3.8737 5 1 0 0 -1 1.7060 6 1 0 1 -1 3.0817 7 1 -1 -1 0 3.1004 8 1 -1 0 0 2.4047 9 1 -1 1 0 1.6139 10 1 0 -1 0 1.2267 11 1 0 1 0 1.2267 12 1 -1 -1 1 3.8027 13 1 -1 0 1 3.8114 14 1 -1 1 1 4.5037 15 1 0 -1 1 3.0817 16 1 0 0 1 1.7060 17 1 0 1 1 3.8737 18 1 1 1 1 6.7449 19 1 1 0 1 3.8008 20 1 1 -1 1 4.5269 21 1 1 1 0 3.1004 22 1 1 0 0 2.4047 23 1 1 -1 0 1.6139 24 1 1 1 -1 3.8027 25 1 1 0 -1 3.8114 26 1 1 -1 -1 4.5037 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3918 atoms have been selected out of 3992 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 350 OPERATED ON BY TRANSFORMATION C010 RESIDUE 606 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 387 129 129 0.00 2 C002 has 681 227 227 0.00 3 C003 has 99 33 33 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1722 574 574 0.00 12 C012 has 120 40 40 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13447 atoms and 4474 groups and 4469 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3992 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1317 Number of atoms = 3986 Number of groups = 1322 Number of bonds = 3979 Number of angles = 1421 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1319 Number of HB donors = 2616 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1317 Number of atoms = 3986 Number of groups = 1322 Number of bonds = 3979 Number of angles = 1421 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1319 Number of HB donors = 2616 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.202" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1317" Evaluating: 1317-7 Parameter: NUMWAT <- "1310" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1310" Comparing "1081" and "1310". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.202" Parameter: BOX -> "34.202" Parameter: BOX -> "34.202" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.20200 B = 34.20200 C = 34.20200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7466 2 1 -1 0 -1 3.7980 3 1 -1 1 -1 4.5235 4 1 0 -1 -1 3.8709 5 1 0 0 -1 1.7041 6 1 0 1 -1 3.0790 7 1 -1 -1 0 3.0977 8 1 -1 0 0 2.4027 9 1 -1 1 0 1.6126 10 1 0 -1 0 1.2262 11 1 0 1 0 1.2262 12 1 -1 -1 1 3.7993 13 1 -1 0 1 3.8087 14 1 -1 1 1 4.5008 15 1 0 -1 1 3.0790 16 1 0 0 1 1.7041 17 1 0 1 1 3.8709 18 1 1 1 1 6.7466 19 1 1 0 1 3.7980 20 1 1 -1 1 4.5235 21 1 1 1 0 3.0977 22 1 1 0 0 2.4027 23 1 1 -1 0 1.6126 24 1 1 1 -1 3.7993 25 1 1 0 -1 3.8087 26 1 1 -1 -1 4.5008 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3912 atoms have been selected out of 3986 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 387 129 129 0.00 2 C002 has 681 227 227 0.00 3 C003 has 99 33 33 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1811 602 602 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1719 573 573 0.00 12 C012 has 120 40 40 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13438 atoms and 4471 groups and 4466 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3986 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1317 Number of atoms = 3986 Number of groups = 1322 Number of bonds = 3979 Number of angles = 1421 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1319 Number of HB donors = 2616 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1317 Number of atoms = 3986 Number of groups = 1322 Number of bonds = 3979 Number of angles = 1421 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1319 Number of HB donors = 2616 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.2" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1317" Evaluating: 1317-7 Parameter: NUMWAT <- "1310" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1310" Comparing "1081" and "1310". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.2" Parameter: BOX -> "34.2" Parameter: BOX -> "34.2" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.20000 B = 34.20000 C = 34.20000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7484 2 1 -1 0 -1 3.7953 3 1 -1 1 -1 4.5201 4 1 0 -1 -1 3.8681 5 1 0 0 -1 1.7022 6 1 0 1 -1 3.0763 7 1 -1 -1 0 3.0949 8 1 -1 0 0 2.4008 9 1 -1 1 0 1.6112 10 1 0 -1 0 1.2258 11 1 0 1 0 1.2258 12 1 -1 -1 1 3.7958 13 1 -1 0 1 3.8059 14 1 -1 1 1 4.4978 15 1 0 -1 1 3.0763 16 1 0 0 1 1.7022 17 1 0 1 1 3.8681 18 1 1 1 1 6.7484 19 1 1 0 1 3.7953 20 1 1 -1 1 4.5201 21 1 1 1 0 3.0949 22 1 1 0 0 2.4008 23 1 1 -1 0 1.6112 24 1 1 1 -1 3.7958 25 1 1 0 -1 3.8059 26 1 1 -1 -1 4.4978 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3912 atoms have been selected out of 3986 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 22 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 387 129 129 0.00 2 C002 has 684 228 228 0.00 3 C003 has 99 33 33 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1814 603 603 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1719 573 573 0.00 12 C012 has 120 40 40 0.00 13 C013 has 483 161 161 0.00 14 C014 has 108 36 36 0.00 Total of13450 atoms and 4475 groups and 4470 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3986 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1316 Number of atoms = 3983 Number of groups = 1321 Number of bonds = 3976 Number of angles = 1420 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1318 Number of HB donors = 2614 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1316 Number of atoms = 3983 Number of groups = 1321 Number of bonds = 3976 Number of angles = 1420 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1318 Number of HB donors = 2614 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.198" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1316" Evaluating: 1316-7 Parameter: NUMWAT <- "1309" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1309" Comparing "1081" and "1309". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.198" Parameter: BOX -> "34.198" Parameter: BOX -> "34.198" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.19800 B = 34.19800 C = 34.19800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7501 2 1 -1 0 -1 3.7925 3 1 -1 1 -1 4.5166 4 1 0 -1 -1 3.8654 5 1 0 0 -1 1.7003 6 1 0 1 -1 3.0735 7 1 -1 -1 0 3.0922 8 1 -1 0 0 2.3989 9 1 -1 1 0 1.6098 10 1 0 -1 0 1.2253 11 1 0 1 0 1.2253 12 1 -1 -1 1 3.7924 13 1 -1 0 1 3.8031 14 1 -1 1 1 4.4949 15 1 0 -1 1 3.0735 16 1 0 0 1 1.7003 17 1 0 1 1 3.8654 18 1 1 1 1 6.7501 19 1 1 0 1 3.7925 20 1 1 -1 1 4.5166 21 1 1 1 0 3.0922 22 1 1 0 0 2.3989 23 1 1 -1 0 1.6098 24 1 1 1 -1 3.7924 25 1 1 0 -1 3.8031 26 1 1 -1 -1 4.4949 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3909 atoms have been selected out of 3983 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 387 129 129 0.00 2 C002 has 684 228 228 0.00 3 C003 has 99 33 33 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1811 602 602 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1719 573 573 0.00 12 C012 has 120 40 40 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13438 atoms and 4471 groups and 4466 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3983 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1316 Number of atoms = 3983 Number of groups = 1321 Number of bonds = 3976 Number of angles = 1420 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1318 Number of HB donors = 2614 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1316 Number of atoms = 3983 Number of groups = 1321 Number of bonds = 3976 Number of angles = 1420 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1318 Number of HB donors = 2614 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.196" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1316" Evaluating: 1316-7 Parameter: NUMWAT <- "1309" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1309" Comparing "1081" and "1309". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.196" Parameter: BOX -> "34.196" Parameter: BOX -> "34.196" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.19600 B = 34.19600 C = 34.19600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7518 2 1 -1 0 -1 3.7897 3 1 -1 1 -1 4.5132 4 1 0 -1 -1 3.8626 5 1 0 0 -1 1.6984 6 1 0 1 -1 3.0708 7 1 -1 -1 0 3.0895 8 1 -1 0 0 2.3970 9 1 -1 1 0 1.6085 10 1 0 -1 0 1.2248 11 1 0 1 0 1.2248 12 1 -1 -1 1 3.7889 13 1 -1 0 1 3.8004 14 1 -1 1 1 4.4920 15 1 0 -1 1 3.0708 16 1 0 0 1 1.6984 17 1 0 1 1 3.8626 18 1 1 1 1 6.7518 19 1 1 0 1 3.7897 20 1 1 -1 1 4.5132 21 1 1 1 0 3.0895 22 1 1 0 0 2.3970 23 1 1 -1 0 1.6085 24 1 1 1 -1 3.7889 25 1 1 0 -1 3.8004 26 1 1 -1 -1 4.4920 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3909 atoms have been selected out of 3983 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 387 129 129 0.00 2 C002 has 684 228 228 0.00 3 C003 has 99 33 33 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1811 602 602 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1719 573 573 0.00 12 C012 has 120 40 40 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13438 atoms and 4471 groups and 4466 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3983 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1316 Number of atoms = 3983 Number of groups = 1321 Number of bonds = 3976 Number of angles = 1420 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1318 Number of HB donors = 2614 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1316 Number of atoms = 3983 Number of groups = 1321 Number of bonds = 3976 Number of angles = 1420 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1318 Number of HB donors = 2614 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.194" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1316" Evaluating: 1316-7 Parameter: NUMWAT <- "1309" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1309" Comparing "1081" and "1309". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.194" Parameter: BOX -> "34.194" Parameter: BOX -> "34.194" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.19400 B = 34.19400 C = 34.19400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7536 2 1 -1 0 -1 3.7870 3 1 -1 1 -1 4.5098 4 1 0 -1 -1 3.8598 5 1 0 0 -1 1.6965 6 1 0 1 -1 3.0680 7 1 -1 -1 0 3.0867 8 1 -1 0 0 2.3950 9 1 -1 1 0 1.6072 10 1 0 -1 0 1.2243 11 1 0 1 0 1.2243 12 1 -1 -1 1 3.7855 13 1 -1 0 1 3.7976 14 1 -1 1 1 4.4891 15 1 0 -1 1 3.0680 16 1 0 0 1 1.6965 17 1 0 1 1 3.8598 18 1 1 1 1 6.7536 19 1 1 0 1 3.7870 20 1 1 -1 1 4.5098 21 1 1 1 0 3.0867 22 1 1 0 0 2.3950 23 1 1 -1 0 1.6072 24 1 1 1 -1 3.7855 25 1 1 0 -1 3.7976 26 1 1 -1 -1 4.4891 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3909 atoms have been selected out of 3983 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 387 129 129 0.00 2 C002 has 684 228 228 0.00 3 C003 has 99 33 33 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1811 602 602 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1719 573 573 0.00 12 C012 has 120 40 40 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13438 atoms and 4471 groups and 4466 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3983 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1316 Number of atoms = 3983 Number of groups = 1321 Number of bonds = 3976 Number of angles = 1420 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1318 Number of HB donors = 2614 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1316 Number of atoms = 3983 Number of groups = 1321 Number of bonds = 3976 Number of angles = 1420 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1318 Number of HB donors = 2614 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.192" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1316" Evaluating: 1316-7 Parameter: NUMWAT <- "1309" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1309" Comparing "1081" and "1309". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.192" Parameter: BOX -> "34.192" Parameter: BOX -> "34.192" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.19200 B = 34.19200 C = 34.19200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7553 2 1 -1 0 -1 3.7842 3 1 -1 1 -1 4.5063 4 1 0 -1 -1 3.8571 5 1 0 0 -1 1.6946 6 1 0 1 -1 3.0653 7 1 -1 -1 0 3.0840 8 1 -1 0 0 2.3931 9 1 -1 1 0 1.6058 10 1 0 -1 0 1.2238 11 1 0 1 0 1.2238 12 1 -1 -1 1 3.7820 13 1 -1 0 1 3.7948 14 1 -1 1 1 4.4862 15 1 0 -1 1 3.0653 16 1 0 0 1 1.6946 17 1 0 1 1 3.8571 18 1 1 1 1 6.7553 19 1 1 0 1 3.7842 20 1 1 -1 1 4.5063 21 1 1 1 0 3.0840 22 1 1 0 0 2.3931 23 1 1 -1 0 1.6058 24 1 1 1 -1 3.7820 25 1 1 0 -1 3.7948 26 1 1 -1 -1 4.4862 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3909 atoms have been selected out of 3983 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 387 129 129 0.00 2 C002 has 684 228 228 0.00 3 C003 has 99 33 33 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1811 602 602 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1722 574 574 0.00 12 C012 has 120 40 40 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13447 atoms and 4474 groups and 4469 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3983 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1316 Number of atoms = 3983 Number of groups = 1321 Number of bonds = 3976 Number of angles = 1420 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1318 Number of HB donors = 2614 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1316 Number of atoms = 3983 Number of groups = 1321 Number of bonds = 3976 Number of angles = 1420 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1318 Number of HB donors = 2614 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.19" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1316" Evaluating: 1316-7 Parameter: NUMWAT <- "1309" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1309" Comparing "1081" and "1309". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.19" Parameter: BOX -> "34.19" Parameter: BOX -> "34.19" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.19000 B = 34.19000 C = 34.19000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7571 2 1 -1 0 -1 3.7814 3 1 -1 1 -1 4.5029 4 1 0 -1 -1 3.8543 5 1 0 0 -1 1.6928 6 1 0 1 -1 3.0625 7 1 -1 -1 0 3.0813 8 1 -1 0 0 2.3912 9 1 -1 1 0 1.6045 10 1 0 -1 0 1.2234 11 1 0 1 0 1.2234 12 1 -1 -1 1 3.7786 13 1 -1 0 1 3.7921 14 1 -1 1 1 4.4832 15 1 0 -1 1 3.0625 16 1 0 0 1 1.6928 17 1 0 1 1 3.8543 18 1 1 1 1 6.7571 19 1 1 0 1 3.7814 20 1 1 -1 1 4.5029 21 1 1 1 0 3.0813 22 1 1 0 0 2.3912 23 1 1 -1 0 1.6045 24 1 1 1 -1 3.7786 25 1 1 0 -1 3.7921 26 1 1 -1 -1 4.4832 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3909 atoms have been selected out of 3983 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 387 129 129 0.00 2 C002 has 684 228 228 0.00 3 C003 has 99 33 33 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1811 602 602 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1722 574 574 0.00 12 C012 has 120 40 40 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13450 atoms and 4475 groups and 4470 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3983 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1316 Number of atoms = 3983 Number of groups = 1321 Number of bonds = 3976 Number of angles = 1420 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1318 Number of HB donors = 2614 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1316 Number of atoms = 3983 Number of groups = 1321 Number of bonds = 3976 Number of angles = 1420 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1318 Number of HB donors = 2614 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.188" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1316" Evaluating: 1316-7 Parameter: NUMWAT <- "1309" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1309" Comparing "1081" and "1309". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.188" Parameter: BOX -> "34.188" Parameter: BOX -> "34.188" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.18800 B = 34.18800 C = 34.18800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7589 2 1 -1 0 -1 3.7787 3 1 -1 1 -1 4.4994 4 1 0 -1 -1 3.8515 5 1 0 0 -1 1.6909 6 1 0 1 -1 3.0598 7 1 -1 -1 0 3.0785 8 1 -1 0 0 2.3892 9 1 -1 1 0 1.6032 10 1 0 -1 0 1.2229 11 1 0 1 0 1.2229 12 1 -1 -1 1 3.7751 13 1 -1 0 1 3.7893 14 1 -1 1 1 4.4803 15 1 0 -1 1 3.0598 16 1 0 0 1 1.6909 17 1 0 1 1 3.8515 18 1 1 1 1 6.7589 19 1 1 0 1 3.7787 20 1 1 -1 1 4.4994 21 1 1 1 0 3.0785 22 1 1 0 0 2.3892 23 1 1 -1 0 1.6032 24 1 1 1 -1 3.7751 25 1 1 0 -1 3.7893 26 1 1 -1 -1 4.4803 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3909 atoms have been selected out of 3983 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 387 129 129 0.00 2 C002 has 687 229 229 0.00 3 C003 has 99 33 33 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1811 602 602 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1722 574 574 0.00 12 C012 has 123 41 41 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13459 atoms and 4478 groups and 4473 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3983 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1316 Number of atoms = 3983 Number of groups = 1321 Number of bonds = 3976 Number of angles = 1420 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1318 Number of HB donors = 2614 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1316 Number of atoms = 3983 Number of groups = 1321 Number of bonds = 3976 Number of angles = 1420 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1318 Number of HB donors = 2614 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.186" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1316" Evaluating: 1316-7 Parameter: NUMWAT <- "1309" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1309" Comparing "1081" and "1309". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.186" Parameter: BOX -> "34.186" Parameter: BOX -> "34.186" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.18600 B = 34.18600 C = 34.18600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7606 2 1 -1 0 -1 3.7759 3 1 -1 1 -1 4.4960 4 1 0 -1 -1 3.8488 5 1 0 0 -1 1.6890 6 1 0 1 -1 3.0571 7 1 -1 -1 0 3.0758 8 1 -1 0 0 2.3873 9 1 -1 1 0 1.6018 10 1 0 -1 0 1.2224 11 1 0 1 0 1.2224 12 1 -1 -1 1 3.7717 13 1 -1 0 1 3.7865 14 1 -1 1 1 4.4774 15 1 0 -1 1 3.0571 16 1 0 0 1 1.6890 17 1 0 1 1 3.8488 18 1 1 1 1 6.7606 19 1 1 0 1 3.7759 20 1 1 -1 1 4.4960 21 1 1 1 0 3.0758 22 1 1 0 0 2.3873 23 1 1 -1 0 1.6018 24 1 1 1 -1 3.7717 25 1 1 0 -1 3.7865 26 1 1 -1 -1 4.4774 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3909 atoms have been selected out of 3983 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 128 OPERATED ON BY TRANSFORMATION C011 RESIDUE 921 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 387 129 129 0.00 2 C002 has 687 229 229 0.00 3 C003 has 99 33 33 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1805 600 600 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1725 575 575 0.00 12 C012 has 123 41 41 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13456 atoms and 4477 groups and 4472 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3983 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1314 Number of atoms = 3977 Number of groups = 1319 Number of bonds = 3970 Number of angles = 1418 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1316 Number of HB donors = 2610 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1314 Number of atoms = 3977 Number of groups = 1319 Number of bonds = 3970 Number of angles = 1418 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1316 Number of HB donors = 2610 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.184" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1314" Evaluating: 1314-7 Parameter: NUMWAT <- "1307" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1307" Comparing "1081" and "1307". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.184" Parameter: BOX -> "34.184" Parameter: BOX -> "34.184" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.18400 B = 34.18400 C = 34.18400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7624 2 1 -1 0 -1 3.7731 3 1 -1 1 -1 4.4926 4 1 0 -1 -1 3.8460 5 1 0 0 -1 1.6871 6 1 0 1 -1 3.0543 7 1 -1 -1 0 3.0730 8 1 -1 0 0 2.3854 9 1 -1 1 0 1.6005 10 1 0 -1 0 1.2220 11 1 0 1 0 1.2220 12 1 -1 -1 1 3.7682 13 1 -1 0 1 3.7837 14 1 -1 1 1 4.4745 15 1 0 -1 1 3.0543 16 1 0 0 1 1.6871 17 1 0 1 1 3.8460 18 1 1 1 1 6.7624 19 1 1 0 1 3.7731 20 1 1 -1 1 4.4926 21 1 1 1 0 3.0730 22 1 1 0 0 2.3854 23 1 1 -1 0 1.6005 24 1 1 1 -1 3.7682 25 1 1 0 -1 3.7837 26 1 1 -1 -1 4.4745 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3903 atoms have been selected out of 3977 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 687 229 229 0.00 3 C003 has 99 33 33 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1805 600 600 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1722 574 574 0.00 12 C012 has 123 41 41 0.00 13 C013 has 480 160 160 0.00 14 C014 has 108 36 36 0.00 Total of13450 atoms and 4475 groups and 4470 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3977 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1314 Number of atoms = 3977 Number of groups = 1319 Number of bonds = 3970 Number of angles = 1418 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1316 Number of HB donors = 2610 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1314 Number of atoms = 3977 Number of groups = 1319 Number of bonds = 3970 Number of angles = 1418 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1316 Number of HB donors = 2610 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.182" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1314" Evaluating: 1314-7 Parameter: NUMWAT <- "1307" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1307" Comparing "1081" and "1307". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.182" Parameter: BOX -> "34.182" Parameter: BOX -> "34.182" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.18200 B = 34.18200 C = 34.18200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7641 2 1 -1 0 -1 3.7703 3 1 -1 1 -1 4.4891 4 1 0 -1 -1 3.8432 5 1 0 0 -1 1.6852 6 1 0 1 -1 3.0516 7 1 -1 -1 0 3.0703 8 1 -1 0 0 2.3835 9 1 -1 1 0 1.5992 10 1 0 -1 0 1.2215 11 1 0 1 0 1.2215 12 1 -1 -1 1 3.7648 13 1 -1 0 1 3.7810 14 1 -1 1 1 4.4716 15 1 0 -1 1 3.0516 16 1 0 0 1 1.6852 17 1 0 1 1 3.8432 18 1 1 1 1 6.7641 19 1 1 0 1 3.7703 20 1 1 -1 1 4.4891 21 1 1 1 0 3.0703 22 1 1 0 0 2.3835 23 1 1 -1 0 1.5992 24 1 1 1 -1 3.7648 25 1 1 0 -1 3.7810 26 1 1 -1 -1 4.4716 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3903 atoms have been selected out of 3977 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 687 229 229 0.00 3 C003 has 99 33 33 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1805 600 600 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1722 574 574 0.00 12 C012 has 123 41 41 0.00 13 C013 has 480 160 160 0.00 14 C014 has 111 37 37 0.00 Total of13453 atoms and 4476 groups and 4471 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3977 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1314 Number of atoms = 3977 Number of groups = 1319 Number of bonds = 3970 Number of angles = 1418 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1316 Number of HB donors = 2610 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1314 Number of atoms = 3977 Number of groups = 1319 Number of bonds = 3970 Number of angles = 1418 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1316 Number of HB donors = 2610 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.18" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1314" Evaluating: 1314-7 Parameter: NUMWAT <- "1307" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1307" Comparing "1081" and "1307". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.18" Parameter: BOX -> "34.18" Parameter: BOX -> "34.18" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.18000 B = 34.18000 C = 34.18000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7659 2 1 -1 0 -1 3.7676 3 1 -1 1 -1 4.4857 4 1 0 -1 -1 3.8405 5 1 0 0 -1 1.6833 6 1 0 1 -1 3.0488 7 1 -1 -1 0 3.0676 8 1 -1 0 0 2.3815 9 1 -1 1 0 1.5979 10 1 0 -1 0 1.2211 11 1 0 1 0 1.2211 12 1 -1 -1 1 3.7613 13 1 -1 0 1 3.7782 14 1 -1 1 1 4.4687 15 1 0 -1 1 3.0488 16 1 0 0 1 1.6833 17 1 0 1 1 3.8405 18 1 1 1 1 6.7659 19 1 1 0 1 3.7676 20 1 1 -1 1 4.4857 21 1 1 1 0 3.0676 22 1 1 0 0 2.3815 23 1 1 -1 0 1.5979 24 1 1 1 -1 3.7613 25 1 1 0 -1 3.7782 26 1 1 -1 -1 4.4687 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3903 atoms have been selected out of 3977 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 697 OPERATED ON BY TRANSFORMATION C011 RESIDUE 868 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 687 229 229 0.00 3 C003 has 99 33 33 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1805 600 600 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1719 573 573 0.00 12 C012 has 123 41 41 0.00 13 C013 has 480 160 160 0.00 14 C014 has 111 37 37 0.00 Total of13450 atoms and 4475 groups and 4470 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3977 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1312 Number of atoms = 3971 Number of groups = 1317 Number of bonds = 3964 Number of angles = 1416 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1314 Number of HB donors = 2606 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1312 Number of atoms = 3971 Number of groups = 1317 Number of bonds = 3964 Number of angles = 1416 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1314 Number of HB donors = 2606 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.178" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1312" Evaluating: 1312-7 Parameter: NUMWAT <- "1305" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1305" Comparing "1081" and "1305". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.178" Parameter: BOX -> "34.178" Parameter: BOX -> "34.178" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.17800 B = 34.17800 C = 34.17800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7676 2 1 -1 0 -1 3.7648 3 1 -1 1 -1 4.4823 4 1 0 -1 -1 3.8377 5 1 0 0 -1 1.6814 6 1 0 1 -1 3.0461 7 1 -1 -1 0 3.0648 8 1 -1 0 0 2.3796 9 1 -1 1 0 2.5908 10 1 0 -1 0 1.2206 11 1 0 1 0 1.2206 12 1 -1 -1 1 3.7579 13 1 -1 0 1 3.7754 14 1 -1 1 1 4.4658 15 1 0 -1 1 3.0461 16 1 0 0 1 1.6814 17 1 0 1 1 3.8377 18 1 1 1 1 6.7676 19 1 1 0 1 3.7648 20 1 1 -1 1 4.4823 21 1 1 1 0 3.0648 22 1 1 0 0 2.3796 23 1 1 -1 0 2.5908 24 1 1 1 -1 3.7579 25 1 1 0 -1 3.7754 26 1 1 -1 -1 4.4658 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3897 atoms have been selected out of 3971 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 523 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 687 229 229 0.00 3 C003 has 99 33 33 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1647 549 549 0.00 6 C006 has 501 167 167 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1802 599 599 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1713 571 571 0.00 12 C012 has 120 40 40 0.00 13 C013 has 480 160 160 0.00 14 C014 has 114 38 38 0.00 Total of13432 atoms and 4469 groups and 4464 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3971 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1311 Number of atoms = 3968 Number of groups = 1316 Number of bonds = 3961 Number of angles = 1415 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1313 Number of HB donors = 2604 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1311 Number of atoms = 3968 Number of groups = 1316 Number of bonds = 3961 Number of angles = 1415 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1313 Number of HB donors = 2604 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.176" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1311" Evaluating: 1311-7 Parameter: NUMWAT <- "1304" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1304" Comparing "1081" and "1304". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.176" Parameter: BOX -> "34.176" Parameter: BOX -> "34.176" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.17600 B = 34.17600 C = 34.17600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7694 2 1 -1 0 -1 3.7620 3 1 -1 1 -1 4.4788 4 1 0 -1 -1 3.8349 5 1 0 0 -1 1.6795 6 1 0 1 -1 3.0434 7 1 -1 -1 0 3.0621 8 1 -1 0 0 2.3777 9 1 -1 1 0 2.5897 10 1 0 -1 0 1.2201 11 1 0 1 0 1.2201 12 1 -1 -1 1 3.7544 13 1 -1 0 1 3.7727 14 1 -1 1 1 4.4629 15 1 0 -1 1 3.0434 16 1 0 0 1 1.6795 17 1 0 1 1 3.8349 18 1 1 1 1 6.7694 19 1 1 0 1 3.7620 20 1 1 -1 1 4.4788 21 1 1 1 0 3.0621 22 1 1 0 0 2.3777 23 1 1 -1 0 2.5897 24 1 1 1 -1 3.7544 25 1 1 0 -1 3.7727 26 1 1 -1 -1 4.4629 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3894 atoms have been selected out of 3968 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 687 229 229 0.00 3 C003 has 102 34 34 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1647 549 549 0.00 6 C006 has 501 167 167 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1799 598 598 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1713 571 571 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 111 37 37 0.00 Total of13423 atoms and 4466 groups and 4461 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3968 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1311 Number of atoms = 3968 Number of groups = 1316 Number of bonds = 3961 Number of angles = 1415 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1313 Number of HB donors = 2604 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1311 Number of atoms = 3968 Number of groups = 1316 Number of bonds = 3961 Number of angles = 1415 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1313 Number of HB donors = 2604 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.174" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1311" Evaluating: 1311-7 Parameter: NUMWAT <- "1304" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1304" Comparing "1081" and "1304". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.174" Parameter: BOX -> "34.174" Parameter: BOX -> "34.174" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.17400 B = 34.17400 C = 34.17400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7712 2 1 -1 0 -1 3.7593 3 1 -1 1 -1 4.4754 4 1 0 -1 -1 3.8322 5 1 0 0 -1 1.6776 6 1 0 1 -1 3.0406 7 1 -1 -1 0 3.0594 8 1 -1 0 0 2.3757 9 1 -1 1 0 2.5885 10 1 0 -1 0 1.2197 11 1 0 1 0 1.2197 12 1 -1 -1 1 3.7510 13 1 -1 0 1 3.7699 14 1 -1 1 1 4.4599 15 1 0 -1 1 3.0406 16 1 0 0 1 1.6776 17 1 0 1 1 3.8322 18 1 1 1 1 6.7712 19 1 1 0 1 3.7593 20 1 1 -1 1 4.4754 21 1 1 1 0 3.0594 22 1 1 0 0 2.3757 23 1 1 -1 0 2.5885 24 1 1 1 -1 3.7510 25 1 1 0 -1 3.7699 26 1 1 -1 -1 4.4599 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3894 atoms have been selected out of 3968 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 615 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 393 131 131 0.00 2 C002 has 690 230 230 0.00 3 C003 has 102 34 34 0.00 4 C004 has 639 213 213 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1799 598 598 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1713 571 571 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 111 37 37 0.00 Total of13426 atoms and 4467 groups and 4462 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3968 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1310 Number of atoms = 3965 Number of groups = 1315 Number of bonds = 3958 Number of angles = 1414 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1312 Number of HB donors = 2602 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1310 Number of atoms = 3965 Number of groups = 1315 Number of bonds = 3958 Number of angles = 1414 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1312 Number of HB donors = 2602 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.172" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1310" Evaluating: 1310-7 Parameter: NUMWAT <- "1303" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1303" Comparing "1081" and "1303". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.172" Parameter: BOX -> "34.172" Parameter: BOX -> "34.172" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.17200 B = 34.17200 C = 34.17200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7729 2 1 -1 0 -1 3.7565 3 1 -1 1 -1 4.4720 4 1 0 -1 -1 3.8294 5 1 0 0 -1 1.6757 6 1 0 1 -1 3.0379 7 1 -1 -1 0 3.0566 8 1 -1 0 0 2.3738 9 1 -1 1 0 2.5873 10 1 0 -1 0 1.2193 11 1 0 1 0 1.2193 12 1 -1 -1 1 3.7475 13 1 -1 0 1 3.7671 14 1 -1 1 1 4.4570 15 1 0 -1 1 3.0379 16 1 0 0 1 1.6757 17 1 0 1 1 3.8294 18 1 1 1 1 6.7729 19 1 1 0 1 3.7565 20 1 1 -1 1 4.4720 21 1 1 1 0 3.0566 22 1 1 0 0 2.3738 23 1 1 -1 0 2.5873 24 1 1 1 -1 3.7475 25 1 1 0 -1 3.7671 26 1 1 -1 -1 4.4570 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3891 atoms have been selected out of 3965 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 687 229 229 0.00 3 C003 has 102 34 34 0.00 4 C004 has 639 213 213 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 501 167 167 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1796 597 597 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1710 570 570 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 111 37 37 0.00 Total of13408 atoms and 4461 groups and 4456 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3965 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1310 Number of atoms = 3965 Number of groups = 1315 Number of bonds = 3958 Number of angles = 1414 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1312 Number of HB donors = 2602 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1310 Number of atoms = 3965 Number of groups = 1315 Number of bonds = 3958 Number of angles = 1414 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1312 Number of HB donors = 2602 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.17" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1310" Evaluating: 1310-7 Parameter: NUMWAT <- "1303" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1303" Comparing "1081" and "1303". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.17" Parameter: BOX -> "34.17" Parameter: BOX -> "34.17" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.17000 B = 34.17000 C = 34.17000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7747 2 1 -1 0 -1 3.7537 3 1 -1 1 -1 4.4685 4 1 0 -1 -1 3.8266 5 1 0 0 -1 1.6738 6 1 0 1 -1 3.0352 7 1 -1 -1 0 3.0539 8 1 -1 0 0 2.3719 9 1 -1 1 0 2.5862 10 1 0 -1 0 1.2188 11 1 0 1 0 1.2188 12 1 -1 -1 1 3.7441 13 1 -1 0 1 3.7644 14 1 -1 1 1 4.4541 15 1 0 -1 1 3.0352 16 1 0 0 1 1.6738 17 1 0 1 1 3.8266 18 1 1 1 1 6.7747 19 1 1 0 1 3.7537 20 1 1 -1 1 4.4685 21 1 1 1 0 3.0539 22 1 1 0 0 2.3719 23 1 1 -1 0 2.5862 24 1 1 1 -1 3.7441 25 1 1 0 -1 3.7644 26 1 1 -1 -1 4.4541 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3891 atoms have been selected out of 3965 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 687 229 229 0.00 3 C003 has 102 34 34 0.00 4 C004 has 639 213 213 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 501 167 167 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1796 597 597 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1710 570 570 0.00 12 C012 has 120 40 40 0.00 13 C013 has 480 160 160 0.00 14 C014 has 111 37 37 0.00 Total of13414 atoms and 4463 groups and 4458 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3965 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1310 Number of atoms = 3965 Number of groups = 1315 Number of bonds = 3958 Number of angles = 1414 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1312 Number of HB donors = 2602 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1310 Number of atoms = 3965 Number of groups = 1315 Number of bonds = 3958 Number of angles = 1414 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1312 Number of HB donors = 2602 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.168" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1310" Evaluating: 1310-7 Parameter: NUMWAT <- "1303" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1303" Comparing "1081" and "1303". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.168" Parameter: BOX -> "34.168" Parameter: BOX -> "34.168" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.16800 B = 34.16800 C = 34.16800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7765 2 1 -1 0 -1 3.7510 3 1 -1 1 -1 4.4651 4 1 0 -1 -1 3.8239 5 1 0 0 -1 1.6719 6 1 0 1 -1 3.0324 7 1 -1 -1 0 3.0512 8 1 -1 0 0 2.3700 9 1 -1 1 0 2.5850 10 1 0 -1 0 1.2184 11 1 0 1 0 1.2184 12 1 -1 -1 1 3.7406 13 1 -1 0 1 3.7616 14 1 -1 1 1 4.4512 15 1 0 -1 1 3.0324 16 1 0 0 1 1.6719 17 1 0 1 1 3.8239 18 1 1 1 1 6.7765 19 1 1 0 1 3.7510 20 1 1 -1 1 4.4651 21 1 1 1 0 3.0512 22 1 1 0 0 2.3700 23 1 1 -1 0 2.5850 24 1 1 1 -1 3.7406 25 1 1 0 -1 3.7616 26 1 1 -1 -1 4.4512 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3891 atoms have been selected out of 3965 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 299 OPERATED ON BY TRANSFORMATION C016 RESIDUE 621 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 393 131 131 0.00 2 C002 has 693 231 231 0.00 3 C003 has 105 35 35 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 504 168 168 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1796 597 597 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 108 36 36 0.90 Total of13387 atoms and 4454 groups and 4449 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3965 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1308 Number of atoms = 3959 Number of groups = 1313 Number of bonds = 3952 Number of angles = 1412 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1310 Number of HB donors = 2598 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1308 Number of atoms = 3959 Number of groups = 1313 Number of bonds = 3952 Number of angles = 1412 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1310 Number of HB donors = 2598 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.166" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1308" Evaluating: 1308-7 Parameter: NUMWAT <- "1301" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1301" Comparing "1081" and "1301". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.166" Parameter: BOX -> "34.166" Parameter: BOX -> "34.166" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.16600 B = 34.16600 C = 34.16600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7782 2 1 -1 0 -1 3.7482 3 1 -1 1 -1 4.4616 4 1 0 -1 -1 3.8211 5 1 0 0 -1 1.6700 6 1 0 1 -1 3.0297 7 1 -1 -1 0 3.0484 8 1 -1 0 0 2.3680 9 1 -1 1 0 2.5838 10 1 0 -1 0 1.2179 11 1 0 1 0 1.2179 12 1 -1 -1 1 3.7372 13 1 -1 0 1 3.7588 14 1 -1 1 1 4.4483 15 1 0 -1 1 3.0297 16 1 0 0 1 1.6700 17 1 0 1 1 3.8211 18 1 1 1 1 6.7782 19 1 1 0 1 3.7482 20 1 1 -1 1 4.4616 21 1 1 1 0 3.0484 22 1 1 0 0 2.3680 23 1 1 -1 0 2.5838 24 1 1 1 -1 3.7372 25 1 1 0 -1 3.7588 26 1 1 -1 -1 4.4483 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3885 atoms have been selected out of 3959 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 687 229 229 0.00 3 C003 has 102 34 34 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 501 167 167 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 108 36 36 0.90 Total of13342 atoms and 4439 groups and 4434 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3959 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1308 Number of atoms = 3959 Number of groups = 1313 Number of bonds = 3952 Number of angles = 1412 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1310 Number of HB donors = 2598 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1308 Number of atoms = 3959 Number of groups = 1313 Number of bonds = 3952 Number of angles = 1412 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1310 Number of HB donors = 2598 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.164" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1308" Evaluating: 1308-7 Parameter: NUMWAT <- "1301" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1301" Comparing "1081" and "1301". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.164" Parameter: BOX -> "34.164" Parameter: BOX -> "34.164" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.16400 B = 34.16400 C = 34.16400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7800 2 1 -1 0 -1 3.7454 3 1 -1 1 -1 4.4582 4 1 0 -1 -1 3.8184 5 1 0 0 -1 1.6681 6 1 0 1 -1 3.0269 7 1 -1 -1 0 3.0457 8 1 -1 0 0 2.3661 9 1 -1 1 0 2.5827 10 1 0 -1 0 1.2175 11 1 0 1 0 1.2175 12 1 -1 -1 1 3.7337 13 1 -1 0 1 3.7561 14 1 -1 1 1 4.4454 15 1 0 -1 1 3.0269 16 1 0 0 1 1.6681 17 1 0 1 1 3.8184 18 1 1 1 1 6.7800 19 1 1 0 1 3.7454 20 1 1 -1 1 4.4582 21 1 1 1 0 3.0457 22 1 1 0 0 2.3661 23 1 1 -1 0 2.5827 24 1 1 1 -1 3.7337 25 1 1 0 -1 3.7561 26 1 1 -1 -1 4.4454 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3885 atoms have been selected out of 3959 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 102 34 34 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 501 167 167 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 108 36 36 0.90 Total of13348 atoms and 4441 groups and 4436 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3959 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1308 Number of atoms = 3959 Number of groups = 1313 Number of bonds = 3952 Number of angles = 1412 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1310 Number of HB donors = 2598 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1308 Number of atoms = 3959 Number of groups = 1313 Number of bonds = 3952 Number of angles = 1412 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1310 Number of HB donors = 2598 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.162" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1308" Evaluating: 1308-7 Parameter: NUMWAT <- "1301" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1301" Comparing "1081" and "1301". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.162" Parameter: BOX -> "34.162" Parameter: BOX -> "34.162" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.16200 B = 34.16200 C = 34.16200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7818 2 1 -1 0 -1 3.7427 3 1 -1 1 -1 4.4548 4 1 0 -1 -1 3.8156 5 1 0 0 -1 1.6662 6 1 0 1 -1 3.0242 7 1 -1 -1 0 3.0430 8 1 -1 0 0 2.3642 9 1 -1 1 0 2.5815 10 1 0 -1 0 1.2171 11 1 0 1 0 1.2171 12 1 -1 -1 1 3.7303 13 1 -1 0 1 3.7533 14 1 -1 1 1 4.4425 15 1 0 -1 1 3.0242 16 1 0 0 1 1.6662 17 1 0 1 1 3.8156 18 1 1 1 1 6.7818 19 1 1 0 1 3.7427 20 1 1 -1 1 4.4548 21 1 1 1 0 3.0430 22 1 1 0 0 2.3642 23 1 1 -1 0 2.5815 24 1 1 1 -1 3.7303 25 1 1 0 -1 3.7533 26 1 1 -1 -1 4.4425 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3885 atoms have been selected out of 3959 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 102 34 34 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 501 167 167 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 108 36 36 0.90 Total of13348 atoms and 4441 groups and 4436 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3959 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1308 Number of atoms = 3959 Number of groups = 1313 Number of bonds = 3952 Number of angles = 1412 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1310 Number of HB donors = 2598 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1308 Number of atoms = 3959 Number of groups = 1313 Number of bonds = 3952 Number of angles = 1412 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1310 Number of HB donors = 2598 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.16" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1308" Evaluating: 1308-7 Parameter: NUMWAT <- "1301" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1301" Comparing "1081" and "1301". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.16" Parameter: BOX -> "34.16" Parameter: BOX -> "34.16" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.16000 B = 34.16000 C = 34.16000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7836 2 1 -1 0 -1 3.7399 3 1 -1 1 -1 4.4513 4 1 0 -1 -1 3.8128 5 1 0 0 -1 1.6643 6 1 0 1 -1 3.0215 7 1 -1 -1 0 3.0402 8 1 -1 0 0 2.3623 9 1 -1 1 0 2.5804 10 1 0 -1 0 1.2167 11 1 0 1 0 1.2167 12 1 -1 -1 1 3.7268 13 1 -1 0 1 3.7505 14 1 -1 1 1 4.4396 15 1 0 -1 1 3.0215 16 1 0 0 1 1.6643 17 1 0 1 1 3.8128 18 1 1 1 1 6.7836 19 1 1 0 1 3.7399 20 1 1 -1 1 4.4513 21 1 1 1 0 3.0402 22 1 1 0 0 2.3623 23 1 1 -1 0 2.5804 24 1 1 1 -1 3.7268 25 1 1 0 -1 3.7505 26 1 1 -1 -1 4.4396 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3885 atoms have been selected out of 3959 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 102 34 34 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 501 167 167 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 108 36 36 0.89 Total of13348 atoms and 4441 groups and 4436 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3959 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1308 Number of atoms = 3959 Number of groups = 1313 Number of bonds = 3952 Number of angles = 1412 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1310 Number of HB donors = 2598 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1308 Number of atoms = 3959 Number of groups = 1313 Number of bonds = 3952 Number of angles = 1412 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1310 Number of HB donors = 2598 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.158" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1308" Evaluating: 1308-7 Parameter: NUMWAT <- "1301" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1301" Comparing "1081" and "1301". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.158" Parameter: BOX -> "34.158" Parameter: BOX -> "34.158" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.15800 B = 34.15800 C = 34.15800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7853 2 1 -1 0 -1 3.7371 3 1 -1 1 -1 4.4479 4 1 0 -1 -1 3.8101 5 1 0 0 -1 1.6624 6 1 0 1 -1 3.0187 7 1 -1 -1 0 3.0375 8 1 -1 0 0 2.3603 9 1 -1 1 0 2.5792 10 1 0 -1 0 1.2162 11 1 0 1 0 1.2162 12 1 -1 -1 1 3.7234 13 1 -1 0 1 3.7478 14 1 -1 1 1 4.4367 15 1 0 -1 1 3.0187 16 1 0 0 1 1.6624 17 1 0 1 1 3.8101 18 1 1 1 1 6.7853 19 1 1 0 1 3.7371 20 1 1 -1 1 4.4479 21 1 1 1 0 3.0375 22 1 1 0 0 2.3603 23 1 1 -1 0 2.5792 24 1 1 1 -1 3.7234 25 1 1 0 -1 3.7478 26 1 1 -1 -1 4.4367 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3885 atoms have been selected out of 3959 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 102 34 34 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 501 167 167 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 108 36 36 0.89 Total of13348 atoms and 4441 groups and 4436 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3959 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1308 Number of atoms = 3959 Number of groups = 1313 Number of bonds = 3952 Number of angles = 1412 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1310 Number of HB donors = 2598 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1308 Number of atoms = 3959 Number of groups = 1313 Number of bonds = 3952 Number of angles = 1412 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1310 Number of HB donors = 2598 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.156" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1308" Evaluating: 1308-7 Parameter: NUMWAT <- "1301" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1301" Comparing "1081" and "1301". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.156" Parameter: BOX -> "34.156" Parameter: BOX -> "34.156" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.15600 B = 34.15600 C = 34.15600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7871 2 1 -1 0 -1 3.7344 3 1 -1 1 -1 4.4445 4 1 0 -1 -1 3.8073 5 1 0 0 -1 1.6605 6 1 0 1 -1 3.0160 7 1 -1 -1 0 3.0348 8 1 -1 0 0 2.3584 9 1 -1 1 0 2.5781 10 1 0 -1 0 1.2158 11 1 0 1 0 1.2158 12 1 -1 -1 1 3.7199 13 1 -1 0 1 3.7450 14 1 -1 1 1 4.4338 15 1 0 -1 1 3.0160 16 1 0 0 1 1.6605 17 1 0 1 1 3.8073 18 1 1 1 1 6.7871 19 1 1 0 1 3.7344 20 1 1 -1 1 4.4445 21 1 1 1 0 3.0348 22 1 1 0 0 2.3584 23 1 1 -1 0 2.5781 24 1 1 1 -1 3.7199 25 1 1 0 -1 3.7450 26 1 1 -1 -1 4.4338 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3885 atoms have been selected out of 3959 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 102 34 34 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 501 167 167 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 111 37 37 0.89 Total of13354 atoms and 4443 groups and 4438 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3959 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1308 Number of atoms = 3959 Number of groups = 1313 Number of bonds = 3952 Number of angles = 1412 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1310 Number of HB donors = 2598 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1308 Number of atoms = 3959 Number of groups = 1313 Number of bonds = 3952 Number of angles = 1412 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1310 Number of HB donors = 2598 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.154" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1308" Evaluating: 1308-7 Parameter: NUMWAT <- "1301" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1301" Comparing "1081" and "1301". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.154" Parameter: BOX -> "34.154" Parameter: BOX -> "34.154" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.15400 B = 34.15400 C = 34.15400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7889 2 1 -1 0 -1 3.7316 3 1 -1 1 -1 4.4410 4 1 0 -1 -1 3.8045 5 1 0 0 -1 1.6586 6 1 0 1 -1 3.0133 7 1 -1 -1 0 3.0320 8 1 -1 0 0 2.3565 9 1 -1 1 0 2.5770 10 1 0 -1 0 1.2154 11 1 0 1 0 1.2154 12 1 -1 -1 1 3.7165 13 1 -1 0 1 3.7422 14 1 -1 1 1 4.4309 15 1 0 -1 1 3.0133 16 1 0 0 1 1.6586 17 1 0 1 1 3.8045 18 1 1 1 1 6.7889 19 1 1 0 1 3.7316 20 1 1 -1 1 4.4410 21 1 1 1 0 3.0320 22 1 1 0 0 2.3565 23 1 1 -1 0 2.5770 24 1 1 1 -1 3.7165 25 1 1 0 -1 3.7422 26 1 1 -1 -1 4.4309 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3885 atoms have been selected out of 3959 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 102 34 34 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 501 167 167 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 111 37 37 0.89 Total of13357 atoms and 4444 groups and 4439 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3959 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1308 Number of atoms = 3959 Number of groups = 1313 Number of bonds = 3952 Number of angles = 1412 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1310 Number of HB donors = 2598 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1308 Number of atoms = 3959 Number of groups = 1313 Number of bonds = 3952 Number of angles = 1412 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1310 Number of HB donors = 2598 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.152" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1308" Evaluating: 1308-7 Parameter: NUMWAT <- "1301" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1301" Comparing "1081" and "1301". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.152" Parameter: BOX -> "34.152" Parameter: BOX -> "34.152" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.15200 B = 34.15200 C = 34.15200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7907 2 1 -1 0 -1 3.7288 3 1 -1 1 -1 4.4376 4 1 0 -1 -1 3.8018 5 1 0 0 -1 1.6567 6 1 0 1 -1 3.0105 7 1 -1 -1 0 3.0293 8 1 -1 0 0 2.3545 9 1 -1 1 0 2.5758 10 1 0 -1 0 1.2150 11 1 0 1 0 1.2150 12 1 -1 -1 1 3.7130 13 1 -1 0 1 3.7395 14 1 -1 1 1 4.4280 15 1 0 -1 1 3.0105 16 1 0 0 1 1.6567 17 1 0 1 1 3.8018 18 1 1 1 1 6.7907 19 1 1 0 1 3.7288 20 1 1 -1 1 4.4376 21 1 1 1 0 3.0293 22 1 1 0 0 2.3545 23 1 1 -1 0 2.5758 24 1 1 1 -1 3.7130 25 1 1 0 -1 3.7395 26 1 1 -1 -1 4.4280 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3885 atoms have been selected out of 3959 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 102 34 34 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 501 167 167 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 111 37 37 0.89 Total of13357 atoms and 4444 groups and 4439 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3959 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1308 Number of atoms = 3959 Number of groups = 1313 Number of bonds = 3952 Number of angles = 1412 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1310 Number of HB donors = 2598 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1308 Number of atoms = 3959 Number of groups = 1313 Number of bonds = 3952 Number of angles = 1412 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1310 Number of HB donors = 2598 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.15" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1308" Evaluating: 1308-7 Parameter: NUMWAT <- "1301" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1301" Comparing "1081" and "1301". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.15" Parameter: BOX -> "34.15" Parameter: BOX -> "34.15" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.15000 B = 34.15000 C = 34.15000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7924 2 1 -1 0 -1 3.7261 3 1 -1 1 -1 4.4342 4 1 0 -1 -1 3.7990 5 1 0 0 -1 1.6548 6 1 0 1 -1 3.0078 7 1 -1 -1 0 3.0266 8 1 -1 0 0 2.3526 9 1 -1 1 0 2.5747 10 1 0 -1 0 1.2146 11 1 0 1 0 1.2146 12 1 -1 -1 1 3.7096 13 1 -1 0 1 3.7367 14 1 -1 1 1 4.4251 15 1 0 -1 1 3.0078 16 1 0 0 1 1.6548 17 1 0 1 1 3.7990 18 1 1 1 1 6.7924 19 1 1 0 1 3.7261 20 1 1 -1 1 4.4342 21 1 1 1 0 3.0266 22 1 1 0 0 2.3526 23 1 1 -1 0 2.5747 24 1 1 1 -1 3.7096 25 1 1 0 -1 3.7367 26 1 1 -1 -1 4.4251 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3885 atoms have been selected out of 3959 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 102 34 34 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 501 167 167 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 114 38 38 0.88 Total of13366 atoms and 4447 groups and 4442 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3959 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1308 Number of atoms = 3959 Number of groups = 1313 Number of bonds = 3952 Number of angles = 1412 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1310 Number of HB donors = 2598 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1308 Number of atoms = 3959 Number of groups = 1313 Number of bonds = 3952 Number of angles = 1412 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1310 Number of HB donors = 2598 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.148" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1308" Evaluating: 1308-7 Parameter: NUMWAT <- "1301" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1301" Comparing "1081" and "1301". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.148" Parameter: BOX -> "34.148" Parameter: BOX -> "34.148" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.14800 B = 34.14800 C = 34.14800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7942 2 1 -1 0 -1 3.7233 3 1 -1 1 -1 4.4307 4 1 0 -1 -1 3.7962 5 1 0 0 -1 1.6529 6 1 0 1 -1 3.0050 7 1 -1 -1 0 3.0238 8 1 -1 0 0 2.3507 9 1 -1 1 0 2.5735 10 1 0 -1 0 1.2142 11 1 0 1 0 1.2142 12 1 -1 -1 1 3.7061 13 1 -1 0 1 3.7339 14 1 -1 1 1 4.4222 15 1 0 -1 1 3.0050 16 1 0 0 1 1.6529 17 1 0 1 1 3.7962 18 1 1 1 1 6.7942 19 1 1 0 1 3.7233 20 1 1 -1 1 4.4307 21 1 1 1 0 3.0238 22 1 1 0 0 2.3507 23 1 1 -1 0 2.5735 24 1 1 1 -1 3.7061 25 1 1 0 -1 3.7339 26 1 1 -1 -1 4.4222 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3885 atoms have been selected out of 3959 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 102 34 34 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 501 167 167 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 114 38 38 0.88 Total of13372 atoms and 4449 groups and 4444 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3959 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1308 Number of atoms = 3959 Number of groups = 1313 Number of bonds = 3952 Number of angles = 1412 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1310 Number of HB donors = 2598 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1308 Number of atoms = 3959 Number of groups = 1313 Number of bonds = 3952 Number of angles = 1412 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1310 Number of HB donors = 2598 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.146" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1308" Evaluating: 1308-7 Parameter: NUMWAT <- "1301" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1301" Comparing "1081" and "1301". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.146" Parameter: BOX -> "34.146" Parameter: BOX -> "34.146" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.14600 B = 34.14600 C = 34.14600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7960 2 1 -1 0 -1 3.7205 3 1 -1 1 -1 4.4273 4 1 0 -1 -1 3.7935 5 1 0 0 -1 1.6510 6 1 0 1 -1 3.0023 7 1 -1 -1 0 3.0211 8 1 -1 0 0 2.3488 9 1 -1 1 0 2.5724 10 1 0 -1 0 1.2138 11 1 0 1 0 1.2138 12 1 -1 -1 1 3.7027 13 1 -1 0 1 3.7312 14 1 -1 1 1 4.4193 15 1 0 -1 1 3.0023 16 1 0 0 1 1.6510 17 1 0 1 1 3.7935 18 1 1 1 1 6.7960 19 1 1 0 1 3.7205 20 1 1 -1 1 4.4273 21 1 1 1 0 3.0211 22 1 1 0 0 2.3488 23 1 1 -1 0 2.5724 24 1 1 1 -1 3.7027 25 1 1 0 -1 3.7312 26 1 1 -1 -1 4.4193 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3885 atoms have been selected out of 3959 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 102 34 34 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 114 38 38 0.88 Total of13375 atoms and 4450 groups and 4445 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3959 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1308 Number of atoms = 3959 Number of groups = 1313 Number of bonds = 3952 Number of angles = 1412 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1310 Number of HB donors = 2598 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1308 Number of atoms = 3959 Number of groups = 1313 Number of bonds = 3952 Number of angles = 1412 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1310 Number of HB donors = 2598 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.144" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1308" Evaluating: 1308-7 Parameter: NUMWAT <- "1301" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1301" Comparing "1081" and "1301". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.144" Parameter: BOX -> "34.144" Parameter: BOX -> "34.144" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.14400 B = 34.14400 C = 34.14400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7978 2 1 -1 0 -1 3.7177 3 1 -1 1 -1 4.4239 4 1 0 -1 -1 3.7907 5 1 0 0 -1 1.6491 6 1 0 1 -1 2.9996 7 1 -1 -1 0 3.0184 8 1 -1 0 0 2.3468 9 1 -1 1 0 2.5713 10 1 0 -1 0 1.2134 11 1 0 1 0 1.2134 12 1 -1 -1 1 3.6992 13 1 -1 0 1 3.7284 14 1 -1 1 1 4.4164 15 1 0 -1 1 2.9996 16 1 0 0 1 1.6491 17 1 0 1 1 3.7907 18 1 1 1 1 6.7978 19 1 1 0 1 3.7177 20 1 1 -1 1 4.4239 21 1 1 1 0 3.0184 22 1 1 0 0 2.3468 23 1 1 -1 0 2.5713 24 1 1 1 -1 3.6992 25 1 1 0 -1 3.7284 26 1 1 -1 -1 4.4164 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3885 atoms have been selected out of 3959 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 684 OPERATED ON BY TRANSFORMATION C011 RESIDUE 852 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 393 131 131 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 495 165 165 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 534 178 178 0.00 10 C010 has 1707 569 569 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 114 38 38 0.88 Total of13372 atoms and 4449 groups and 4444 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3959 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1306 Number of atoms = 3953 Number of groups = 1311 Number of bonds = 3946 Number of angles = 1410 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1308 Number of HB donors = 2594 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1306 Number of atoms = 3953 Number of groups = 1311 Number of bonds = 3946 Number of angles = 1410 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1308 Number of HB donors = 2594 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.142" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1306" Evaluating: 1306-7 Parameter: NUMWAT <- "1299" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1299" Comparing "1081" and "1299". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.142" Parameter: BOX -> "34.142" Parameter: BOX -> "34.142" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.14200 B = 34.14200 C = 34.14200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7996 2 1 -1 0 -1 3.7150 3 1 -1 1 -1 4.4204 4 1 0 -1 -1 3.7880 5 1 0 0 -1 1.6473 6 1 0 1 -1 2.9968 7 1 -1 -1 0 3.0156 8 1 -1 0 0 2.3449 9 1 -1 1 0 2.5702 10 1 0 -1 0 1.2130 11 1 0 1 0 1.2130 12 1 -1 -1 1 3.6958 13 1 -1 0 1 3.7256 14 1 -1 1 1 4.4135 15 1 0 -1 1 2.9968 16 1 0 0 1 1.6473 17 1 0 1 1 3.7880 18 1 1 1 1 6.7996 19 1 1 0 1 3.7150 20 1 1 -1 1 4.4204 21 1 1 1 0 3.0156 22 1 1 0 0 2.3449 23 1 1 -1 0 2.5702 24 1 1 1 -1 3.6958 25 1 1 0 -1 3.7256 26 1 1 -1 -1 4.4135 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3879 atoms have been selected out of 3953 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 690 230 230 0.00 3 C003 has 99 33 33 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 495 165 165 0.00 7 C007 has 732 244 244 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.88 Total of13309 atoms and 4428 groups and 4423 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3953 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1306 Number of atoms = 3953 Number of groups = 1311 Number of bonds = 3946 Number of angles = 1410 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1308 Number of HB donors = 2594 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1306 Number of atoms = 3953 Number of groups = 1311 Number of bonds = 3946 Number of angles = 1410 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1308 Number of HB donors = 2594 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.14" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1306" Evaluating: 1306-7 Parameter: NUMWAT <- "1299" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1299" Comparing "1081" and "1299". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.14" Parameter: BOX -> "34.14" Parameter: BOX -> "34.14" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.14000 B = 34.14000 C = 34.14000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8014 2 1 -1 0 -1 3.7122 3 1 -1 1 -1 4.4170 4 1 0 -1 -1 3.7852 5 1 0 0 -1 1.6454 6 1 0 1 -1 2.9941 7 1 -1 -1 0 3.0129 8 1 -1 0 0 2.3430 9 1 -1 1 0 2.5690 10 1 0 -1 0 1.2126 11 1 0 1 0 1.2126 12 1 -1 -1 1 3.6923 13 1 -1 0 1 3.7229 14 1 -1 1 1 4.4106 15 1 0 -1 1 2.9941 16 1 0 0 1 1.6454 17 1 0 1 1 3.7852 18 1 1 1 1 6.8014 19 1 1 0 1 3.7122 20 1 1 -1 1 4.4170 21 1 1 1 0 3.0129 22 1 1 0 0 2.3430 23 1 1 -1 0 2.5690 24 1 1 1 -1 3.6923 25 1 1 0 -1 3.7229 26 1 1 -1 -1 4.4106 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3879 atoms have been selected out of 3953 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 690 230 230 0.00 3 C003 has 99 33 33 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 495 165 165 0.00 7 C007 has 732 244 244 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.87 Total of13309 atoms and 4428 groups and 4423 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3953 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1306 Number of atoms = 3953 Number of groups = 1311 Number of bonds = 3946 Number of angles = 1410 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1308 Number of HB donors = 2594 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1306 Number of atoms = 3953 Number of groups = 1311 Number of bonds = 3946 Number of angles = 1410 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1308 Number of HB donors = 2594 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.138" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1306" Evaluating: 1306-7 Parameter: NUMWAT <- "1299" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1299" Comparing "1081" and "1299". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.138" Parameter: BOX -> "34.138" Parameter: BOX -> "34.138" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.13800 B = 34.13800 C = 34.13800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8031 2 1 -1 0 -1 3.7094 3 1 -1 1 -1 4.4136 4 1 0 -1 -1 3.7824 5 1 0 0 -1 1.6435 6 1 0 1 -1 2.9914 7 1 -1 -1 0 3.0102 8 1 -1 0 0 2.3411 9 1 -1 1 0 2.5679 10 1 0 -1 0 1.2122 11 1 0 1 0 1.2122 12 1 -1 -1 1 3.6889 13 1 -1 0 1 3.7201 14 1 -1 1 1 4.4077 15 1 0 -1 1 2.9914 16 1 0 0 1 1.6435 17 1 0 1 1 3.7824 18 1 1 1 1 6.8031 19 1 1 0 1 3.7094 20 1 1 -1 1 4.4136 21 1 1 1 0 3.0102 22 1 1 0 0 2.3411 23 1 1 -1 0 2.5679 24 1 1 1 -1 3.6889 25 1 1 0 -1 3.7201 26 1 1 -1 -1 4.4077 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3879 atoms have been selected out of 3953 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 690 230 230 0.00 3 C003 has 99 33 33 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 495 165 165 0.00 7 C007 has 732 244 244 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.87 Total of13309 atoms and 4428 groups and 4423 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3953 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1306 Number of atoms = 3953 Number of groups = 1311 Number of bonds = 3946 Number of angles = 1410 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1308 Number of HB donors = 2594 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1306 Number of atoms = 3953 Number of groups = 1311 Number of bonds = 3946 Number of angles = 1410 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1308 Number of HB donors = 2594 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.136" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1306" Evaluating: 1306-7 Parameter: NUMWAT <- "1299" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1299" Comparing "1081" and "1299". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.136" Parameter: BOX -> "34.136" Parameter: BOX -> "34.136" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.13600 B = 34.13600 C = 34.13600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8049 2 1 -1 0 -1 3.7067 3 1 -1 1 -1 4.4101 4 1 0 -1 -1 3.7797 5 1 0 0 -1 1.6416 6 1 0 1 -1 2.9886 7 1 -1 -1 0 3.0074 8 1 -1 0 0 2.3391 9 1 -1 1 0 2.5668 10 1 0 -1 0 1.2118 11 1 0 1 0 1.2118 12 1 -1 -1 1 3.6854 13 1 -1 0 1 3.7173 14 1 -1 1 1 4.4048 15 1 0 -1 1 2.9886 16 1 0 0 1 1.6416 17 1 0 1 1 3.7797 18 1 1 1 1 6.8049 19 1 1 0 1 3.7067 20 1 1 -1 1 4.4101 21 1 1 1 0 3.0074 22 1 1 0 0 2.3391 23 1 1 -1 0 2.5668 24 1 1 1 -1 3.6854 25 1 1 0 -1 3.7173 26 1 1 -1 -1 4.4048 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3879 atoms have been selected out of 3953 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 690 230 230 0.00 3 C003 has 99 33 33 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 495 165 165 0.00 7 C007 has 732 244 244 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.87 Total of13309 atoms and 4428 groups and 4423 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3953 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1306 Number of atoms = 3953 Number of groups = 1311 Number of bonds = 3946 Number of angles = 1410 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1308 Number of HB donors = 2594 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1306 Number of atoms = 3953 Number of groups = 1311 Number of bonds = 3946 Number of angles = 1410 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1308 Number of HB donors = 2594 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.134" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1306" Evaluating: 1306-7 Parameter: NUMWAT <- "1299" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1299" Comparing "1081" and "1299". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.134" Parameter: BOX -> "34.134" Parameter: BOX -> "34.134" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.13400 B = 34.13400 C = 34.13400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8067 2 1 -1 0 -1 3.7039 3 1 -1 1 -1 4.4067 4 1 0 -1 -1 3.7769 5 1 0 0 -1 1.6397 6 1 0 1 -1 2.9859 7 1 -1 -1 0 3.0047 8 1 -1 0 0 2.3372 9 1 -1 1 0 2.5657 10 1 0 -1 0 1.2114 11 1 0 1 0 1.2114 12 1 -1 -1 1 3.6820 13 1 -1 0 1 3.7146 14 1 -1 1 1 4.4019 15 1 0 -1 1 2.9859 16 1 0 0 1 1.6397 17 1 0 1 1 3.7769 18 1 1 1 1 6.8067 19 1 1 0 1 3.7039 20 1 1 -1 1 4.4067 21 1 1 1 0 3.0047 22 1 1 0 0 2.3372 23 1 1 -1 0 2.5657 24 1 1 1 -1 3.6820 25 1 1 0 -1 3.7146 26 1 1 -1 -1 4.4019 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3879 atoms have been selected out of 3953 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 864 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 687 229 229 0.00 3 C003 has 99 33 33 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 492 164 164 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.87 Total of13312 atoms and 4429 groups and 4424 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3953 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1305 Number of atoms = 3950 Number of groups = 1310 Number of bonds = 3943 Number of angles = 1409 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1307 Number of HB donors = 2592 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1305 Number of atoms = 3950 Number of groups = 1310 Number of bonds = 3943 Number of angles = 1409 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1307 Number of HB donors = 2592 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.132" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1305" Evaluating: 1305-7 Parameter: NUMWAT <- "1298" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1298" Comparing "1081" and "1298". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.132" Parameter: BOX -> "34.132" Parameter: BOX -> "34.132" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.13200 B = 34.13200 C = 34.13200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8085 2 1 -1 0 -1 3.7011 3 1 -1 1 -1 4.4032 4 1 0 -1 -1 3.7741 5 1 0 0 -1 1.6378 6 1 0 1 -1 2.9832 7 1 -1 -1 0 3.0020 8 1 -1 0 0 2.3353 9 1 -1 1 0 2.5646 10 1 0 -1 0 1.2110 11 1 0 1 0 1.2110 12 1 -1 -1 1 3.6785 13 1 -1 0 1 3.7118 14 1 -1 1 1 4.3990 15 1 0 -1 1 2.9832 16 1 0 0 1 1.6378 17 1 0 1 1 3.7741 18 1 1 1 1 6.8085 19 1 1 0 1 3.7011 20 1 1 -1 1 4.4032 21 1 1 1 0 3.0020 22 1 1 0 0 2.3353 23 1 1 -1 0 2.5646 24 1 1 1 -1 3.6785 25 1 1 0 -1 3.7118 26 1 1 -1 -1 4.3990 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3876 atoms have been selected out of 3950 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 687 229 229 0.00 3 C003 has 99 33 33 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 492 164 164 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.87 Total of13303 atoms and 4426 groups and 4421 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3950 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1305 Number of atoms = 3950 Number of groups = 1310 Number of bonds = 3943 Number of angles = 1409 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1307 Number of HB donors = 2592 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1305 Number of atoms = 3950 Number of groups = 1310 Number of bonds = 3943 Number of angles = 1409 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1307 Number of HB donors = 2592 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.13" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1305" Evaluating: 1305-7 Parameter: NUMWAT <- "1298" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1298" Comparing "1081" and "1298". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.13" Parameter: BOX -> "34.13" Parameter: BOX -> "34.13" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.13000 B = 34.13000 C = 34.13000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8103 2 1 -1 0 -1 3.6984 3 1 -1 1 -1 4.3998 4 1 0 -1 -1 3.7714 5 1 0 0 -1 1.6359 6 1 0 1 -1 2.9804 7 1 -1 -1 0 2.9993 8 1 -1 0 0 2.3334 9 1 -1 1 0 2.5635 10 1 0 -1 0 1.2107 11 1 0 1 0 1.2107 12 1 -1 -1 1 3.6751 13 1 -1 0 1 3.7090 14 1 -1 1 1 4.3961 15 1 0 -1 1 2.9804 16 1 0 0 1 1.6359 17 1 0 1 1 3.7714 18 1 1 1 1 6.8103 19 1 1 0 1 3.6984 20 1 1 -1 1 4.3998 21 1 1 1 0 2.9993 22 1 1 0 0 2.3334 23 1 1 -1 0 2.5635 24 1 1 1 -1 3.6751 25 1 1 0 -1 3.7090 26 1 1 -1 -1 4.3961 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3876 atoms have been selected out of 3950 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 687 229 229 0.00 3 C003 has 99 33 33 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 492 164 164 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.86 Total of13303 atoms and 4426 groups and 4421 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3950 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1305 Number of atoms = 3950 Number of groups = 1310 Number of bonds = 3943 Number of angles = 1409 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1307 Number of HB donors = 2592 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1305 Number of atoms = 3950 Number of groups = 1310 Number of bonds = 3943 Number of angles = 1409 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1307 Number of HB donors = 2592 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.128" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1305" Evaluating: 1305-7 Parameter: NUMWAT <- "1298" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1298" Comparing "1081" and "1298". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.128" Parameter: BOX -> "34.128" Parameter: BOX -> "34.128" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.12800 B = 34.12800 C = 34.12800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8121 2 1 -1 0 -1 3.6956 3 1 -1 1 -1 4.3964 4 1 0 -1 -1 3.7686 5 1 0 0 -1 1.6340 6 1 0 1 -1 2.9777 7 1 -1 -1 0 2.9965 8 1 -1 0 0 2.3314 9 1 -1 1 0 2.5623 10 1 0 -1 0 1.2103 11 1 0 1 0 1.2103 12 1 -1 -1 1 3.6716 13 1 -1 0 1 3.7063 14 1 -1 1 1 4.3932 15 1 0 -1 1 2.9777 16 1 0 0 1 1.6340 17 1 0 1 1 3.7686 18 1 1 1 1 6.8121 19 1 1 0 1 3.6956 20 1 1 -1 1 4.3964 21 1 1 1 0 2.9965 22 1 1 0 0 2.3314 23 1 1 -1 0 2.5623 24 1 1 1 -1 3.6716 25 1 1 0 -1 3.7063 26 1 1 -1 -1 4.3932 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3876 atoms have been selected out of 3950 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 687 229 229 0.00 3 C003 has 99 33 33 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 492 164 164 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.86 Total of13306 atoms and 4427 groups and 4422 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3950 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1305 Number of atoms = 3950 Number of groups = 1310 Number of bonds = 3943 Number of angles = 1409 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1307 Number of HB donors = 2592 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1305 Number of atoms = 3950 Number of groups = 1310 Number of bonds = 3943 Number of angles = 1409 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1307 Number of HB donors = 2592 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.126" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1305" Evaluating: 1305-7 Parameter: NUMWAT <- "1298" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1298" Comparing "1081" and "1298". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.126" Parameter: BOX -> "34.126" Parameter: BOX -> "34.126" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.12600 B = 34.12600 C = 34.12600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8139 2 1 -1 0 -1 3.6928 3 1 -1 1 -1 4.3929 4 1 0 -1 -1 3.7659 5 1 0 0 -1 1.6321 6 1 0 1 -1 2.9750 7 1 -1 -1 0 2.9938 8 1 -1 0 0 2.3295 9 1 -1 1 0 2.5612 10 1 0 -1 0 1.2099 11 1 0 1 0 1.2099 12 1 -1 -1 1 3.6682 13 1 -1 0 1 3.7035 14 1 -1 1 1 4.3903 15 1 0 -1 1 2.9750 16 1 0 0 1 1.6321 17 1 0 1 1 3.7659 18 1 1 1 1 6.8139 19 1 1 0 1 3.6928 20 1 1 -1 1 4.3929 21 1 1 1 0 2.9938 22 1 1 0 0 2.3295 23 1 1 -1 0 2.5612 24 1 1 1 -1 3.6682 25 1 1 0 -1 3.7035 26 1 1 -1 -1 4.3903 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3876 atoms have been selected out of 3950 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 687 229 229 0.00 3 C003 has 99 33 33 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 492 164 164 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.86 Total of13306 atoms and 4427 groups and 4422 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3950 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1305 Number of atoms = 3950 Number of groups = 1310 Number of bonds = 3943 Number of angles = 1409 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1307 Number of HB donors = 2592 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1305 Number of atoms = 3950 Number of groups = 1310 Number of bonds = 3943 Number of angles = 1409 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1307 Number of HB donors = 2592 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.124" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1305" Evaluating: 1305-7 Parameter: NUMWAT <- "1298" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1298" Comparing "1081" and "1298". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.124" Parameter: BOX -> "34.124" Parameter: BOX -> "34.124" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.12400 B = 34.12400 C = 34.12400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8157 2 1 -1 0 -1 3.6901 3 1 -1 1 -1 4.3895 4 1 0 -1 -1 3.7631 5 1 0 0 -1 1.6302 6 1 0 1 -1 2.9722 7 1 -1 -1 0 2.9911 8 1 -1 0 0 2.3276 9 1 -1 1 0 2.5601 10 1 0 -1 0 1.2095 11 1 0 1 0 1.2095 12 1 -1 -1 1 3.6647 13 1 -1 0 1 3.7007 14 1 -1 1 1 4.3874 15 1 0 -1 1 2.9722 16 1 0 0 1 1.6302 17 1 0 1 1 3.7631 18 1 1 1 1 6.8157 19 1 1 0 1 3.6901 20 1 1 -1 1 4.3895 21 1 1 1 0 2.9911 22 1 1 0 0 2.3276 23 1 1 -1 0 2.5601 24 1 1 1 -1 3.6647 25 1 1 0 -1 3.7007 26 1 1 -1 -1 4.3874 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3876 atoms have been selected out of 3950 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 687 229 229 0.00 3 C003 has 99 33 33 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 492 164 164 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.86 Total of13306 atoms and 4427 groups and 4422 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3950 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1305 Number of atoms = 3950 Number of groups = 1310 Number of bonds = 3943 Number of angles = 1409 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1307 Number of HB donors = 2592 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1305 Number of atoms = 3950 Number of groups = 1310 Number of bonds = 3943 Number of angles = 1409 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1307 Number of HB donors = 2592 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.122" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1305" Evaluating: 1305-7 Parameter: NUMWAT <- "1298" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1298" Comparing "1081" and "1298". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.122" Parameter: BOX -> "34.122" Parameter: BOX -> "34.122" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.12200 B = 34.12200 C = 34.12200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8175 2 1 -1 0 -1 3.6873 3 1 -1 1 -1 4.3861 4 1 0 -1 -1 3.7603 5 1 0 0 -1 1.6283 6 1 0 1 -1 2.9695 7 1 -1 -1 0 2.9883 8 1 -1 0 0 2.3257 9 1 -1 1 0 2.5590 10 1 0 -1 0 1.2092 11 1 0 1 0 1.2092 12 1 -1 -1 1 3.6613 13 1 -1 0 1 3.6980 14 1 -1 1 1 4.3845 15 1 0 -1 1 2.9695 16 1 0 0 1 1.6283 17 1 0 1 1 3.7603 18 1 1 1 1 6.8175 19 1 1 0 1 3.6873 20 1 1 -1 1 4.3861 21 1 1 1 0 2.9883 22 1 1 0 0 2.3257 23 1 1 -1 0 2.5590 24 1 1 1 -1 3.6613 25 1 1 0 -1 3.6980 26 1 1 -1 -1 4.3845 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3876 atoms have been selected out of 3950 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 687 229 229 0.00 3 C003 has 99 33 33 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 492 164 164 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.86 Total of13306 atoms and 4427 groups and 4422 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3950 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1305 Number of atoms = 3950 Number of groups = 1310 Number of bonds = 3943 Number of angles = 1409 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1307 Number of HB donors = 2592 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1305 Number of atoms = 3950 Number of groups = 1310 Number of bonds = 3943 Number of angles = 1409 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1307 Number of HB donors = 2592 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.12" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1305" Evaluating: 1305-7 Parameter: NUMWAT <- "1298" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1298" Comparing "1081" and "1298". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.12" Parameter: BOX -> "34.12" Parameter: BOX -> "34.12" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.12000 B = 34.12000 C = 34.12000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8193 2 1 -1 0 -1 3.6845 3 1 -1 1 -1 4.3826 4 1 0 -1 -1 3.7576 5 1 0 0 -1 1.6264 6 1 0 1 -1 2.9667 7 1 -1 -1 0 2.9856 8 1 -1 0 0 2.3237 9 1 -1 1 0 2.5579 10 1 0 -1 0 1.2088 11 1 0 1 0 1.2088 12 1 -1 -1 1 3.6578 13 1 -1 0 1 3.6952 14 1 -1 1 1 4.3817 15 1 0 -1 1 2.9667 16 1 0 0 1 1.6264 17 1 0 1 1 3.7576 18 1 1 1 1 6.8193 19 1 1 0 1 3.6845 20 1 1 -1 1 4.3826 21 1 1 1 0 2.9856 22 1 1 0 0 2.3237 23 1 1 -1 0 2.5579 24 1 1 1 -1 3.6578 25 1 1 0 -1 3.6952 26 1 1 -1 -1 4.3817 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3876 atoms have been selected out of 3950 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 687 229 229 0.00 3 C003 has 99 33 33 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 492 164 164 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.85 Total of13306 atoms and 4427 groups and 4422 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3950 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1305 Number of atoms = 3950 Number of groups = 1310 Number of bonds = 3943 Number of angles = 1409 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1307 Number of HB donors = 2592 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1305 Number of atoms = 3950 Number of groups = 1310 Number of bonds = 3943 Number of angles = 1409 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1307 Number of HB donors = 2592 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.118" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1305" Evaluating: 1305-7 Parameter: NUMWAT <- "1298" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1298" Comparing "1081" and "1298". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.118" Parameter: BOX -> "34.118" Parameter: BOX -> "34.118" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.11800 B = 34.11800 C = 34.11800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8211 2 1 -1 0 -1 3.6818 3 1 -1 1 -1 4.3792 4 1 0 -1 -1 3.7548 5 1 0 0 -1 1.6246 6 1 0 1 -1 2.9640 7 1 -1 -1 0 2.9829 8 1 -1 0 0 2.3218 9 1 -1 1 0 2.5568 10 1 0 -1 0 1.2084 11 1 0 1 0 1.2084 12 1 -1 -1 1 3.6544 13 1 -1 0 1 3.6924 14 1 -1 1 1 4.3788 15 1 0 -1 1 2.9640 16 1 0 0 1 1.6246 17 1 0 1 1 3.7548 18 1 1 1 1 6.8211 19 1 1 0 1 3.6818 20 1 1 -1 1 4.3792 21 1 1 1 0 2.9829 22 1 1 0 0 2.3218 23 1 1 -1 0 2.5568 24 1 1 1 -1 3.6544 25 1 1 0 -1 3.6924 26 1 1 -1 -1 4.3788 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3876 atoms have been selected out of 3950 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 687 229 229 0.00 3 C003 has 99 33 33 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 492 164 164 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.85 Total of13309 atoms and 4428 groups and 4423 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3950 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1305 Number of atoms = 3950 Number of groups = 1310 Number of bonds = 3943 Number of angles = 1409 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1307 Number of HB donors = 2592 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1305 Number of atoms = 3950 Number of groups = 1310 Number of bonds = 3943 Number of angles = 1409 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1307 Number of HB donors = 2592 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.116" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1305" Evaluating: 1305-7 Parameter: NUMWAT <- "1298" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1298" Comparing "1081" and "1298". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.116" Parameter: BOX -> "34.116" Parameter: BOX -> "34.116" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.11600 B = 34.11600 C = 34.11600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8229 2 1 -1 0 -1 3.6790 3 1 -1 1 -1 4.3758 4 1 0 -1 -1 3.7521 5 1 0 0 -1 1.6227 6 1 0 1 -1 2.9613 7 1 -1 -1 0 2.9801 8 1 -1 0 0 2.3199 9 1 -1 1 0 2.5558 10 1 0 -1 0 1.2081 11 1 0 1 0 1.2081 12 1 -1 -1 1 3.6509 13 1 -1 0 1 3.6897 14 1 -1 1 1 4.3759 15 1 0 -1 1 2.9613 16 1 0 0 1 1.6227 17 1 0 1 1 3.7521 18 1 1 1 1 6.8229 19 1 1 0 1 3.6790 20 1 1 -1 1 4.3758 21 1 1 1 0 2.9801 22 1 1 0 0 2.3199 23 1 1 -1 0 2.5558 24 1 1 1 -1 3.6509 25 1 1 0 -1 3.6897 26 1 1 -1 -1 4.3759 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3876 atoms have been selected out of 3950 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 687 229 229 0.00 3 C003 has 99 33 33 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 492 164 164 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.85 Total of13312 atoms and 4429 groups and 4424 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3950 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1305 Number of atoms = 3950 Number of groups = 1310 Number of bonds = 3943 Number of angles = 1409 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1307 Number of HB donors = 2592 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1305 Number of atoms = 3950 Number of groups = 1310 Number of bonds = 3943 Number of angles = 1409 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1307 Number of HB donors = 2592 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.114" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1305" Evaluating: 1305-7 Parameter: NUMWAT <- "1298" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1298" Comparing "1081" and "1298". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.114" Parameter: BOX -> "34.114" Parameter: BOX -> "34.114" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.11400 B = 34.11400 C = 34.11400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8247 2 1 -1 0 -1 3.6762 3 1 -1 1 -1 4.3723 4 1 0 -1 -1 3.7493 5 1 0 0 -1 1.6208 6 1 0 1 -1 2.9585 7 1 -1 -1 0 2.9774 8 1 -1 0 0 2.3180 9 1 -1 1 0 2.5547 10 1 0 -1 0 1.2077 11 1 0 1 0 1.2077 12 1 -1 -1 1 3.6475 13 1 -1 0 1 3.6869 14 1 -1 1 1 4.3730 15 1 0 -1 1 2.9585 16 1 0 0 1 1.6208 17 1 0 1 1 3.7493 18 1 1 1 1 6.8247 19 1 1 0 1 3.6762 20 1 1 -1 1 4.3723 21 1 1 1 0 2.9774 22 1 1 0 0 2.3180 23 1 1 -1 0 2.5547 24 1 1 1 -1 3.6475 25 1 1 0 -1 3.6869 26 1 1 -1 -1 4.3730 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3876 atoms have been selected out of 3950 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 687 229 229 0.00 3 C003 has 99 33 33 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 492 164 164 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.85 Total of13312 atoms and 4429 groups and 4424 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3950 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1305 Number of atoms = 3950 Number of groups = 1310 Number of bonds = 3943 Number of angles = 1409 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1307 Number of HB donors = 2592 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1305 Number of atoms = 3950 Number of groups = 1310 Number of bonds = 3943 Number of angles = 1409 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1307 Number of HB donors = 2592 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.112" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1305" Evaluating: 1305-7 Parameter: NUMWAT <- "1298" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1298" Comparing "1081" and "1298". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.112" Parameter: BOX -> "34.112" Parameter: BOX -> "34.112" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.11200 B = 34.11200 C = 34.11200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8265 2 1 -1 0 -1 3.6735 3 1 -1 1 -1 4.3689 4 1 0 -1 -1 3.7465 5 1 0 0 -1 1.6189 6 1 0 1 -1 2.9558 7 1 -1 -1 0 2.9747 8 1 -1 0 0 2.3160 9 1 -1 1 0 2.5536 10 1 0 -1 0 1.2074 11 1 0 1 0 1.2074 12 1 -1 -1 1 3.6440 13 1 -1 0 1 3.6841 14 1 -1 1 1 4.3701 15 1 0 -1 1 2.9558 16 1 0 0 1 1.6189 17 1 0 1 1 3.7465 18 1 1 1 1 6.8265 19 1 1 0 1 3.6735 20 1 1 -1 1 4.3689 21 1 1 1 0 2.9747 22 1 1 0 0 2.3160 23 1 1 -1 0 2.5536 24 1 1 1 -1 3.6440 25 1 1 0 -1 3.6841 26 1 1 -1 -1 4.3701 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3876 atoms have been selected out of 3950 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 690 230 230 0.00 3 C003 has 99 33 33 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 492 164 164 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.85 Total of13315 atoms and 4430 groups and 4425 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3950 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1305 Number of atoms = 3950 Number of groups = 1310 Number of bonds = 3943 Number of angles = 1409 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1307 Number of HB donors = 2592 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1305 Number of atoms = 3950 Number of groups = 1310 Number of bonds = 3943 Number of angles = 1409 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1307 Number of HB donors = 2592 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.11" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1305" Evaluating: 1305-7 Parameter: NUMWAT <- "1298" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1298" Comparing "1081" and "1298". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.11" Parameter: BOX -> "34.11" Parameter: BOX -> "34.11" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.11000 B = 34.11000 C = 34.11000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8283 2 1 -1 0 -1 3.6707 3 1 -1 1 -1 4.3655 4 1 0 -1 -1 3.7438 5 1 0 0 -1 1.6170 6 1 0 1 -1 2.9531 7 1 -1 -1 0 2.9720 8 1 -1 0 0 2.3141 9 1 -1 1 0 2.5525 10 1 0 -1 0 1.2070 11 1 0 1 0 1.2070 12 1 -1 -1 1 3.6406 13 1 -1 0 1 3.6814 14 1 -1 1 1 4.3672 15 1 0 -1 1 2.9531 16 1 0 0 1 1.6170 17 1 0 1 1 3.7438 18 1 1 1 1 6.8283 19 1 1 0 1 3.6707 20 1 1 -1 1 4.3655 21 1 1 1 0 2.9720 22 1 1 0 0 2.3141 23 1 1 -1 0 2.5525 24 1 1 1 -1 3.6406 25 1 1 0 -1 3.6814 26 1 1 -1 -1 4.3672 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3876 atoms have been selected out of 3950 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 690 230 230 0.00 3 C003 has 99 33 33 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 492 164 164 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.84 Total of13315 atoms and 4430 groups and 4425 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3950 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1305 Number of atoms = 3950 Number of groups = 1310 Number of bonds = 3943 Number of angles = 1409 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1307 Number of HB donors = 2592 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1305 Number of atoms = 3950 Number of groups = 1310 Number of bonds = 3943 Number of angles = 1409 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1307 Number of HB donors = 2592 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.108" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1305" Evaluating: 1305-7 Parameter: NUMWAT <- "1298" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1298" Comparing "1081" and "1298". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.108" Parameter: BOX -> "34.108" Parameter: BOX -> "34.108" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.10800 B = 34.10800 C = 34.10800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8301 2 1 -1 0 -1 3.6679 3 1 -1 1 -1 4.3620 4 1 0 -1 -1 3.7410 5 1 0 0 -1 1.6151 6 1 0 1 -1 2.9503 7 1 -1 -1 0 2.9692 8 1 -1 0 0 2.3122 9 1 -1 1 0 2.5514 10 1 0 -1 0 1.2067 11 1 0 1 0 1.2067 12 1 -1 -1 1 3.6372 13 1 -1 0 1 3.6786 14 1 -1 1 1 4.3643 15 1 0 -1 1 2.9503 16 1 0 0 1 1.6151 17 1 0 1 1 3.7410 18 1 1 1 1 6.8301 19 1 1 0 1 3.6679 20 1 1 -1 1 4.3620 21 1 1 1 0 2.9692 22 1 1 0 0 2.3122 23 1 1 -1 0 2.5514 24 1 1 1 -1 3.6372 25 1 1 0 -1 3.6786 26 1 1 -1 -1 4.3643 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3876 atoms have been selected out of 3950 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1065 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 690 230 230 0.00 3 C003 has 99 33 33 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 495 165 165 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.84 Total of13318 atoms and 4431 groups and 4426 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3950 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1304 Number of atoms = 3947 Number of groups = 1309 Number of bonds = 3940 Number of angles = 1408 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1306 Number of HB donors = 2590 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1304 Number of atoms = 3947 Number of groups = 1309 Number of bonds = 3940 Number of angles = 1408 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1306 Number of HB donors = 2590 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.106" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1304" Evaluating: 1304-7 Parameter: NUMWAT <- "1297" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1297" Comparing "1081" and "1297". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.106" Parameter: BOX -> "34.106" Parameter: BOX -> "34.106" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.10600 B = 34.10600 C = 34.10600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8319 2 1 -1 0 -1 3.6652 3 1 -1 1 -1 4.3586 4 1 0 -1 -1 3.7382 5 1 0 0 -1 1.6132 6 1 0 1 -1 2.9476 7 1 -1 -1 0 2.9665 8 1 -1 0 0 2.3103 9 1 -1 1 0 2.5503 10 1 0 -1 0 1.2064 11 1 0 1 0 1.2064 12 1 -1 -1 1 3.6337 13 1 -1 0 1 3.6758 14 1 -1 1 1 4.3615 15 1 0 -1 1 2.9476 16 1 0 0 1 1.6132 17 1 0 1 1 3.7382 18 1 1 1 1 6.8319 19 1 1 0 1 3.6652 20 1 1 -1 1 4.3586 21 1 1 1 0 2.9665 22 1 1 0 0 2.3103 23 1 1 -1 0 2.5503 24 1 1 1 -1 3.6337 25 1 1 0 -1 3.6758 26 1 1 -1 -1 4.3615 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3873 atoms have been selected out of 3947 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 690 230 230 0.00 3 C003 has 99 33 33 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 492 164 164 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.84 Total of13306 atoms and 4427 groups and 4422 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3947 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1304 Number of atoms = 3947 Number of groups = 1309 Number of bonds = 3940 Number of angles = 1408 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1306 Number of HB donors = 2590 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1304 Number of atoms = 3947 Number of groups = 1309 Number of bonds = 3940 Number of angles = 1408 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1306 Number of HB donors = 2590 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.104" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1304" Evaluating: 1304-7 Parameter: NUMWAT <- "1297" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1297" Comparing "1081" and "1297". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.104" Parameter: BOX -> "34.104" Parameter: BOX -> "34.104" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.10400 B = 34.10400 C = 34.10400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8337 2 1 -1 0 -1 3.6624 3 1 -1 1 -1 4.3552 4 1 0 -1 -1 3.7355 5 1 0 0 -1 1.6113 6 1 0 1 -1 2.9449 7 1 -1 -1 0 2.9638 8 1 -1 0 0 2.3083 9 1 -1 1 0 2.5493 10 1 0 -1 0 1.2060 11 1 0 1 0 1.2060 12 1 -1 -1 1 3.6303 13 1 -1 0 1 3.6731 14 1 -1 1 1 4.3586 15 1 0 -1 1 2.9449 16 1 0 0 1 1.6113 17 1 0 1 1 3.7355 18 1 1 1 1 6.8337 19 1 1 0 1 3.6624 20 1 1 -1 1 4.3552 21 1 1 1 0 2.9638 22 1 1 0 0 2.3083 23 1 1 -1 0 2.5493 24 1 1 1 -1 3.6303 25 1 1 0 -1 3.6731 26 1 1 -1 -1 4.3586 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3873 atoms have been selected out of 3947 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 690 230 230 0.00 3 C003 has 99 33 33 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 492 164 164 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.84 Total of13306 atoms and 4427 groups and 4422 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3947 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1304 Number of atoms = 3947 Number of groups = 1309 Number of bonds = 3940 Number of angles = 1408 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1306 Number of HB donors = 2590 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1304 Number of atoms = 3947 Number of groups = 1309 Number of bonds = 3940 Number of angles = 1408 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1306 Number of HB donors = 2590 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.102" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1304" Evaluating: 1304-7 Parameter: NUMWAT <- "1297" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1297" Comparing "1081" and "1297". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.102" Parameter: BOX -> "34.102" Parameter: BOX -> "34.102" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.10200 B = 34.10200 C = 34.10200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8355 2 1 -1 0 -1 3.6596 3 1 -1 1 -1 4.3517 4 1 0 -1 -1 3.7327 5 1 0 0 -1 1.6095 6 1 0 1 -1 2.9421 7 1 -1 -1 0 2.9610 8 1 -1 0 0 2.3064 9 1 -1 1 0 2.5482 10 1 0 -1 0 1.2057 11 1 0 1 0 1.2057 12 1 -1 -1 1 3.6268 13 1 -1 0 1 3.6703 14 1 -1 1 1 4.3557 15 1 0 -1 1 2.9421 16 1 0 0 1 1.6095 17 1 0 1 1 3.7327 18 1 1 1 1 6.8355 19 1 1 0 1 3.6596 20 1 1 -1 1 4.3517 21 1 1 1 0 2.9610 22 1 1 0 0 2.3064 23 1 1 -1 0 2.5482 24 1 1 1 -1 3.6268 25 1 1 0 -1 3.6703 26 1 1 -1 -1 4.3557 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3873 atoms have been selected out of 3947 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 690 230 230 0.00 3 C003 has 99 33 33 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 492 164 164 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.84 Total of13315 atoms and 4430 groups and 4425 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3947 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1304 Number of atoms = 3947 Number of groups = 1309 Number of bonds = 3940 Number of angles = 1408 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1306 Number of HB donors = 2590 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1304 Number of atoms = 3947 Number of groups = 1309 Number of bonds = 3940 Number of angles = 1408 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1306 Number of HB donors = 2590 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.1" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1304" Evaluating: 1304-7 Parameter: NUMWAT <- "1297" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1297" Comparing "1081" and "1297". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.1" Parameter: BOX -> "34.1" Parameter: BOX -> "34.1" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.10000 B = 34.10000 C = 34.10000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8373 2 1 -1 0 -1 3.6569 3 1 -1 1 -1 4.3483 4 1 0 -1 -1 3.7300 5 1 0 0 -1 1.6076 6 1 0 1 -1 2.9394 7 1 -1 -1 0 2.9583 8 1 -1 0 0 2.3045 9 1 -1 1 0 2.5471 10 1 0 -1 0 1.2054 11 1 0 1 0 1.2054 12 1 -1 -1 1 3.6234 13 1 -1 0 1 3.6675 14 1 -1 1 1 4.3528 15 1 0 -1 1 2.9394 16 1 0 0 1 1.6076 17 1 0 1 1 3.7300 18 1 1 1 1 6.8373 19 1 1 0 1 3.6569 20 1 1 -1 1 4.3483 21 1 1 1 0 2.9583 22 1 1 0 0 2.3045 23 1 1 -1 0 2.5471 24 1 1 1 -1 3.6234 25 1 1 0 -1 3.6675 26 1 1 -1 -1 4.3528 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3873 atoms have been selected out of 3947 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 492 164 164 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.83 Total of13321 atoms and 4432 groups and 4427 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3947 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1304 Number of atoms = 3947 Number of groups = 1309 Number of bonds = 3940 Number of angles = 1408 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1306 Number of HB donors = 2590 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1304 Number of atoms = 3947 Number of groups = 1309 Number of bonds = 3940 Number of angles = 1408 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1306 Number of HB donors = 2590 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.098" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1304" Evaluating: 1304-7 Parameter: NUMWAT <- "1297" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1297" Comparing "1081" and "1297". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.098" Parameter: BOX -> "34.098" Parameter: BOX -> "34.098" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.09800 B = 34.09800 C = 34.09800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8392 2 1 -1 0 -1 3.6541 3 1 -1 1 -1 4.3449 4 1 0 -1 -1 3.7272 5 1 0 0 -1 1.6057 6 1 0 1 -1 2.9367 7 1 -1 -1 0 2.9556 8 1 -1 0 0 2.3026 9 1 -1 1 0 2.5460 10 1 0 -1 0 1.2050 11 1 0 1 0 1.2050 12 1 -1 -1 1 3.6199 13 1 -1 0 1 3.6648 14 1 -1 1 1 4.3499 15 1 0 -1 1 2.9367 16 1 0 0 1 1.6057 17 1 0 1 1 3.7272 18 1 1 1 1 6.8392 19 1 1 0 1 3.6541 20 1 1 -1 1 4.3449 21 1 1 1 0 2.9556 22 1 1 0 0 2.3026 23 1 1 -1 0 2.5460 24 1 1 1 -1 3.6199 25 1 1 0 -1 3.6648 26 1 1 -1 -1 4.3499 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3873 atoms have been selected out of 3947 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 492 164 164 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.83 Total of13321 atoms and 4432 groups and 4427 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3947 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1304 Number of atoms = 3947 Number of groups = 1309 Number of bonds = 3940 Number of angles = 1408 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1306 Number of HB donors = 2590 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1304 Number of atoms = 3947 Number of groups = 1309 Number of bonds = 3940 Number of angles = 1408 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1306 Number of HB donors = 2590 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.096" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1304" Evaluating: 1304-7 Parameter: NUMWAT <- "1297" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1297" Comparing "1081" and "1297". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.096" Parameter: BOX -> "34.096" Parameter: BOX -> "34.096" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.09600 B = 34.09600 C = 34.09600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8410 2 1 -1 0 -1 3.6513 3 1 -1 1 -1 4.3414 4 1 0 -1 -1 3.7244 5 1 0 0 -1 1.6038 6 1 0 1 -1 2.9339 7 1 -1 -1 0 2.9529 8 1 -1 0 0 2.3007 9 1 -1 1 0 2.5450 10 1 0 -1 0 1.2047 11 1 0 1 0 1.2047 12 1 -1 -1 1 3.6165 13 1 -1 0 1 3.6620 14 1 -1 1 1 4.3471 15 1 0 -1 1 2.9339 16 1 0 0 1 1.6038 17 1 0 1 1 3.7244 18 1 1 1 1 6.8410 19 1 1 0 1 3.6513 20 1 1 -1 1 4.3414 21 1 1 1 0 2.9529 22 1 1 0 0 2.3007 23 1 1 -1 0 2.5450 24 1 1 1 -1 3.6165 25 1 1 0 -1 3.6620 26 1 1 -1 -1 4.3471 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3873 atoms have been selected out of 3947 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1131 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 492 164 164 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1710 570 570 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 120 40 40 0.83 Total of13324 atoms and 4433 groups and 4428 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3947 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.094" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1303" Evaluating: 1303-7 Parameter: NUMWAT <- "1296" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1296" Comparing "1081" and "1296". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.094" Parameter: BOX -> "34.094" Parameter: BOX -> "34.094" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.09400 B = 34.09400 C = 34.09400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8428 2 1 -1 0 -1 3.6486 3 1 -1 1 -1 4.3380 4 1 0 -1 -1 3.7217 5 1 0 0 -1 1.6019 6 1 0 1 -1 2.9312 7 1 -1 -1 0 2.9501 8 1 -1 0 0 2.2987 9 1 -1 1 0 2.5439 10 1 0 -1 0 1.2044 11 1 0 1 0 1.2044 12 1 -1 -1 1 3.6130 13 1 -1 0 1 3.6593 14 1 -1 1 1 4.3442 15 1 0 -1 1 2.9312 16 1 0 0 1 1.6019 17 1 0 1 1 3.7217 18 1 1 1 1 6.8428 19 1 1 0 1 3.6486 20 1 1 -1 1 4.3380 21 1 1 1 0 2.9501 22 1 1 0 0 2.2987 23 1 1 -1 0 2.5439 24 1 1 1 -1 3.6130 25 1 1 0 -1 3.6593 26 1 1 -1 -1 4.3442 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3870 atoms have been selected out of 3944 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 492 164 164 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1707 569 569 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 120 40 40 0.83 Total of13318 atoms and 4431 groups and 4426 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3944 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.092" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1303" Evaluating: 1303-7 Parameter: NUMWAT <- "1296" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1296" Comparing "1081" and "1296". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.092" Parameter: BOX -> "34.092" Parameter: BOX -> "34.092" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.09200 B = 34.09200 C = 34.09200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8446 2 1 -1 0 -1 3.6458 3 1 -1 1 -1 4.3346 4 1 0 -1 -1 3.7189 5 1 0 0 -1 1.6000 6 1 0 1 -1 2.9285 7 1 -1 -1 0 2.9474 8 1 -1 0 0 2.2968 9 1 -1 1 0 2.5429 10 1 0 -1 0 1.2041 11 1 0 1 0 1.2041 12 1 -1 -1 1 3.6096 13 1 -1 0 1 3.6565 14 1 -1 1 1 4.3413 15 1 0 -1 1 2.9285 16 1 0 0 1 1.6000 17 1 0 1 1 3.7189 18 1 1 1 1 6.8446 19 1 1 0 1 3.6458 20 1 1 -1 1 4.3346 21 1 1 1 0 2.9474 22 1 1 0 0 2.2968 23 1 1 -1 0 2.5429 24 1 1 1 -1 3.6096 25 1 1 0 -1 3.6565 26 1 1 -1 -1 4.3413 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3870 atoms have been selected out of 3944 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 492 164 164 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1707 569 569 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 120 40 40 0.83 Total of13318 atoms and 4431 groups and 4426 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3944 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.09" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1303" Evaluating: 1303-7 Parameter: NUMWAT <- "1296" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1296" Comparing "1081" and "1296". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.09" Parameter: BOX -> "34.09" Parameter: BOX -> "34.09" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.09000 B = 34.09000 C = 34.09000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8464 2 1 -1 0 -1 3.6431 3 1 -1 1 -1 4.3311 4 1 0 -1 -1 3.7162 5 1 0 0 -1 1.5981 6 1 0 1 -1 2.9258 7 1 -1 -1 0 2.9447 8 1 -1 0 0 2.2949 9 1 -1 1 0 2.5418 10 1 0 -1 0 1.2038 11 1 0 1 0 1.2038 12 1 -1 -1 1 3.6061 13 1 -1 0 1 3.6537 14 1 -1 1 1 4.3384 15 1 0 -1 1 2.9258 16 1 0 0 1 1.5981 17 1 0 1 1 3.7162 18 1 1 1 1 6.8464 19 1 1 0 1 3.6431 20 1 1 -1 1 4.3311 21 1 1 1 0 2.9447 22 1 1 0 0 2.2949 23 1 1 -1 0 2.5418 24 1 1 1 -1 3.6061 25 1 1 0 -1 3.6537 26 1 1 -1 -1 4.3384 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3870 atoms have been selected out of 3944 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 492 164 164 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1707 569 569 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 120 40 40 0.82 Total of13321 atoms and 4432 groups and 4427 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3944 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.088" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1303" Evaluating: 1303-7 Parameter: NUMWAT <- "1296" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1296" Comparing "1081" and "1296". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.088" Parameter: BOX -> "34.088" Parameter: BOX -> "34.088" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.08800 B = 34.08800 C = 34.08800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8482 2 1 -1 0 -1 3.6403 3 1 -1 1 -1 4.3277 4 1 0 -1 -1 3.7134 5 1 0 0 -1 1.5962 6 1 0 1 -1 2.9230 7 1 -1 -1 0 2.9420 8 1 -1 0 0 2.2930 9 1 -1 1 0 2.5407 10 1 0 -1 0 1.2035 11 1 0 1 0 1.2035 12 1 -1 -1 1 3.6027 13 1 -1 0 1 3.6510 14 1 -1 1 1 4.3356 15 1 0 -1 1 2.9230 16 1 0 0 1 1.5962 17 1 0 1 1 3.7134 18 1 1 1 1 6.8482 19 1 1 0 1 3.6403 20 1 1 -1 1 4.3277 21 1 1 1 0 2.9420 22 1 1 0 0 2.2930 23 1 1 -1 0 2.5407 24 1 1 1 -1 3.6027 25 1 1 0 -1 3.6510 26 1 1 -1 -1 4.3356 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3870 atoms have been selected out of 3944 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 495 165 165 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1707 569 569 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 120 40 40 0.82 Total of13327 atoms and 4434 groups and 4429 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3944 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.086" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1303" Evaluating: 1303-7 Parameter: NUMWAT <- "1296" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1296" Comparing "1081" and "1296". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.086" Parameter: BOX -> "34.086" Parameter: BOX -> "34.086" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.08600 B = 34.08600 C = 34.08600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8501 2 1 -1 0 -1 3.6375 3 1 -1 1 -1 4.3243 4 1 0 -1 -1 3.7106 5 1 0 0 -1 1.5944 6 1 0 1 -1 2.9203 7 1 -1 -1 0 2.9392 8 1 -1 0 0 2.2910 9 1 -1 1 0 2.5397 10 1 0 -1 0 1.2031 11 1 0 1 0 1.2031 12 1 -1 -1 1 3.5992 13 1 -1 0 1 3.6482 14 1 -1 1 1 4.3327 15 1 0 -1 1 2.9203 16 1 0 0 1 1.5944 17 1 0 1 1 3.7106 18 1 1 1 1 6.8501 19 1 1 0 1 3.6375 20 1 1 -1 1 4.3243 21 1 1 1 0 2.9392 22 1 1 0 0 2.2910 23 1 1 -1 0 2.5397 24 1 1 1 -1 3.5992 25 1 1 0 -1 3.6482 26 1 1 -1 -1 4.3327 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3870 atoms have been selected out of 3944 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 498 166 166 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1707 569 569 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 120 40 40 0.82 Total of13330 atoms and 4435 groups and 4430 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3944 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.084" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1303" Evaluating: 1303-7 Parameter: NUMWAT <- "1296" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1296" Comparing "1081" and "1296". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.084" Parameter: BOX -> "34.084" Parameter: BOX -> "34.084" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.08400 B = 34.08400 C = 34.08400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8519 2 1 -1 0 -1 3.6348 3 1 -1 1 -1 4.3208 4 1 0 -1 -1 3.7079 5 1 0 0 -1 1.5925 6 1 0 1 -1 2.9176 7 1 -1 -1 0 2.9365 8 1 -1 0 0 2.2891 9 1 -1 1 0 2.5386 10 1 0 -1 0 1.2028 11 1 0 1 0 1.2028 12 1 -1 -1 1 3.5958 13 1 -1 0 1 3.6454 14 1 -1 1 1 4.3298 15 1 0 -1 1 2.9176 16 1 0 0 1 1.5925 17 1 0 1 1 3.7079 18 1 1 1 1 6.8519 19 1 1 0 1 3.6348 20 1 1 -1 1 4.3208 21 1 1 1 0 2.9365 22 1 1 0 0 2.2891 23 1 1 -1 0 2.5386 24 1 1 1 -1 3.5958 25 1 1 0 -1 3.6454 26 1 1 -1 -1 4.3298 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3870 atoms have been selected out of 3944 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 498 166 166 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1707 569 569 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 120 40 40 0.82 Total of13330 atoms and 4435 groups and 4430 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3944 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.082" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1303" Evaluating: 1303-7 Parameter: NUMWAT <- "1296" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1296" Comparing "1081" and "1296". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.082" Parameter: BOX -> "34.082" Parameter: BOX -> "34.082" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.08200 B = 34.08200 C = 34.08200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8537 2 1 -1 0 -1 3.6320 3 1 -1 1 -1 4.3174 4 1 0 -1 -1 3.7051 5 1 0 0 -1 1.5906 6 1 0 1 -1 2.9148 7 1 -1 -1 0 2.9338 8 1 -1 0 0 2.2872 9 1 -1 1 0 2.5376 10 1 0 -1 0 1.2025 11 1 0 1 0 1.2025 12 1 -1 -1 1 3.5923 13 1 -1 0 1 3.6427 14 1 -1 1 1 4.3269 15 1 0 -1 1 2.9148 16 1 0 0 1 1.5906 17 1 0 1 1 3.7051 18 1 1 1 1 6.8537 19 1 1 0 1 3.6320 20 1 1 -1 1 4.3174 21 1 1 1 0 2.9338 22 1 1 0 0 2.2872 23 1 1 -1 0 2.5376 24 1 1 1 -1 3.5923 25 1 1 0 -1 3.6427 26 1 1 -1 -1 4.3269 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3870 atoms have been selected out of 3944 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 501 167 167 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1707 569 569 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 120 40 40 0.82 Total of13333 atoms and 4436 groups and 4431 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3944 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.08" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1303" Evaluating: 1303-7 Parameter: NUMWAT <- "1296" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1296" Comparing "1081" and "1296". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.08" Parameter: BOX -> "34.08" Parameter: BOX -> "34.08" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.08000 B = 34.08000 C = 34.08000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8555 2 1 -1 0 -1 3.6292 3 1 -1 1 -1 4.3139 4 1 0 -1 -1 3.7024 5 1 0 0 -1 1.5887 6 1 0 1 -1 2.9121 7 1 -1 -1 0 2.9310 8 1 -1 0 0 2.2853 9 1 -1 1 0 2.5366 10 1 0 -1 0 1.2022 11 1 0 1 0 1.2022 12 1 -1 -1 1 3.5889 13 1 -1 0 1 3.6399 14 1 -1 1 1 4.3241 15 1 0 -1 1 2.9121 16 1 0 0 1 1.5887 17 1 0 1 1 3.7024 18 1 1 1 1 6.8555 19 1 1 0 1 3.6292 20 1 1 -1 1 4.3139 21 1 1 1 0 2.9310 22 1 1 0 0 2.2853 23 1 1 -1 0 2.5366 24 1 1 1 -1 3.5889 25 1 1 0 -1 3.6399 26 1 1 -1 -1 4.3241 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3870 atoms have been selected out of 3944 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 501 167 167 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1707 569 569 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 120 40 40 0.81 Total of13333 atoms and 4436 groups and 4431 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3944 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.078" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1303" Evaluating: 1303-7 Parameter: NUMWAT <- "1296" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1296" Comparing "1081" and "1296". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.078" Parameter: BOX -> "34.078" Parameter: BOX -> "34.078" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.07800 B = 34.07800 C = 34.07800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8574 2 1 -1 0 -1 3.6265 3 1 -1 1 -1 4.3105 4 1 0 -1 -1 3.6996 5 1 0 0 -1 1.5868 6 1 0 1 -1 2.9094 7 1 -1 -1 0 2.9283 8 1 -1 0 0 2.2834 9 1 -1 1 0 2.5355 10 1 0 -1 0 1.2019 11 1 0 1 0 1.2019 12 1 -1 -1 1 3.5854 13 1 -1 0 1 3.6371 14 1 -1 1 1 4.3212 15 1 0 -1 1 2.9094 16 1 0 0 1 1.5868 17 1 0 1 1 3.6996 18 1 1 1 1 6.8574 19 1 1 0 1 3.6265 20 1 1 -1 1 4.3105 21 1 1 1 0 2.9283 22 1 1 0 0 2.2834 23 1 1 -1 0 2.5355 24 1 1 1 -1 3.5854 25 1 1 0 -1 3.6371 26 1 1 -1 -1 4.3212 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3870 atoms have been selected out of 3944 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 501 167 167 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1707 569 569 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 120 40 40 0.81 Total of13333 atoms and 4436 groups and 4431 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3944 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.076" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1303" Evaluating: 1303-7 Parameter: NUMWAT <- "1296" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1296" Comparing "1081" and "1296". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.076" Parameter: BOX -> "34.076" Parameter: BOX -> "34.076" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.07600 B = 34.07600 C = 34.07600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8592 2 1 -1 0 -1 3.6237 3 1 -1 1 -1 4.3071 4 1 0 -1 -1 3.6968 5 1 0 0 -1 1.5849 6 1 0 1 -1 2.9066 7 1 -1 -1 0 2.9256 8 1 -1 0 0 2.2814 9 1 -1 1 0 2.5345 10 1 0 -1 0 1.2017 11 1 0 1 0 1.2017 12 1 -1 -1 1 3.5820 13 1 -1 0 1 3.6344 14 1 -1 1 1 4.3183 15 1 0 -1 1 2.9066 16 1 0 0 1 1.5849 17 1 0 1 1 3.6968 18 1 1 1 1 6.8592 19 1 1 0 1 3.6237 20 1 1 -1 1 4.3071 21 1 1 1 0 2.9256 22 1 1 0 0 2.2814 23 1 1 -1 0 2.5345 24 1 1 1 -1 3.5820 25 1 1 0 -1 3.6344 26 1 1 -1 -1 4.3183 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3870 atoms have been selected out of 3944 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 501 167 167 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1707 569 569 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 120 40 40 0.81 Total of13333 atoms and 4436 groups and 4431 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3944 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.074" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1303" Evaluating: 1303-7 Parameter: NUMWAT <- "1296" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1296" Comparing "1081" and "1296". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.074" Parameter: BOX -> "34.074" Parameter: BOX -> "34.074" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.07400 B = 34.07400 C = 34.07400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8610 2 1 -1 0 -1 3.6209 3 1 -1 1 -1 4.3036 4 1 0 -1 -1 3.6941 5 1 0 0 -1 1.5831 6 1 0 1 -1 2.9039 7 1 -1 -1 0 2.9229 8 1 -1 0 0 2.2795 9 1 -1 1 0 2.5334 10 1 0 -1 0 1.2014 11 1 0 1 0 1.2014 12 1 -1 -1 1 3.5785 13 1 -1 0 1 3.6316 14 1 -1 1 1 4.3155 15 1 0 -1 1 2.9039 16 1 0 0 1 1.5831 17 1 0 1 1 3.6941 18 1 1 1 1 6.8610 19 1 1 0 1 3.6209 20 1 1 -1 1 4.3036 21 1 1 1 0 2.9229 22 1 1 0 0 2.2795 23 1 1 -1 0 2.5334 24 1 1 1 -1 3.5785 25 1 1 0 -1 3.6316 26 1 1 -1 -1 4.3155 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3870 atoms have been selected out of 3944 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 501 167 167 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1707 569 569 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 0.81 Total of13336 atoms and 4437 groups and 4432 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3944 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.072" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1303" Evaluating: 1303-7 Parameter: NUMWAT <- "1296" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1296" Comparing "1081" and "1296". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.072" Parameter: BOX -> "34.072" Parameter: BOX -> "34.072" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.07200 B = 34.07200 C = 34.07200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8628 2 1 -1 0 -1 3.6182 3 1 -1 1 -1 4.3002 4 1 0 -1 -1 3.6913 5 1 0 0 -1 1.5812 6 1 0 1 -1 2.9012 7 1 -1 -1 0 2.9201 8 1 -1 0 0 2.2776 9 1 -1 1 0 2.5324 10 1 0 -1 0 1.2011 11 1 0 1 0 1.2011 12 1 -1 -1 1 3.5751 13 1 -1 0 1 3.6288 14 1 -1 1 1 4.3126 15 1 0 -1 1 2.9012 16 1 0 0 1 1.5812 17 1 0 1 1 3.6913 18 1 1 1 1 6.8628 19 1 1 0 1 3.6182 20 1 1 -1 1 4.3002 21 1 1 1 0 2.9201 22 1 1 0 0 2.2776 23 1 1 -1 0 2.5324 24 1 1 1 -1 3.5751 25 1 1 0 -1 3.6288 26 1 1 -1 -1 4.3126 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3870 atoms have been selected out of 3944 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 501 167 167 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1707 569 569 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 126 42 42 0.81 Total of13339 atoms and 4438 groups and 4433 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3944 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.07" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1303" Evaluating: 1303-7 Parameter: NUMWAT <- "1296" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1296" Comparing "1081" and "1296". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.07" Parameter: BOX -> "34.07" Parameter: BOX -> "34.07" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.07000 B = 34.07000 C = 34.07000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8647 2 1 -1 0 -1 3.6154 3 1 -1 1 -1 4.2968 4 1 0 -1 -1 3.6886 5 1 0 0 -1 1.5793 6 1 0 1 -1 2.8984 7 1 -1 -1 0 2.9174 8 1 -1 0 0 2.2757 9 1 -1 1 0 2.5314 10 1 0 -1 0 1.2008 11 1 0 1 0 1.2008 12 1 -1 -1 1 3.5716 13 1 -1 0 1 3.6261 14 1 -1 1 1 4.3097 15 1 0 -1 1 2.8984 16 1 0 0 1 1.5793 17 1 0 1 1 3.6886 18 1 1 1 1 6.8647 19 1 1 0 1 3.6154 20 1 1 -1 1 4.2968 21 1 1 1 0 2.9174 22 1 1 0 0 2.2757 23 1 1 -1 0 2.5314 24 1 1 1 -1 3.5716 25 1 1 0 -1 3.6261 26 1 1 -1 -1 4.3097 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3870 atoms have been selected out of 3944 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1707 569 569 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 126 42 42 0.80 Total of13342 atoms and 4439 groups and 4434 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3944 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.068" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1303" Evaluating: 1303-7 Parameter: NUMWAT <- "1296" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1296" Comparing "1081" and "1296". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.068" Parameter: BOX -> "34.068" Parameter: BOX -> "34.068" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.06800 B = 34.06800 C = 34.06800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8665 2 1 -1 0 -1 3.6126 3 1 -1 1 -1 4.2933 4 1 0 -1 -1 3.6858 5 1 0 0 -1 1.5774 6 1 0 1 -1 2.8957 7 1 -1 -1 0 2.9147 8 1 -1 0 0 2.2737 9 1 -1 1 0 2.5304 10 1 0 -1 0 1.2005 11 1 0 1 0 1.2005 12 1 -1 -1 1 3.5682 13 1 -1 0 1 3.6233 14 1 -1 1 1 4.3069 15 1 0 -1 1 2.8957 16 1 0 0 1 1.5774 17 1 0 1 1 3.6858 18 1 1 1 1 6.8665 19 1 1 0 1 3.6126 20 1 1 -1 1 4.2933 21 1 1 1 0 2.9147 22 1 1 0 0 2.2737 23 1 1 -1 0 2.5304 24 1 1 1 -1 3.5682 25 1 1 0 -1 3.6233 26 1 1 -1 -1 4.3069 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3870 atoms have been selected out of 3944 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 507 169 169 0.00 10 C010 has 1707 569 569 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 126 42 42 0.80 Total of13345 atoms and 4440 groups and 4435 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3944 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.066" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1303" Evaluating: 1303-7 Parameter: NUMWAT <- "1296" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1296" Comparing "1081" and "1296". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.066" Parameter: BOX -> "34.066" Parameter: BOX -> "34.066" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.06600 B = 34.06600 C = 34.06600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8683 2 1 -1 0 -1 3.6099 3 1 -1 1 -1 4.2899 4 1 0 -1 -1 3.6830 5 1 0 0 -1 1.5755 6 1 0 1 -1 2.8930 7 1 -1 -1 0 2.9120 8 1 -1 0 0 2.2718 9 1 -1 1 0 2.5293 10 1 0 -1 0 1.2002 11 1 0 1 0 1.2002 12 1 -1 -1 1 3.5647 13 1 -1 0 1 3.6206 14 1 -1 1 1 4.3040 15 1 0 -1 1 2.8930 16 1 0 0 1 1.5755 17 1 0 1 1 3.6830 18 1 1 1 1 6.8683 19 1 1 0 1 3.6099 20 1 1 -1 1 4.2899 21 1 1 1 0 2.9120 22 1 1 0 0 2.2718 23 1 1 -1 0 2.5293 24 1 1 1 -1 3.5647 25 1 1 0 -1 3.6206 26 1 1 -1 -1 4.3040 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3870 atoms have been selected out of 3944 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 507 169 169 0.00 10 C010 has 1707 569 569 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 126 42 42 0.80 Total of13345 atoms and 4440 groups and 4435 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3944 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1303 Number of atoms = 3944 Number of groups = 1308 Number of bonds = 3937 Number of angles = 1407 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1305 Number of HB donors = 2588 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.064" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1303" Evaluating: 1303-7 Parameter: NUMWAT <- "1296" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1296" Comparing "1081" and "1296". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.064" Parameter: BOX -> "34.064" Parameter: BOX -> "34.064" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.06400 B = 34.06400 C = 34.06400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8702 2 1 -1 0 -1 3.6071 3 1 -1 1 -1 4.2865 4 1 0 -1 -1 3.6803 5 1 0 0 -1 1.5736 6 1 0 1 -1 2.8903 7 1 -1 -1 0 2.9092 8 1 -1 0 0 2.2699 9 1 -1 1 0 2.5283 10 1 0 -1 0 1.2000 11 1 0 1 0 1.2000 12 1 -1 -1 1 3.5613 13 1 -1 0 1 3.6178 14 1 -1 1 1 4.3011 15 1 0 -1 1 2.8903 16 1 0 0 1 1.5736 17 1 0 1 1 3.6803 18 1 1 1 1 6.8702 19 1 1 0 1 3.6071 20 1 1 -1 1 4.2865 21 1 1 1 0 2.9092 22 1 1 0 0 2.2699 23 1 1 -1 0 2.5283 24 1 1 1 -1 3.5613 25 1 1 0 -1 3.6178 26 1 1 -1 -1 4.3011 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3870 atoms have been selected out of 3944 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 174 OPERATED ON BY TRANSFORMATION C008 RESIDUE 504 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1707 569 569 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 126 42 42 0.80 Total of13339 atoms and 4438 groups and 4433 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3944 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1301 Number of atoms = 3938 Number of groups = 1306 Number of bonds = 3931 Number of angles = 1405 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1303 Number of HB donors = 2584 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1301 Number of atoms = 3938 Number of groups = 1306 Number of bonds = 3931 Number of angles = 1405 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1303 Number of HB donors = 2584 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.062" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1301" Evaluating: 1301-7 Parameter: NUMWAT <- "1294" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1294" Comparing "1081" and "1294". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.062" Parameter: BOX -> "34.062" Parameter: BOX -> "34.062" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.06200 B = 34.06200 C = 34.06200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8720 2 1 -1 0 -1 3.6044 3 1 -1 1 -1 4.2830 4 1 0 -1 -1 3.6775 5 1 0 0 -1 1.5718 6 1 0 1 -1 2.8875 7 1 -1 -1 0 2.9065 8 1 -1 0 0 2.2680 9 1 -1 1 0 3.9891 10 1 0 -1 0 1.1997 11 1 0 1 0 1.1997 12 1 -1 -1 1 3.5578 13 1 -1 0 1 3.6150 14 1 -1 1 1 4.2983 15 1 0 -1 1 2.8875 16 1 0 0 1 1.5718 17 1 0 1 1 3.6775 18 1 1 1 1 6.8720 19 1 1 0 1 3.6044 20 1 1 -1 1 4.2830 21 1 1 1 0 2.9065 22 1 1 0 0 2.2680 23 1 1 -1 0 3.9891 24 1 1 1 -1 3.5578 25 1 1 0 -1 3.6150 26 1 1 -1 -1 4.2983 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3864 atoms have been selected out of 3938 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 390 130 130 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 126 42 42 0.80 Total of13324 atoms and 4433 groups and 4428 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3938 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1301 Number of atoms = 3938 Number of groups = 1306 Number of bonds = 3931 Number of angles = 1405 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1303 Number of HB donors = 2584 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1301 Number of atoms = 3938 Number of groups = 1306 Number of bonds = 3931 Number of angles = 1405 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1303 Number of HB donors = 2584 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.06" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1301" Evaluating: 1301-7 Parameter: NUMWAT <- "1294" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1294" Comparing "1081" and "1294". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.06" Parameter: BOX -> "34.06" Parameter: BOX -> "34.06" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.06000 B = 34.06000 C = 34.06000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8738 2 1 -1 0 -1 3.6016 3 1 -1 1 -1 4.2796 4 1 0 -1 -1 3.6748 5 1 0 0 -1 1.5699 6 1 0 1 -1 2.8848 7 1 -1 -1 0 2.9038 8 1 -1 0 0 2.2661 9 1 -1 1 0 3.9870 10 1 0 -1 0 1.1994 11 1 0 1 0 1.1994 12 1 -1 -1 1 3.5544 13 1 -1 0 1 3.6123 14 1 -1 1 1 4.2954 15 1 0 -1 1 2.8848 16 1 0 0 1 1.5699 17 1 0 1 1 3.6748 18 1 1 1 1 6.8738 19 1 1 0 1 3.6016 20 1 1 -1 1 4.2796 21 1 1 1 0 2.9038 22 1 1 0 0 2.2661 23 1 1 -1 0 3.9870 24 1 1 1 -1 3.5544 25 1 1 0 -1 3.6123 26 1 1 -1 -1 4.2954 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3864 atoms have been selected out of 3938 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 393 131 131 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 126 42 42 0.79 Total of13327 atoms and 4434 groups and 4429 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3938 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1301 Number of atoms = 3938 Number of groups = 1306 Number of bonds = 3931 Number of angles = 1405 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1303 Number of HB donors = 2584 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1301 Number of atoms = 3938 Number of groups = 1306 Number of bonds = 3931 Number of angles = 1405 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1303 Number of HB donors = 2584 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.058" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1301" Evaluating: 1301-7 Parameter: NUMWAT <- "1294" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1294" Comparing "1081" and "1294". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.058" Parameter: BOX -> "34.058" Parameter: BOX -> "34.058" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.05800 B = 34.05800 C = 34.05800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8757 2 1 -1 0 -1 3.5988 3 1 -1 1 -1 4.2762 4 1 0 -1 -1 3.6720 5 1 0 0 -1 1.5680 6 1 0 1 -1 2.8821 7 1 -1 -1 0 2.9011 8 1 -1 0 0 2.2641 9 1 -1 1 0 3.9850 10 1 0 -1 0 1.1992 11 1 0 1 0 1.1992 12 1 -1 -1 1 3.5509 13 1 -1 0 1 3.6095 14 1 -1 1 1 4.2925 15 1 0 -1 1 2.8821 16 1 0 0 1 1.5680 17 1 0 1 1 3.6720 18 1 1 1 1 6.8757 19 1 1 0 1 3.5988 20 1 1 -1 1 4.2762 21 1 1 1 0 2.9011 22 1 1 0 0 2.2641 23 1 1 -1 0 3.9850 24 1 1 1 -1 3.5509 25 1 1 0 -1 3.6095 26 1 1 -1 -1 4.2925 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3864 atoms have been selected out of 3938 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 393 131 131 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 126 42 42 0.79 Total of13327 atoms and 4434 groups and 4429 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3938 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1301 Number of atoms = 3938 Number of groups = 1306 Number of bonds = 3931 Number of angles = 1405 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1303 Number of HB donors = 2584 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1301 Number of atoms = 3938 Number of groups = 1306 Number of bonds = 3931 Number of angles = 1405 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1303 Number of HB donors = 2584 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.056" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1301" Evaluating: 1301-7 Parameter: NUMWAT <- "1294" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1294" Comparing "1081" and "1294". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.056" Parameter: BOX -> "34.056" Parameter: BOX -> "34.056" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.05600 B = 34.05600 C = 34.05600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8775 2 1 -1 0 -1 3.5961 3 1 -1 1 -1 4.2727 4 1 0 -1 -1 3.6692 5 1 0 0 -1 1.5661 6 1 0 1 -1 2.8793 7 1 -1 -1 0 2.8984 8 1 -1 0 0 2.2622 9 1 -1 1 0 3.9829 10 1 0 -1 0 1.1989 11 1 0 1 0 1.1989 12 1 -1 -1 1 3.5475 13 1 -1 0 1 3.6067 14 1 -1 1 1 4.2897 15 1 0 -1 1 2.8793 16 1 0 0 1 1.5661 17 1 0 1 1 3.6692 18 1 1 1 1 6.8775 19 1 1 0 1 3.5961 20 1 1 -1 1 4.2727 21 1 1 1 0 2.8984 22 1 1 0 0 2.2622 23 1 1 -1 0 3.9829 24 1 1 1 -1 3.5475 25 1 1 0 -1 3.6067 26 1 1 -1 -1 4.2897 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3864 atoms have been selected out of 3938 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 393 131 131 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 474 158 158 0.00 14 C014 has 126 42 42 0.79 Total of13327 atoms and 4434 groups and 4429 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3938 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1301 Number of atoms = 3938 Number of groups = 1306 Number of bonds = 3931 Number of angles = 1405 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1303 Number of HB donors = 2584 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1301 Number of atoms = 3938 Number of groups = 1306 Number of bonds = 3931 Number of angles = 1405 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1303 Number of HB donors = 2584 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.054" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1301" Evaluating: 1301-7 Parameter: NUMWAT <- "1294" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1294" Comparing "1081" and "1294". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.054" Parameter: BOX -> "34.054" Parameter: BOX -> "34.054" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.05400 B = 34.05400 C = 34.05400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8794 2 1 -1 0 -1 3.5933 3 1 -1 1 -1 4.2693 4 1 0 -1 -1 3.6665 5 1 0 0 -1 1.5642 6 1 0 1 -1 2.8766 7 1 -1 -1 0 2.8956 8 1 -1 0 0 2.2603 9 1 -1 1 0 3.9808 10 1 0 -1 0 1.1987 11 1 0 1 0 1.1987 12 1 -1 -1 1 3.5440 13 1 -1 0 1 3.6040 14 1 -1 1 1 4.2868 15 1 0 -1 1 2.8766 16 1 0 0 1 1.5642 17 1 0 1 1 3.6665 18 1 1 1 1 6.8794 19 1 1 0 1 3.5933 20 1 1 -1 1 4.2693 21 1 1 1 0 2.8956 22 1 1 0 0 2.2603 23 1 1 -1 0 3.9808 24 1 1 1 -1 3.5440 25 1 1 0 -1 3.6040 26 1 1 -1 -1 4.2868 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3864 atoms have been selected out of 3938 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 393 131 131 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1707 569 569 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.79 Total of13333 atoms and 4436 groups and 4431 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3938 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1301 Number of atoms = 3938 Number of groups = 1306 Number of bonds = 3931 Number of angles = 1405 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1303 Number of HB donors = 2584 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1301 Number of atoms = 3938 Number of groups = 1306 Number of bonds = 3931 Number of angles = 1405 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1303 Number of HB donors = 2584 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.052" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1301" Evaluating: 1301-7 Parameter: NUMWAT <- "1294" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1294" Comparing "1081" and "1294". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.052" Parameter: BOX -> "34.052" Parameter: BOX -> "34.052" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.05200 B = 34.05200 C = 34.05200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8812 2 1 -1 0 -1 3.5905 3 1 -1 1 -1 4.2659 4 1 0 -1 -1 3.6637 5 1 0 0 -1 1.5624 6 1 0 1 -1 2.8739 7 1 -1 -1 0 2.8929 8 1 -1 0 0 2.2584 9 1 -1 1 0 3.9788 10 1 0 -1 0 1.1984 11 1 0 1 0 1.1984 12 1 -1 -1 1 3.5406 13 1 -1 0 1 3.6012 14 1 -1 1 1 4.2840 15 1 0 -1 1 2.8739 16 1 0 0 1 1.5624 17 1 0 1 1 3.6637 18 1 1 1 1 6.8812 19 1 1 0 1 3.5905 20 1 1 -1 1 4.2659 21 1 1 1 0 2.8929 22 1 1 0 0 2.2584 23 1 1 -1 0 3.9788 24 1 1 1 -1 3.5406 25 1 1 0 -1 3.6012 26 1 1 -1 -1 4.2840 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3864 atoms have been selected out of 3938 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 393 131 131 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1707 569 569 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.79 Total of13333 atoms and 4436 groups and 4431 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3938 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1301 Number of atoms = 3938 Number of groups = 1306 Number of bonds = 3931 Number of angles = 1405 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1303 Number of HB donors = 2584 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1301 Number of atoms = 3938 Number of groups = 1306 Number of bonds = 3931 Number of angles = 1405 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1303 Number of HB donors = 2584 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.05" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1301" Evaluating: 1301-7 Parameter: NUMWAT <- "1294" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1294" Comparing "1081" and "1294". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.05" Parameter: BOX -> "34.05" Parameter: BOX -> "34.05" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.05000 B = 34.05000 C = 34.05000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8830 2 1 -1 0 -1 3.5878 3 1 -1 1 -1 4.2624 4 1 0 -1 -1 3.6610 5 1 0 0 -1 1.5605 6 1 0 1 -1 2.8712 7 1 -1 -1 0 2.8902 8 1 -1 0 0 2.2565 9 1 -1 1 0 3.9767 10 1 0 -1 0 1.1982 11 1 0 1 0 1.1982 12 1 -1 -1 1 3.5372 13 1 -1 0 1 3.5985 14 1 -1 1 1 4.2811 15 1 0 -1 1 2.8712 16 1 0 0 1 1.5605 17 1 0 1 1 3.6610 18 1 1 1 1 6.8830 19 1 1 0 1 3.5878 20 1 1 -1 1 4.2624 21 1 1 1 0 2.8902 22 1 1 0 0 2.2565 23 1 1 -1 0 3.9767 24 1 1 1 -1 3.5372 25 1 1 0 -1 3.5985 26 1 1 -1 -1 4.2811 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3864 atoms have been selected out of 3938 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 393 131 131 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1707 569 569 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.78 Total of13333 atoms and 4436 groups and 4431 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3938 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1301 Number of atoms = 3938 Number of groups = 1306 Number of bonds = 3931 Number of angles = 1405 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1303 Number of HB donors = 2584 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1301 Number of atoms = 3938 Number of groups = 1306 Number of bonds = 3931 Number of angles = 1405 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1303 Number of HB donors = 2584 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.048" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1301" Evaluating: 1301-7 Parameter: NUMWAT <- "1294" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1294" Comparing "1081" and "1294". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.048" Parameter: BOX -> "34.048" Parameter: BOX -> "34.048" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.04800 B = 34.04800 C = 34.04800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8849 2 1 -1 0 -1 3.5850 3 1 -1 1 -1 4.2590 4 1 0 -1 -1 3.6582 5 1 0 0 -1 1.5586 6 1 0 1 -1 2.8684 7 1 -1 -1 0 2.8875 8 1 -1 0 0 2.2545 9 1 -1 1 0 3.9747 10 1 0 -1 0 1.1979 11 1 0 1 0 1.1979 12 1 -1 -1 1 3.5337 13 1 -1 0 1 3.5957 14 1 -1 1 1 4.2782 15 1 0 -1 1 2.8684 16 1 0 0 1 1.5586 17 1 0 1 1 3.6582 18 1 1 1 1 6.8849 19 1 1 0 1 3.5850 20 1 1 -1 1 4.2590 21 1 1 1 0 2.8875 22 1 1 0 0 2.2545 23 1 1 -1 0 3.9747 24 1 1 1 -1 3.5337 25 1 1 0 -1 3.5957 26 1 1 -1 -1 4.2782 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3864 atoms have been selected out of 3938 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 393 131 131 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1707 569 569 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.78 Total of13333 atoms and 4436 groups and 4431 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3938 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1301 Number of atoms = 3938 Number of groups = 1306 Number of bonds = 3931 Number of angles = 1405 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1303 Number of HB donors = 2584 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1301 Number of atoms = 3938 Number of groups = 1306 Number of bonds = 3931 Number of angles = 1405 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1303 Number of HB donors = 2584 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.046" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1301" Evaluating: 1301-7 Parameter: NUMWAT <- "1294" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1294" Comparing "1081" and "1294". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.046" Parameter: BOX -> "34.046" Parameter: BOX -> "34.046" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.04600 B = 34.04600 C = 34.04600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8867 2 1 -1 0 -1 3.5822 3 1 -1 1 -1 4.2556 4 1 0 -1 -1 3.6555 5 1 0 0 -1 1.5567 6 1 0 1 -1 2.8657 7 1 -1 -1 0 2.8847 8 1 -1 0 0 2.2526 9 1 -1 1 0 3.9726 10 1 0 -1 0 1.1977 11 1 0 1 0 1.1977 12 1 -1 -1 1 3.5303 13 1 -1 0 1 3.5929 14 1 -1 1 1 4.2754 15 1 0 -1 1 2.8657 16 1 0 0 1 1.5567 17 1 0 1 1 3.6555 18 1 1 1 1 6.8867 19 1 1 0 1 3.5822 20 1 1 -1 1 4.2556 21 1 1 1 0 2.8847 22 1 1 0 0 2.2526 23 1 1 -1 0 3.9726 24 1 1 1 -1 3.5303 25 1 1 0 -1 3.5929 26 1 1 -1 -1 4.2754 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3864 atoms have been selected out of 3938 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 393 131 131 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 501 167 167 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1707 569 569 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.78 Total of13336 atoms and 4437 groups and 4432 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3938 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1301 Number of atoms = 3938 Number of groups = 1306 Number of bonds = 3931 Number of angles = 1405 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1303 Number of HB donors = 2584 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1301 Number of atoms = 3938 Number of groups = 1306 Number of bonds = 3931 Number of angles = 1405 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1303 Number of HB donors = 2584 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.044" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1301" Evaluating: 1301-7 Parameter: NUMWAT <- "1294" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1294" Comparing "1081" and "1294". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.044" Parameter: BOX -> "34.044" Parameter: BOX -> "34.044" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.04400 B = 34.04400 C = 34.04400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8886 2 1 -1 0 -1 3.5795 3 1 -1 1 -1 4.2521 4 1 0 -1 -1 3.6527 5 1 0 0 -1 1.5548 6 1 0 1 -1 2.8630 7 1 -1 -1 0 2.8820 8 1 -1 0 0 2.2507 9 1 -1 1 0 3.9706 10 1 0 -1 0 1.1974 11 1 0 1 0 1.1974 12 1 -1 -1 1 3.5268 13 1 -1 0 1 3.5902 14 1 -1 1 1 4.2725 15 1 0 -1 1 2.8630 16 1 0 0 1 1.5548 17 1 0 1 1 3.6527 18 1 1 1 1 6.8886 19 1 1 0 1 3.5795 20 1 1 -1 1 4.2521 21 1 1 1 0 2.8820 22 1 1 0 0 2.2507 23 1 1 -1 0 3.9706 24 1 1 1 -1 3.5268 25 1 1 0 -1 3.5902 26 1 1 -1 -1 4.2725 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3864 atoms have been selected out of 3938 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 365 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 393 131 131 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 501 167 167 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1707 569 569 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.78 Total of13339 atoms and 4438 groups and 4433 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3938 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1300 Number of atoms = 3935 Number of groups = 1305 Number of bonds = 3928 Number of angles = 1404 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1302 Number of HB donors = 2582 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1300 Number of atoms = 3935 Number of groups = 1305 Number of bonds = 3928 Number of angles = 1404 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1302 Number of HB donors = 2582 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.042" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1300" Evaluating: 1300-7 Parameter: NUMWAT <- "1293" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1293" Comparing "1081" and "1293". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.042" Parameter: BOX -> "34.042" Parameter: BOX -> "34.042" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.04200 B = 34.04200 C = 34.04200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8904 2 1 -1 0 -1 3.5767 3 1 -1 1 -1 4.2487 4 1 0 -1 -1 3.6499 5 1 0 0 -1 1.5530 6 1 0 1 -1 2.8603 7 1 -1 -1 0 2.8793 8 1 -1 0 0 2.2488 9 1 -1 1 0 3.9685 10 1 0 -1 0 1.1972 11 1 0 1 0 1.1972 12 1 -1 -1 1 3.5234 13 1 -1 0 1 3.5874 14 1 -1 1 1 4.2697 15 1 0 -1 1 2.8603 16 1 0 0 1 1.5530 17 1 0 1 1 3.6499 18 1 1 1 1 6.8904 19 1 1 0 1 3.5767 20 1 1 -1 1 4.2487 21 1 1 1 0 2.8793 22 1 1 0 0 2.2488 23 1 1 -1 0 3.9685 24 1 1 1 -1 3.5234 25 1 1 0 -1 3.5874 26 1 1 -1 -1 4.2697 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3861 atoms have been selected out of 3935 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1006 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 396 132 132 0.00 2 C002 has 696 232 232 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 501 167 167 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.78 Total of13327 atoms and 4434 groups and 4429 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3935 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.04" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1299" Evaluating: 1299-7 Parameter: NUMWAT <- "1292" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1292" Comparing "1081" and "1292". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.04" Parameter: BOX -> "34.04" Parameter: BOX -> "34.04" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.04000 B = 34.04000 C = 34.04000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8923 2 1 -1 0 -1 3.5740 3 1 -1 1 -1 4.2453 4 1 0 -1 -1 3.6472 5 1 0 0 -1 1.5511 6 1 0 1 -1 2.8575 7 1 -1 -1 0 2.8766 8 1 -1 0 0 2.2469 9 1 -1 1 0 3.9665 10 1 0 -1 0 1.1970 11 1 0 1 0 1.1970 12 1 -1 -1 1 3.5199 13 1 -1 0 1 3.5846 14 1 -1 1 1 4.2668 15 1 0 -1 1 2.8575 16 1 0 0 1 1.5511 17 1 0 1 1 3.6472 18 1 1 1 1 6.8923 19 1 1 0 1 3.5740 20 1 1 -1 1 4.2453 21 1 1 1 0 2.8766 22 1 1 0 0 2.2469 23 1 1 -1 0 3.9665 24 1 1 1 -1 3.5199 25 1 1 0 -1 3.5846 26 1 1 -1 -1 4.2668 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3858 atoms have been selected out of 3932 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 393 131 131 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 501 167 167 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.77 Total of13309 atoms and 4428 groups and 4423 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3932 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.038" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1299" Evaluating: 1299-7 Parameter: NUMWAT <- "1292" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1292" Comparing "1081" and "1292". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.038" Parameter: BOX -> "34.038" Parameter: BOX -> "34.038" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.03800 B = 34.03800 C = 34.03800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8941 2 1 -1 0 -1 3.5712 3 1 -1 1 -1 4.2419 4 1 0 -1 -1 3.6444 5 1 0 0 -1 1.5492 6 1 0 1 -1 2.8548 7 1 -1 -1 0 2.8739 8 1 -1 0 0 2.2449 9 1 -1 1 0 3.9644 10 1 0 -1 0 1.1967 11 1 0 1 0 1.1967 12 1 -1 -1 1 3.5165 13 1 -1 0 1 3.5819 14 1 -1 1 1 4.2640 15 1 0 -1 1 2.8548 16 1 0 0 1 1.5492 17 1 0 1 1 3.6444 18 1 1 1 1 6.8941 19 1 1 0 1 3.5712 20 1 1 -1 1 4.2419 21 1 1 1 0 2.8739 22 1 1 0 0 2.2449 23 1 1 -1 0 3.9644 24 1 1 1 -1 3.5165 25 1 1 0 -1 3.5819 26 1 1 -1 -1 4.2640 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3858 atoms have been selected out of 3932 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 393 131 131 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 501 167 167 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.77 Total of13312 atoms and 4429 groups and 4424 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3932 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.036" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1299" Evaluating: 1299-7 Parameter: NUMWAT <- "1292" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1292" Comparing "1081" and "1292". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.036" Parameter: BOX -> "34.036" Parameter: BOX -> "34.036" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.03600 B = 34.03600 C = 34.03600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8960 2 1 -1 0 -1 3.5684 3 1 -1 1 -1 4.2384 4 1 0 -1 -1 3.6417 5 1 0 0 -1 1.5473 6 1 0 1 -1 2.8521 7 1 -1 -1 0 2.8711 8 1 -1 0 0 2.2430 9 1 -1 1 0 3.9624 10 1 0 -1 0 1.1965 11 1 0 1 0 1.1965 12 1 -1 -1 1 3.5130 13 1 -1 0 1 3.5791 14 1 -1 1 1 4.2611 15 1 0 -1 1 2.8521 16 1 0 0 1 1.5473 17 1 0 1 1 3.6417 18 1 1 1 1 6.8960 19 1 1 0 1 3.5684 20 1 1 -1 1 4.2384 21 1 1 1 0 2.8711 22 1 1 0 0 2.2430 23 1 1 -1 0 3.9624 24 1 1 1 -1 3.5130 25 1 1 0 -1 3.5791 26 1 1 -1 -1 4.2611 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3858 atoms have been selected out of 3932 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 393 131 131 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 501 167 167 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.77 Total of13312 atoms and 4429 groups and 4424 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3932 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.034" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1299" Evaluating: 1299-7 Parameter: NUMWAT <- "1292" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1292" Comparing "1081" and "1292". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.034" Parameter: BOX -> "34.034" Parameter: BOX -> "34.034" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.03400 B = 34.03400 C = 34.03400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8978 2 1 -1 0 -1 3.5657 3 1 -1 1 -1 4.2350 4 1 0 -1 -1 3.6389 5 1 0 0 -1 1.5454 6 1 0 1 -1 2.8493 7 1 -1 -1 0 2.8684 8 1 -1 0 0 2.2411 9 1 -1 1 0 3.9603 10 1 0 -1 0 1.1963 11 1 0 1 0 1.1963 12 1 -1 -1 1 3.5096 13 1 -1 0 1 3.5764 14 1 -1 1 1 4.2583 15 1 0 -1 1 2.8493 16 1 0 0 1 1.5454 17 1 0 1 1 3.6389 18 1 1 1 1 6.8978 19 1 1 0 1 3.5657 20 1 1 -1 1 4.2350 21 1 1 1 0 2.8684 22 1 1 0 0 2.2411 23 1 1 -1 0 3.9603 24 1 1 1 -1 3.5096 25 1 1 0 -1 3.5764 26 1 1 -1 -1 4.2583 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3858 atoms have been selected out of 3932 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 393 131 131 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 501 167 167 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.77 Total of13315 atoms and 4430 groups and 4425 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3932 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.032" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1299" Evaluating: 1299-7 Parameter: NUMWAT <- "1292" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1292" Comparing "1081" and "1292". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.032" Parameter: BOX -> "34.032" Parameter: BOX -> "34.032" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.03200 B = 34.03200 C = 34.03200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8997 2 1 -1 0 -1 3.5629 3 1 -1 1 -1 4.2316 4 1 0 -1 -1 3.6362 5 1 0 0 -1 1.5436 6 1 0 1 -1 2.8466 7 1 -1 -1 0 2.8657 8 1 -1 0 0 2.2392 9 1 -1 1 0 3.9583 10 1 0 -1 0 1.1961 11 1 0 1 0 1.1961 12 1 -1 -1 1 3.5061 13 1 -1 0 1 3.5736 14 1 -1 1 1 4.2554 15 1 0 -1 1 2.8466 16 1 0 0 1 1.5436 17 1 0 1 1 3.6362 18 1 1 1 1 6.8997 19 1 1 0 1 3.5629 20 1 1 -1 1 4.2316 21 1 1 1 0 2.8657 22 1 1 0 0 2.2392 23 1 1 -1 0 3.9583 24 1 1 1 -1 3.5061 25 1 1 0 -1 3.5736 26 1 1 -1 -1 4.2554 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3858 atoms have been selected out of 3932 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 393 131 131 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 501 167 167 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.77 Total of13321 atoms and 4432 groups and 4427 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3932 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.03" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1299" Evaluating: 1299-7 Parameter: NUMWAT <- "1292" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1292" Comparing "1081" and "1292". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.03" Parameter: BOX -> "34.03" Parameter: BOX -> "34.03" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.03000 B = 34.03000 C = 34.03000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9015 2 1 -1 0 -1 3.5601 3 1 -1 1 -1 4.2281 4 1 0 -1 -1 3.6334 5 1 0 0 -1 1.5417 6 1 0 1 -1 2.8439 7 1 -1 -1 0 2.8630 8 1 -1 0 0 2.2373 9 1 -1 1 0 3.9562 10 1 0 -1 0 1.1959 11 1 0 1 0 1.1959 12 1 -1 -1 1 3.5027 13 1 -1 0 1 3.5708 14 1 -1 1 1 4.2526 15 1 0 -1 1 2.8439 16 1 0 0 1 1.5417 17 1 0 1 1 3.6334 18 1 1 1 1 6.9015 19 1 1 0 1 3.5601 20 1 1 -1 1 4.2281 21 1 1 1 0 2.8630 22 1 1 0 0 2.2373 23 1 1 -1 0 3.9562 24 1 1 1 -1 3.5027 25 1 1 0 -1 3.5708 26 1 1 -1 -1 4.2526 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3858 atoms have been selected out of 3932 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 396 132 132 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 501 167 167 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.76 Total of13327 atoms and 4434 groups and 4429 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3932 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.028" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1299" Evaluating: 1299-7 Parameter: NUMWAT <- "1292" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1292" Comparing "1081" and "1292". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.028" Parameter: BOX -> "34.028" Parameter: BOX -> "34.028" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.02800 B = 34.02800 C = 34.02800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9034 2 1 -1 0 -1 3.5574 3 1 -1 1 -1 4.2247 4 1 0 -1 -1 3.6306 5 1 0 0 -1 1.5398 6 1 0 1 -1 2.8412 7 1 -1 -1 0 2.8602 8 1 -1 0 0 2.2354 9 1 -1 1 0 3.9542 10 1 0 -1 0 1.1957 11 1 0 1 0 1.1957 12 1 -1 -1 1 3.4992 13 1 -1 0 1 3.5681 14 1 -1 1 1 4.2497 15 1 0 -1 1 2.8412 16 1 0 0 1 1.5398 17 1 0 1 1 3.6306 18 1 1 1 1 6.9034 19 1 1 0 1 3.5574 20 1 1 -1 1 4.2247 21 1 1 1 0 2.8602 22 1 1 0 0 2.2354 23 1 1 -1 0 3.9542 24 1 1 1 -1 3.4992 25 1 1 0 -1 3.5681 26 1 1 -1 -1 4.2497 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3858 atoms have been selected out of 3932 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 396 132 132 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 501 167 167 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.76 Total of13330 atoms and 4435 groups and 4430 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3932 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.026" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1299" Evaluating: 1299-7 Parameter: NUMWAT <- "1292" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1292" Comparing "1081" and "1292". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.026" Parameter: BOX -> "34.026" Parameter: BOX -> "34.026" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.02600 B = 34.02600 C = 34.02600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9053 2 1 -1 0 -1 3.5546 3 1 -1 1 -1 4.2213 4 1 0 -1 -1 3.6279 5 1 0 0 -1 1.5379 6 1 0 1 -1 2.8384 7 1 -1 -1 0 2.8575 8 1 -1 0 0 2.2334 9 1 -1 1 0 3.9522 10 1 0 -1 0 1.1954 11 1 0 1 0 1.1954 12 1 -1 -1 1 3.4958 13 1 -1 0 1 3.5653 14 1 -1 1 1 4.2469 15 1 0 -1 1 2.8384 16 1 0 0 1 1.5379 17 1 0 1 1 3.6279 18 1 1 1 1 6.9053 19 1 1 0 1 3.5546 20 1 1 -1 1 4.2213 21 1 1 1 0 2.8575 22 1 1 0 0 2.2334 23 1 1 -1 0 3.9522 24 1 1 1 -1 3.4958 25 1 1 0 -1 3.5653 26 1 1 -1 -1 4.2469 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3858 atoms have been selected out of 3932 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 396 132 132 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 501 167 167 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.76 Total of13330 atoms and 4435 groups and 4430 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3932 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.024" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1299" Evaluating: 1299-7 Parameter: NUMWAT <- "1292" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1292" Comparing "1081" and "1292". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.024" Parameter: BOX -> "34.024" Parameter: BOX -> "34.024" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.02400 B = 34.02400 C = 34.02400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9071 2 1 -1 0 -1 3.5519 3 1 -1 1 -1 4.2178 4 1 0 -1 -1 3.6251 5 1 0 0 -1 1.5361 6 1 0 1 -1 2.8357 7 1 -1 -1 0 2.8548 8 1 -1 0 0 2.2315 9 1 -1 1 0 3.9501 10 1 0 -1 0 1.1952 11 1 0 1 0 1.1952 12 1 -1 -1 1 3.4923 13 1 -1 0 1 3.5626 14 1 -1 1 1 4.2440 15 1 0 -1 1 2.8357 16 1 0 0 1 1.5361 17 1 0 1 1 3.6251 18 1 1 1 1 6.9071 19 1 1 0 1 3.5519 20 1 1 -1 1 4.2178 21 1 1 1 0 2.8548 22 1 1 0 0 2.2315 23 1 1 -1 0 3.9501 24 1 1 1 -1 3.4923 25 1 1 0 -1 3.5626 26 1 1 -1 -1 4.2440 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3858 atoms have been selected out of 3932 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 396 132 132 0.00 2 C002 has 693 231 231 0.00 3 C003 has 99 33 33 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 501 167 167 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.76 Total of13330 atoms and 4435 groups and 4430 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3932 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.022" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1299" Evaluating: 1299-7 Parameter: NUMWAT <- "1292" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1292" Comparing "1081" and "1292". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.022" Parameter: BOX -> "34.022" Parameter: BOX -> "34.022" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.02200 B = 34.02200 C = 34.02200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9090 2 1 -1 0 -1 3.5491 3 1 -1 1 -1 4.2144 4 1 0 -1 -1 3.6224 5 1 0 0 -1 1.5342 6 1 0 1 -1 2.8330 7 1 -1 -1 0 2.8521 8 1 -1 0 0 2.2296 9 1 -1 1 0 3.9481 10 1 0 -1 0 1.1950 11 1 0 1 0 1.1950 12 1 -1 -1 1 3.4889 13 1 -1 0 1 3.5598 14 1 -1 1 1 4.2412 15 1 0 -1 1 2.8330 16 1 0 0 1 1.5342 17 1 0 1 1 3.6224 18 1 1 1 1 6.9090 19 1 1 0 1 3.5491 20 1 1 -1 1 4.2144 21 1 1 1 0 2.8521 22 1 1 0 0 2.2296 23 1 1 -1 0 3.9481 24 1 1 1 -1 3.4889 25 1 1 0 -1 3.5598 26 1 1 -1 -1 4.2412 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3858 atoms have been selected out of 3932 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 396 132 132 0.00 2 C002 has 696 232 232 0.00 3 C003 has 99 33 33 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 501 167 167 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.76 Total of13336 atoms and 4437 groups and 4432 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3932 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.02" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1299" Evaluating: 1299-7 Parameter: NUMWAT <- "1292" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1292" Comparing "1081" and "1292". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.02" Parameter: BOX -> "34.02" Parameter: BOX -> "34.02" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.02000 B = 34.02000 C = 34.02000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9108 2 1 -1 0 -1 3.5463 3 1 -1 1 -1 4.2110 4 1 0 -1 -1 3.6196 5 1 0 0 -1 1.5323 6 1 0 1 -1 2.8303 7 1 -1 -1 0 2.8494 8 1 -1 0 0 2.2277 9 1 -1 1 0 3.9460 10 1 0 -1 0 1.1948 11 1 0 1 0 1.1948 12 1 -1 -1 1 3.4854 13 1 -1 0 1 3.5570 14 1 -1 1 1 4.2383 15 1 0 -1 1 2.8303 16 1 0 0 1 1.5323 17 1 0 1 1 3.6196 18 1 1 1 1 6.9108 19 1 1 0 1 3.5463 20 1 1 -1 1 4.2110 21 1 1 1 0 2.8494 22 1 1 0 0 2.2277 23 1 1 -1 0 3.9460 24 1 1 1 -1 3.4854 25 1 1 0 -1 3.5570 26 1 1 -1 -1 4.2383 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3858 atoms have been selected out of 3932 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 396 132 132 0.00 2 C002 has 696 232 232 0.00 3 C003 has 99 33 33 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 501 167 167 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.75 Total of13336 atoms and 4437 groups and 4432 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3932 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.018" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1299" Evaluating: 1299-7 Parameter: NUMWAT <- "1292" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1292" Comparing "1081" and "1292". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.018" Parameter: BOX -> "34.018" Parameter: BOX -> "34.018" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.01800 B = 34.01800 C = 34.01800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9127 2 1 -1 0 -1 3.5436 3 1 -1 1 -1 4.2075 4 1 0 -1 -1 3.6169 5 1 0 0 -1 1.5304 6 1 0 1 -1 2.8275 7 1 -1 -1 0 2.8466 8 1 -1 0 0 2.2258 9 1 -1 1 0 3.9440 10 1 0 -1 0 1.1946 11 1 0 1 0 1.1946 12 1 -1 -1 1 3.4820 13 1 -1 0 1 3.5543 14 1 -1 1 1 4.2355 15 1 0 -1 1 2.8275 16 1 0 0 1 1.5304 17 1 0 1 1 3.6169 18 1 1 1 1 6.9127 19 1 1 0 1 3.5436 20 1 1 -1 1 4.2075 21 1 1 1 0 2.8466 22 1 1 0 0 2.2258 23 1 1 -1 0 3.9440 24 1 1 1 -1 3.4820 25 1 1 0 -1 3.5543 26 1 1 -1 -1 4.2355 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3858 atoms have been selected out of 3932 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 396 132 132 0.00 2 C002 has 696 232 232 0.00 3 C003 has 102 34 34 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 501 167 167 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.75 Total of13339 atoms and 4438 groups and 4433 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3932 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.016" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1299" Evaluating: 1299-7 Parameter: NUMWAT <- "1292" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1292" Comparing "1081" and "1292". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.016" Parameter: BOX -> "34.016" Parameter: BOX -> "34.016" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.01600 B = 34.01600 C = 34.01600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9146 2 1 -1 0 -1 3.5408 3 1 -1 1 -1 4.2041 4 1 0 -1 -1 3.6141 5 1 0 0 -1 1.5286 6 1 0 1 -1 2.8248 7 1 -1 -1 0 2.8439 8 1 -1 0 0 2.2239 9 1 -1 1 0 3.9420 10 1 0 -1 0 1.1944 11 1 0 1 0 1.1944 12 1 -1 -1 1 3.4785 13 1 -1 0 1 3.5515 14 1 -1 1 1 4.2326 15 1 0 -1 1 2.8248 16 1 0 0 1 1.5286 17 1 0 1 1 3.6141 18 1 1 1 1 6.9146 19 1 1 0 1 3.5408 20 1 1 -1 1 4.2041 21 1 1 1 0 2.8439 22 1 1 0 0 2.2239 23 1 1 -1 0 3.9420 24 1 1 1 -1 3.4785 25 1 1 0 -1 3.5515 26 1 1 -1 -1 4.2326 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3858 atoms have been selected out of 3932 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 396 132 132 0.00 2 C002 has 696 232 232 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 501 167 167 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.75 Total of13342 atoms and 4439 groups and 4434 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3932 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.014" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1299" Evaluating: 1299-7 Parameter: NUMWAT <- "1292" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1292" Comparing "1081" and "1292". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.014" Parameter: BOX -> "34.014" Parameter: BOX -> "34.014" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.01400 B = 34.01400 C = 34.01400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9164 2 1 -1 0 -1 3.5380 3 1 -1 1 -1 4.2007 4 1 0 -1 -1 3.6113 5 1 0 0 -1 1.5267 6 1 0 1 -1 2.8221 7 1 -1 -1 0 2.8412 8 1 -1 0 0 2.2219 9 1 -1 1 0 3.9399 10 1 0 -1 0 1.1943 11 1 0 1 0 1.1943 12 1 -1 -1 1 3.4751 13 1 -1 0 1 3.5488 14 1 -1 1 1 4.2298 15 1 0 -1 1 2.8221 16 1 0 0 1 1.5267 17 1 0 1 1 3.6113 18 1 1 1 1 6.9164 19 1 1 0 1 3.5380 20 1 1 -1 1 4.2007 21 1 1 1 0 2.8412 22 1 1 0 0 2.2219 23 1 1 -1 0 3.9399 24 1 1 1 -1 3.4751 25 1 1 0 -1 3.5488 26 1 1 -1 -1 4.2298 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3858 atoms have been selected out of 3932 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 396 132 132 0.00 2 C002 has 696 232 232 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 501 167 167 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.75 Total of13345 atoms and 4440 groups and 4435 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3932 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.012" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1299" Evaluating: 1299-7 Parameter: NUMWAT <- "1292" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1292" Comparing "1081" and "1292". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.012" Parameter: BOX -> "34.012" Parameter: BOX -> "34.012" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.01200 B = 34.01200 C = 34.01200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9183 2 1 -1 0 -1 3.5353 3 1 -1 1 -1 4.1972 4 1 0 -1 -1 3.6086 5 1 0 0 -1 1.5248 6 1 0 1 -1 2.8194 7 1 -1 -1 0 2.8385 8 1 -1 0 0 2.2200 9 1 -1 1 0 3.9379 10 1 0 -1 0 1.1941 11 1 0 1 0 1.1941 12 1 -1 -1 1 3.4717 13 1 -1 0 1 3.5460 14 1 -1 1 1 4.2270 15 1 0 -1 1 2.8194 16 1 0 0 1 1.5248 17 1 0 1 1 3.6086 18 1 1 1 1 6.9183 19 1 1 0 1 3.5353 20 1 1 -1 1 4.1972 21 1 1 1 0 2.8385 22 1 1 0 0 2.2200 23 1 1 -1 0 3.9379 24 1 1 1 -1 3.4717 25 1 1 0 -1 3.5460 26 1 1 -1 -1 4.2270 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3858 atoms have been selected out of 3932 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 399 133 133 0.00 2 C002 has 696 232 232 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 504 168 168 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1796 597 597 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.75 Total of13354 atoms and 4443 groups and 4438 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3932 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.01" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1299" Evaluating: 1299-7 Parameter: NUMWAT <- "1292" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1292" Comparing "1081" and "1292". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.01" Parameter: BOX -> "34.01" Parameter: BOX -> "34.01" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.01000 B = 34.01000 C = 34.01000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9202 2 1 -1 0 -1 3.5325 3 1 -1 1 -1 4.1938 4 1 0 -1 -1 3.6058 5 1 0 0 -1 1.5229 6 1 0 1 -1 2.8166 7 1 -1 -1 0 2.8358 8 1 -1 0 0 2.2181 9 1 -1 1 0 3.9359 10 1 0 -1 0 1.1939 11 1 0 1 0 1.1939 12 1 -1 -1 1 3.4682 13 1 -1 0 1 3.5432 14 1 -1 1 1 4.2241 15 1 0 -1 1 2.8166 16 1 0 0 1 1.5229 17 1 0 1 1 3.6058 18 1 1 1 1 6.9202 19 1 1 0 1 3.5325 20 1 1 -1 1 4.1938 21 1 1 1 0 2.8358 22 1 1 0 0 2.2181 23 1 1 -1 0 3.9359 24 1 1 1 -1 3.4682 25 1 1 0 -1 3.5432 26 1 1 -1 -1 4.2241 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3858 atoms have been selected out of 3932 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 399 133 133 0.00 2 C002 has 696 232 232 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 504 168 168 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1796 597 597 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.74 Total of13354 atoms and 4443 groups and 4438 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3932 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.008" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1299" Evaluating: 1299-7 Parameter: NUMWAT <- "1292" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1292" Comparing "1081" and "1292". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.008" Parameter: BOX -> "34.008" Parameter: BOX -> "34.008" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.00800 B = 34.00800 C = 34.00800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9220 2 1 -1 0 -1 3.5298 3 1 -1 1 -1 4.1904 4 1 0 -1 -1 3.6031 5 1 0 0 -1 1.5211 6 1 0 1 -1 2.8139 7 1 -1 -1 0 2.8330 8 1 -1 0 0 2.2162 9 1 -1 1 0 3.9338 10 1 0 -1 0 1.1937 11 1 0 1 0 1.1937 12 1 -1 -1 1 3.4648 13 1 -1 0 1 3.5405 14 1 -1 1 1 4.2213 15 1 0 -1 1 2.8139 16 1 0 0 1 1.5211 17 1 0 1 1 3.6031 18 1 1 1 1 6.9220 19 1 1 0 1 3.5298 20 1 1 -1 1 4.1904 21 1 1 1 0 2.8330 22 1 1 0 0 2.2162 23 1 1 -1 0 3.9338 24 1 1 1 -1 3.4648 25 1 1 0 -1 3.5405 26 1 1 -1 -1 4.2213 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3858 atoms have been selected out of 3932 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 399 133 133 0.00 2 C002 has 696 232 232 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 504 168 168 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1796 597 597 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.74 Total of13354 atoms and 4443 groups and 4438 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3932 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.006" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1299" Evaluating: 1299-7 Parameter: NUMWAT <- "1292" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1292" Comparing "1081" and "1292". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.006" Parameter: BOX -> "34.006" Parameter: BOX -> "34.006" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.00600 B = 34.00600 C = 34.00600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9239 2 1 -1 0 -1 3.5270 3 1 -1 1 -1 4.1869 4 1 0 -1 -1 3.6003 5 1 0 0 -1 1.5192 6 1 0 1 -1 2.8112 7 1 -1 -1 0 2.8303 8 1 -1 0 0 2.2143 9 1 -1 1 0 3.9318 10 1 0 -1 0 1.1935 11 1 0 1 0 1.1935 12 1 -1 -1 1 3.4613 13 1 -1 0 1 3.5377 14 1 -1 1 1 4.2184 15 1 0 -1 1 2.8112 16 1 0 0 1 1.5192 17 1 0 1 1 3.6003 18 1 1 1 1 6.9239 19 1 1 0 1 3.5270 20 1 1 -1 1 4.1869 21 1 1 1 0 2.8303 22 1 1 0 0 2.2143 23 1 1 -1 0 3.9318 24 1 1 1 -1 3.4613 25 1 1 0 -1 3.5377 26 1 1 -1 -1 4.2184 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3858 atoms have been selected out of 3932 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 399 133 133 0.00 2 C002 has 696 232 232 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 504 168 168 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1796 597 597 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.74 Total of13354 atoms and 4443 groups and 4438 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3932 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.004" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1299" Evaluating: 1299-7 Parameter: NUMWAT <- "1292" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1292" Comparing "1081" and "1292". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.004" Parameter: BOX -> "34.004" Parameter: BOX -> "34.004" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.00400 B = 34.00400 C = 34.00400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9258 2 1 -1 0 -1 3.5242 3 1 -1 1 -1 4.1835 4 1 0 -1 -1 3.5976 5 1 0 0 -1 1.5173 6 1 0 1 -1 2.8085 7 1 -1 -1 0 2.8276 8 1 -1 0 0 2.2123 9 1 -1 1 0 3.9298 10 1 0 -1 0 1.1934 11 1 0 1 0 1.1934 12 1 -1 -1 1 3.4579 13 1 -1 0 1 3.5350 14 1 -1 1 1 4.2156 15 1 0 -1 1 2.8085 16 1 0 0 1 1.5173 17 1 0 1 1 3.5976 18 1 1 1 1 6.9258 19 1 1 0 1 3.5242 20 1 1 -1 1 4.1835 21 1 1 1 0 2.8276 22 1 1 0 0 2.2123 23 1 1 -1 0 3.9298 24 1 1 1 -1 3.4579 25 1 1 0 -1 3.5350 26 1 1 -1 -1 4.2156 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3858 atoms have been selected out of 3932 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 399 133 133 0.00 2 C002 has 699 233 233 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 504 168 168 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1796 597 597 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.74 Total of13357 atoms and 4444 groups and 4439 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3932 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1299 Number of atoms = 3932 Number of groups = 1304 Number of bonds = 3925 Number of angles = 1403 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1301 Number of HB donors = 2580 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.002" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1299" Evaluating: 1299-7 Parameter: NUMWAT <- "1292" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1292" Comparing "1081" and "1292". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34.002" Parameter: BOX -> "34.002" Parameter: BOX -> "34.002" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.00200 B = 34.00200 C = 34.00200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9277 2 1 -1 0 -1 3.5215 3 1 -1 1 -1 4.1801 4 1 0 -1 -1 3.5948 5 1 0 0 -1 1.5154 6 1 0 1 -1 2.8058 7 1 -1 -1 0 2.8249 8 1 -1 0 0 2.2104 9 1 -1 1 0 3.9277 10 1 0 -1 0 1.1932 11 1 0 1 0 1.1932 12 1 -1 -1 1 3.4544 13 1 -1 0 1 3.5322 14 1 -1 1 1 4.2128 15 1 0 -1 1 2.8058 16 1 0 0 1 1.5154 17 1 0 1 1 3.5948 18 1 1 1 1 6.9277 19 1 1 0 1 3.5215 20 1 1 -1 1 4.1801 21 1 1 1 0 2.8249 22 1 1 0 0 2.2104 23 1 1 -1 0 3.9277 24 1 1 1 -1 3.4544 25 1 1 0 -1 3.5322 26 1 1 -1 -1 4.2128 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3858 atoms have been selected out of 3932 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 390 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 399 133 133 0.00 2 C002 has 699 233 233 0.00 3 C003 has 105 35 35 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 504 168 168 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1796 597 597 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.74 Total of13363 atoms and 4446 groups and 4441 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3932 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1298 Number of atoms = 3929 Number of groups = 1303 Number of bonds = 3922 Number of angles = 1402 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1300 Number of HB donors = 2578 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1298 Number of atoms = 3929 Number of groups = 1303 Number of bonds = 3922 Number of angles = 1402 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1300 Number of HB donors = 2578 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1298" Evaluating: 1298-7 Parameter: NUMWAT <- "1291" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1291" Comparing "1081" and "1291". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "34" Parameter: BOX -> "34" Parameter: BOX -> "34" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 34.00000 B = 34.00000 C = 34.00000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9295 2 1 -1 0 -1 3.5187 3 1 -1 1 -1 4.1766 4 1 0 -1 -1 3.5921 5 1 0 0 -1 1.5136 6 1 0 1 -1 2.8030 7 1 -1 -1 0 2.8222 8 1 -1 0 0 2.2085 9 1 -1 1 0 3.9257 10 1 0 -1 0 1.1930 11 1 0 1 0 1.1930 12 1 -1 -1 1 3.4510 13 1 -1 0 1 3.5294 14 1 -1 1 1 4.2099 15 1 0 -1 1 2.8030 16 1 0 0 1 1.5136 17 1 0 1 1 3.5921 18 1 1 1 1 6.9295 19 1 1 0 1 3.5187 20 1 1 -1 1 4.1766 21 1 1 1 0 2.8222 22 1 1 0 0 2.2085 23 1 1 -1 0 3.9257 24 1 1 1 -1 3.4510 25 1 1 0 -1 3.5294 26 1 1 -1 -1 4.2099 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3855 atoms have been selected out of 3929 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 399 133 133 0.00 2 C002 has 699 233 233 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 507 169 169 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1796 597 597 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.73 Total of13354 atoms and 4443 groups and 4438 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3929 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1298 Number of atoms = 3929 Number of groups = 1303 Number of bonds = 3922 Number of angles = 1402 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1300 Number of HB donors = 2578 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1298 Number of atoms = 3929 Number of groups = 1303 Number of bonds = 3922 Number of angles = 1402 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1300 Number of HB donors = 2578 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.998" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1298" Evaluating: 1298-7 Parameter: NUMWAT <- "1291" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1291" Comparing "1081" and "1291". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.998" Parameter: BOX -> "33.998" Parameter: BOX -> "33.998" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.99800 B = 33.99800 C = 33.99800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9314 2 1 -1 0 -1 3.5160 3 1 -1 1 -1 4.1732 4 1 0 -1 -1 3.5893 5 1 0 0 -1 1.5117 6 1 0 1 -1 2.8003 7 1 -1 -1 0 2.8195 8 1 -1 0 0 2.2066 9 1 -1 1 0 3.9237 10 1 0 -1 0 1.1929 11 1 0 1 0 1.1929 12 1 -1 -1 1 3.4475 13 1 -1 0 1 3.5267 14 1 -1 1 1 4.2071 15 1 0 -1 1 2.8003 16 1 0 0 1 1.5117 17 1 0 1 1 3.5893 18 1 1 1 1 6.9314 19 1 1 0 1 3.5160 20 1 1 -1 1 4.1732 21 1 1 1 0 2.8195 22 1 1 0 0 2.2066 23 1 1 -1 0 3.9237 24 1 1 1 -1 3.4475 25 1 1 0 -1 3.5267 26 1 1 -1 -1 4.2071 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3855 atoms have been selected out of 3929 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 399 133 133 0.00 2 C002 has 699 233 233 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 507 169 169 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1796 597 597 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.73 Total of13357 atoms and 4444 groups and 4439 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3929 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1298 Number of atoms = 3929 Number of groups = 1303 Number of bonds = 3922 Number of angles = 1402 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1300 Number of HB donors = 2578 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1298 Number of atoms = 3929 Number of groups = 1303 Number of bonds = 3922 Number of angles = 1402 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1300 Number of HB donors = 2578 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.996" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1298" Evaluating: 1298-7 Parameter: NUMWAT <- "1291" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1291" Comparing "1081" and "1291". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.996" Parameter: BOX -> "33.996" Parameter: BOX -> "33.996" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.99600 B = 33.99600 C = 33.99600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9333 2 1 -1 0 -1 3.5132 3 1 -1 1 -1 4.1698 4 1 0 -1 -1 3.5865 5 1 0 0 -1 1.5098 6 1 0 1 -1 2.7976 7 1 -1 -1 0 2.8167 8 1 -1 0 0 2.2047 9 1 -1 1 0 3.9216 10 1 0 -1 0 1.1927 11 1 0 1 0 1.1927 12 1 -1 -1 1 3.4441 13 1 -1 0 1 3.5239 14 1 -1 1 1 4.2043 15 1 0 -1 1 2.7976 16 1 0 0 1 1.5098 17 1 0 1 1 3.5865 18 1 1 1 1 6.9333 19 1 1 0 1 3.5132 20 1 1 -1 1 4.1698 21 1 1 1 0 2.8167 22 1 1 0 0 2.2047 23 1 1 -1 0 3.9216 24 1 1 1 -1 3.4441 25 1 1 0 -1 3.5239 26 1 1 -1 -1 4.2043 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3855 atoms have been selected out of 3929 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 68 OPERATED ON BY TRANSFORMATION C022 RESIDUE 376 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 399 133 133 0.00 2 C002 has 699 233 233 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 510 170 170 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1799 598 598 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1704 568 568 0.00 12 C012 has 123 41 41 0.00 13 C013 has 483 161 161 0.00 14 C014 has 129 43 43 0.73 Total of13372 atoms and 4449 groups and 4444 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3929 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1296 Number of atoms = 3923 Number of groups = 1301 Number of bonds = 3916 Number of angles = 1400 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1298 Number of HB donors = 2574 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1296 Number of atoms = 3923 Number of groups = 1301 Number of bonds = 3916 Number of angles = 1400 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1298 Number of HB donors = 2574 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.994" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1296" Evaluating: 1296-7 Parameter: NUMWAT <- "1289" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1289" Comparing "1081" and "1289". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.994" Parameter: BOX -> "33.994" Parameter: BOX -> "33.994" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.99400 B = 33.99400 C = 33.99400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9352 2 1 -1 0 -1 3.5104 3 1 -1 1 -1 4.1663 4 1 0 -1 -1 3.5838 5 1 0 0 -1 1.5080 6 1 0 1 -1 2.7949 7 1 -1 -1 0 2.8140 8 1 -1 0 0 2.2028 9 1 -1 1 0 3.9196 10 1 0 -1 0 1.1926 11 1 0 1 0 1.1926 12 1 -1 -1 1 3.4406 13 1 -1 0 1 3.5212 14 1 -1 1 1 4.2014 15 1 0 -1 1 2.7949 16 1 0 0 1 1.5080 17 1 0 1 1 3.5838 18 1 1 1 1 6.9352 19 1 1 0 1 3.5104 20 1 1 -1 1 4.1663 21 1 1 1 0 2.8140 22 1 1 0 0 2.2028 23 1 1 -1 0 3.9196 24 1 1 1 -1 3.4406 25 1 1 0 -1 3.5212 26 1 1 -1 -1 4.2014 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3849 atoms have been selected out of 3923 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 399 133 133 0.00 2 C002 has 699 233 233 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 513 171 171 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1793 596 596 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 120 40 40 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.73 Total of13342 atoms and 4439 groups and 4434 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3923 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1296 Number of atoms = 3923 Number of groups = 1301 Number of bonds = 3916 Number of angles = 1400 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1298 Number of HB donors = 2574 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1296 Number of atoms = 3923 Number of groups = 1301 Number of bonds = 3916 Number of angles = 1400 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1298 Number of HB donors = 2574 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.992" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1296" Evaluating: 1296-7 Parameter: NUMWAT <- "1289" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1289" Comparing "1081" and "1289". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.992" Parameter: BOX -> "33.992" Parameter: BOX -> "33.992" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.99200 B = 33.99200 C = 33.99200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9370 2 1 -1 0 -1 3.5077 3 1 -1 1 -1 4.1629 4 1 0 -1 -1 3.5810 5 1 0 0 -1 1.5061 6 1 0 1 -1 2.7921 7 1 -1 -1 0 2.8113 8 1 -1 0 0 2.2009 9 1 -1 1 0 3.9176 10 1 0 -1 0 1.1924 11 1 0 1 0 1.1924 12 1 -1 -1 1 3.4372 13 1 -1 0 1 3.5184 14 1 -1 1 1 4.1986 15 1 0 -1 1 2.7921 16 1 0 0 1 1.5061 17 1 0 1 1 3.5810 18 1 1 1 1 6.9370 19 1 1 0 1 3.5077 20 1 1 -1 1 4.1629 21 1 1 1 0 2.8113 22 1 1 0 0 2.2009 23 1 1 -1 0 3.9176 24 1 1 1 -1 3.4372 25 1 1 0 -1 3.5184 26 1 1 -1 -1 4.1986 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3849 atoms have been selected out of 3923 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 203 OPERATED ON BY TRANSFORMATION C008 RESIDUE 558 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 399 133 133 0.00 2 C002 has 699 233 233 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 513 171 171 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1701 567 567 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 123 41 41 0.73 Total of13324 atoms and 4433 groups and 4428 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3923 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1294 Number of atoms = 3917 Number of groups = 1299 Number of bonds = 3910 Number of angles = 1398 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1296 Number of HB donors = 2570 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1294 Number of atoms = 3917 Number of groups = 1299 Number of bonds = 3910 Number of angles = 1398 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1296 Number of HB donors = 2570 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.99" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1294" Evaluating: 1294-7 Parameter: NUMWAT <- "1287" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1287" Comparing "1081" and "1287". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.99" Parameter: BOX -> "33.99" Parameter: BOX -> "33.99" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.99000 B = 33.99000 C = 33.99000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9389 2 1 -1 0 -1 3.5049 3 1 -1 1 -1 4.1595 4 1 0 -1 -1 3.5783 5 1 0 0 -1 1.5042 6 1 0 1 -1 2.7894 7 1 -1 -1 0 2.8086 8 1 -1 0 0 2.1989 9 1 -1 1 0 3.9156 10 1 0 -1 0 1.1923 11 1 0 1 0 1.1923 12 1 -1 -1 1 3.4337 13 1 -1 0 1 3.5156 14 1 -1 1 1 4.1958 15 1 0 -1 1 2.7894 16 1 0 0 1 1.5042 17 1 0 1 1 3.5783 18 1 1 1 1 6.9389 19 1 1 0 1 3.5049 20 1 1 -1 1 4.1595 21 1 1 1 0 2.8086 22 1 1 0 0 2.1989 23 1 1 -1 0 3.9156 24 1 1 1 -1 3.4337 25 1 1 0 -1 3.5156 26 1 1 -1 -1 4.1958 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3843 atoms have been selected out of 3917 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 399 133 133 0.00 2 C002 has 699 233 233 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 513 171 171 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1698 566 566 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 0.72 Total of13315 atoms and 4430 groups and 4425 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3917 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1294 Number of atoms = 3917 Number of groups = 1299 Number of bonds = 3910 Number of angles = 1398 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1296 Number of HB donors = 2570 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1294 Number of atoms = 3917 Number of groups = 1299 Number of bonds = 3910 Number of angles = 1398 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1296 Number of HB donors = 2570 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.988" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1294" Evaluating: 1294-7 Parameter: NUMWAT <- "1287" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1287" Comparing "1081" and "1287". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.988" Parameter: BOX -> "33.988" Parameter: BOX -> "33.988" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.98800 B = 33.98800 C = 33.98800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9408 2 1 -1 0 -1 3.5022 3 1 -1 1 -1 4.1560 4 1 0 -1 -1 3.5755 5 1 0 0 -1 1.5023 6 1 0 1 -1 2.7867 7 1 -1 -1 0 2.8059 8 1 -1 0 0 2.1970 9 1 -1 1 0 3.9135 10 1 0 -1 0 1.1921 11 1 0 1 0 1.1921 12 1 -1 -1 1 3.4303 13 1 -1 0 1 3.5129 14 1 -1 1 1 4.1929 15 1 0 -1 1 2.7867 16 1 0 0 1 1.5023 17 1 0 1 1 3.5755 18 1 1 1 1 6.9408 19 1 1 0 1 3.5022 20 1 1 -1 1 4.1560 21 1 1 1 0 2.8059 22 1 1 0 0 2.1970 23 1 1 -1 0 3.9135 24 1 1 1 -1 3.4303 25 1 1 0 -1 3.5129 26 1 1 -1 -1 4.1929 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3843 atoms have been selected out of 3917 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 399 133 133 0.00 2 C002 has 699 233 233 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 513 171 171 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1698 566 566 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 0.72 Total of13315 atoms and 4430 groups and 4425 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3917 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1294 Number of atoms = 3917 Number of groups = 1299 Number of bonds = 3910 Number of angles = 1398 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1296 Number of HB donors = 2570 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1294 Number of atoms = 3917 Number of groups = 1299 Number of bonds = 3910 Number of angles = 1398 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1296 Number of HB donors = 2570 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.986" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1294" Evaluating: 1294-7 Parameter: NUMWAT <- "1287" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1287" Comparing "1081" and "1287". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.986" Parameter: BOX -> "33.986" Parameter: BOX -> "33.986" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.98600 B = 33.98600 C = 33.98600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9420 2 1 -1 0 -1 3.4994 3 1 -1 1 -1 4.1526 4 1 0 -1 -1 3.5728 5 1 0 0 -1 1.5005 6 1 0 1 -1 2.7840 7 1 -1 -1 0 2.8032 8 1 -1 0 0 2.1951 9 1 -1 1 0 3.9115 10 1 0 -1 0 1.1920 11 1 0 1 0 1.1920 12 1 -1 -1 1 3.4268 13 1 -1 0 1 3.5101 14 1 -1 1 1 4.1901 15 1 0 -1 1 2.7840 16 1 0 0 1 1.5005 17 1 0 1 1 3.5728 18 1 1 1 1 6.9420 19 1 1 0 1 3.4994 20 1 1 -1 1 4.1526 21 1 1 1 0 2.8032 22 1 1 0 0 2.1951 23 1 1 -1 0 3.9115 24 1 1 1 -1 3.4268 25 1 1 0 -1 3.5101 26 1 1 -1 -1 4.1901 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3843 atoms have been selected out of 3917 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 399 133 133 0.00 2 C002 has 699 233 233 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 513 171 171 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1698 566 566 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 0.72 Total of13315 atoms and 4430 groups and 4425 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3917 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1294 Number of atoms = 3917 Number of groups = 1299 Number of bonds = 3910 Number of angles = 1398 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1296 Number of HB donors = 2570 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1294 Number of atoms = 3917 Number of groups = 1299 Number of bonds = 3910 Number of angles = 1398 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1296 Number of HB donors = 2570 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.984" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1294" Evaluating: 1294-7 Parameter: NUMWAT <- "1287" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1287" Comparing "1081" and "1287". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.984" Parameter: BOX -> "33.984" Parameter: BOX -> "33.984" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.98400 B = 33.98400 C = 33.98400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9399 2 1 -1 0 -1 3.4966 3 1 -1 1 -1 4.1492 4 1 0 -1 -1 3.5700 5 1 0 0 -1 1.4986 6 1 0 1 -1 2.7813 7 1 -1 -1 0 2.8004 8 1 -1 0 0 2.1932 9 1 -1 1 0 3.9095 10 1 0 -1 0 1.1918 11 1 0 1 0 1.1918 12 1 -1 -1 1 3.4234 13 1 -1 0 1 3.5074 14 1 -1 1 1 4.1873 15 1 0 -1 1 2.7813 16 1 0 0 1 1.4986 17 1 0 1 1 3.5700 18 1 1 1 1 6.9399 19 1 1 0 1 3.4966 20 1 1 -1 1 4.1492 21 1 1 1 0 2.8004 22 1 1 0 0 2.1932 23 1 1 -1 0 3.9095 24 1 1 1 -1 3.4234 25 1 1 0 -1 3.5074 26 1 1 -1 -1 4.1873 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3843 atoms have been selected out of 3917 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 399 133 133 0.00 2 C002 has 699 233 233 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 513 171 171 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1698 566 566 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 0.72 Total of13315 atoms and 4430 groups and 4425 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3917 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1294 Number of atoms = 3917 Number of groups = 1299 Number of bonds = 3910 Number of angles = 1398 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1296 Number of HB donors = 2570 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1294 Number of atoms = 3917 Number of groups = 1299 Number of bonds = 3910 Number of angles = 1398 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1296 Number of HB donors = 2570 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.982" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1294" Evaluating: 1294-7 Parameter: NUMWAT <- "1287" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1287" Comparing "1081" and "1287". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.982" Parameter: BOX -> "33.982" Parameter: BOX -> "33.982" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.98200 B = 33.98200 C = 33.98200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9377 2 1 -1 0 -1 3.4939 3 1 -1 1 -1 4.1458 4 1 0 -1 -1 3.5673 5 1 0 0 -1 1.4967 6 1 0 1 -1 2.7785 7 1 -1 -1 0 2.7977 8 1 -1 0 0 2.1913 9 1 -1 1 0 3.9075 10 1 0 -1 0 1.1917 11 1 0 1 0 1.1917 12 1 -1 -1 1 3.4199 13 1 -1 0 1 3.5046 14 1 -1 1 1 4.1844 15 1 0 -1 1 2.7785 16 1 0 0 1 1.4967 17 1 0 1 1 3.5673 18 1 1 1 1 6.9377 19 1 1 0 1 3.4939 20 1 1 -1 1 4.1458 21 1 1 1 0 2.7977 22 1 1 0 0 2.1913 23 1 1 -1 0 3.9075 24 1 1 1 -1 3.4199 25 1 1 0 -1 3.5046 26 1 1 -1 -1 4.1844 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3843 atoms have been selected out of 3917 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 399 133 133 0.00 2 C002 has 699 233 233 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 513 171 171 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1698 566 566 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 0.72 Total of13321 atoms and 4432 groups and 4427 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3917 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1294 Number of atoms = 3917 Number of groups = 1299 Number of bonds = 3910 Number of angles = 1398 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1296 Number of HB donors = 2570 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1294 Number of atoms = 3917 Number of groups = 1299 Number of bonds = 3910 Number of angles = 1398 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1296 Number of HB donors = 2570 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.98" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1294" Evaluating: 1294-7 Parameter: NUMWAT <- "1287" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1287" Comparing "1081" and "1287". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.98" Parameter: BOX -> "33.98" Parameter: BOX -> "33.98" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.98000 B = 33.98000 C = 33.98000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9356 2 1 -1 0 -1 3.4911 3 1 -1 1 -1 4.1423 4 1 0 -1 -1 3.5645 5 1 0 0 -1 1.4949 6 1 0 1 -1 2.7758 7 1 -1 -1 0 2.7950 8 1 -1 0 0 2.1894 9 1 -1 1 0 3.9055 10 1 0 -1 0 1.1916 11 1 0 1 0 1.1916 12 1 -1 -1 1 3.4165 13 1 -1 0 1 3.5018 14 1 -1 1 1 4.1816 15 1 0 -1 1 2.7758 16 1 0 0 1 1.4949 17 1 0 1 1 3.5645 18 1 1 1 1 6.9356 19 1 1 0 1 3.4911 20 1 1 -1 1 4.1423 21 1 1 1 0 2.7950 22 1 1 0 0 2.1894 23 1 1 -1 0 3.9055 24 1 1 1 -1 3.4165 25 1 1 0 -1 3.5018 26 1 1 -1 -1 4.1816 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3843 atoms have been selected out of 3917 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 399 133 133 0.00 2 C002 has 699 233 233 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 513 171 171 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1698 566 566 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 0.71 Total of13321 atoms and 4432 groups and 4427 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3917 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1294 Number of atoms = 3917 Number of groups = 1299 Number of bonds = 3910 Number of angles = 1398 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1296 Number of HB donors = 2570 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1294 Number of atoms = 3917 Number of groups = 1299 Number of bonds = 3910 Number of angles = 1398 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1296 Number of HB donors = 2570 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.978" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1294" Evaluating: 1294-7 Parameter: NUMWAT <- "1287" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1287" Comparing "1081" and "1287". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.978" Parameter: BOX -> "33.978" Parameter: BOX -> "33.978" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.97800 B = 33.97800 C = 33.97800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9334 2 1 -1 0 -1 3.4884 3 1 -1 1 -1 4.1389 4 1 0 -1 -1 3.5618 5 1 0 0 -1 1.4930 6 1 0 1 -1 2.7731 7 1 -1 -1 0 2.7923 8 1 -1 0 0 2.1874 9 1 -1 1 0 3.9034 10 1 0 -1 0 1.1914 11 1 0 1 0 1.1914 12 1 -1 -1 1 3.4131 13 1 -1 0 1 3.4991 14 1 -1 1 1 4.1788 15 1 0 -1 1 2.7731 16 1 0 0 1 1.4930 17 1 0 1 1 3.5618 18 1 1 1 1 6.9334 19 1 1 0 1 3.4884 20 1 1 -1 1 4.1389 21 1 1 1 0 2.7923 22 1 1 0 0 2.1874 23 1 1 -1 0 3.9034 24 1 1 1 -1 3.4131 25 1 1 0 -1 3.4991 26 1 1 -1 -1 4.1788 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3843 atoms have been selected out of 3917 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 205 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 399 133 133 0.00 2 C002 has 705 235 235 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 516 172 172 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1698 566 566 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 123 41 41 0.71 Total of13327 atoms and 4434 groups and 4429 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3917 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1293 Number of atoms = 3914 Number of groups = 1298 Number of bonds = 3907 Number of angles = 1397 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1295 Number of HB donors = 2568 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1293 Number of atoms = 3914 Number of groups = 1298 Number of bonds = 3907 Number of angles = 1397 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1295 Number of HB donors = 2568 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.976" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1293" Evaluating: 1293-7 Parameter: NUMWAT <- "1286" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1286" Comparing "1081" and "1286". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.976" Parameter: BOX -> "33.976" Parameter: BOX -> "33.976" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.97600 B = 33.97600 C = 33.97600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9312 2 1 -1 0 -1 3.4856 3 1 -1 1 -1 4.1355 4 1 0 -1 -1 3.5590 5 1 0 0 -1 1.4911 6 1 0 1 -1 2.7704 7 1 -1 -1 0 2.7896 8 1 -1 0 0 2.1855 9 1 -1 1 0 3.9014 10 1 0 -1 0 1.1913 11 1 0 1 0 1.1913 12 1 -1 -1 1 3.4096 13 1 -1 0 1 3.4963 14 1 -1 1 1 4.1760 15 1 0 -1 1 2.7704 16 1 0 0 1 1.4911 17 1 0 1 1 3.5590 18 1 1 1 1 6.9312 19 1 1 0 1 3.4856 20 1 1 -1 1 4.1355 21 1 1 1 0 2.7896 22 1 1 0 0 2.1855 23 1 1 -1 0 3.9014 24 1 1 1 -1 3.4096 25 1 1 0 -1 3.4963 26 1 1 -1 -1 4.1760 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3840 atoms have been selected out of 3914 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 399 133 133 0.00 2 C002 has 702 234 234 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 513 171 171 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1784 593 593 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1698 566 566 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 123 41 41 0.71 Total of13315 atoms and 4430 groups and 4425 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3914 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1293 Number of atoms = 3914 Number of groups = 1298 Number of bonds = 3907 Number of angles = 1397 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1295 Number of HB donors = 2568 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1293 Number of atoms = 3914 Number of groups = 1298 Number of bonds = 3907 Number of angles = 1397 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1295 Number of HB donors = 2568 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.974" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1293" Evaluating: 1293-7 Parameter: NUMWAT <- "1286" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1286" Comparing "1081" and "1286". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.974" Parameter: BOX -> "33.974" Parameter: BOX -> "33.974" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.97400 B = 33.97400 C = 33.97400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9291 2 1 -1 0 -1 3.4828 3 1 -1 1 -1 4.1320 4 1 0 -1 -1 3.5562 5 1 0 0 -1 1.4893 6 1 0 1 -1 2.7677 7 1 -1 -1 0 2.7869 8 1 -1 0 0 2.1836 9 1 -1 1 0 3.8994 10 1 0 -1 0 1.1912 11 1 0 1 0 1.1912 12 1 -1 -1 1 3.4062 13 1 -1 0 1 3.4936 14 1 -1 1 1 4.1732 15 1 0 -1 1 2.7677 16 1 0 0 1 1.4893 17 1 0 1 1 3.5562 18 1 1 1 1 6.9291 19 1 1 0 1 3.4828 20 1 1 -1 1 4.1320 21 1 1 1 0 2.7869 22 1 1 0 0 2.1836 23 1 1 -1 0 3.8994 24 1 1 1 -1 3.4062 25 1 1 0 -1 3.4936 26 1 1 -1 -1 4.1732 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3840 atoms have been selected out of 3914 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 399 133 133 0.00 2 C002 has 702 234 234 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 513 171 171 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1784 593 593 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1698 566 566 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 123 41 41 0.71 Total of13315 atoms and 4430 groups and 4425 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3914 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1293 Number of atoms = 3914 Number of groups = 1298 Number of bonds = 3907 Number of angles = 1397 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1295 Number of HB donors = 2568 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1293 Number of atoms = 3914 Number of groups = 1298 Number of bonds = 3907 Number of angles = 1397 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1295 Number of HB donors = 2568 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.972" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1293" Evaluating: 1293-7 Parameter: NUMWAT <- "1286" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1286" Comparing "1081" and "1286". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.972" Parameter: BOX -> "33.972" Parameter: BOX -> "33.972" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.97200 B = 33.97200 C = 33.97200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9269 2 1 -1 0 -1 3.4801 3 1 -1 1 -1 4.1286 4 1 0 -1 -1 3.5535 5 1 0 0 -1 1.4874 6 1 0 1 -1 2.7649 7 1 -1 -1 0 2.7842 8 1 -1 0 0 2.1817 9 1 -1 1 0 3.8974 10 1 0 -1 0 1.1911 11 1 0 1 0 1.1911 12 1 -1 -1 1 3.4027 13 1 -1 0 1 3.4908 14 1 -1 1 1 4.1703 15 1 0 -1 1 2.7649 16 1 0 0 1 1.4874 17 1 0 1 1 3.5535 18 1 1 1 1 6.9269 19 1 1 0 1 3.4801 20 1 1 -1 1 4.1286 21 1 1 1 0 2.7842 22 1 1 0 0 2.1817 23 1 1 -1 0 3.8974 24 1 1 1 -1 3.4027 25 1 1 0 -1 3.4908 26 1 1 -1 -1 4.1703 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3840 atoms have been selected out of 3914 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 399 133 133 0.00 2 C002 has 702 234 234 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 513 171 171 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1784 593 593 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1698 566 566 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 123 41 41 0.71 Total of13315 atoms and 4430 groups and 4425 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3914 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1293 Number of atoms = 3914 Number of groups = 1298 Number of bonds = 3907 Number of angles = 1397 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1295 Number of HB donors = 2568 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1293 Number of atoms = 3914 Number of groups = 1298 Number of bonds = 3907 Number of angles = 1397 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1295 Number of HB donors = 2568 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.97" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1293" Evaluating: 1293-7 Parameter: NUMWAT <- "1286" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1286" Comparing "1081" and "1286". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.97" Parameter: BOX -> "33.97" Parameter: BOX -> "33.97" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.97000 B = 33.97000 C = 33.97000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9248 2 1 -1 0 -1 3.4773 3 1 -1 1 -1 4.1252 4 1 0 -1 -1 3.5507 5 1 0 0 -1 1.4855 6 1 0 1 -1 2.7622 7 1 -1 -1 0 2.7814 8 1 -1 0 0 2.1798 9 1 -1 1 0 3.8954 10 1 0 -1 0 1.1909 11 1 0 1 0 1.1909 12 1 -1 -1 1 3.3993 13 1 -1 0 1 3.4881 14 1 -1 1 1 4.1675 15 1 0 -1 1 2.7622 16 1 0 0 1 1.4855 17 1 0 1 1 3.5507 18 1 1 1 1 6.9248 19 1 1 0 1 3.4773 20 1 1 -1 1 4.1252 21 1 1 1 0 2.7814 22 1 1 0 0 2.1798 23 1 1 -1 0 3.8954 24 1 1 1 -1 3.3993 25 1 1 0 -1 3.4881 26 1 1 -1 -1 4.1675 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3840 atoms have been selected out of 3914 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 399 133 133 0.00 2 C002 has 702 234 234 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 513 171 171 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1784 593 593 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1698 566 566 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 123 41 41 0.70 Total of13315 atoms and 4430 groups and 4425 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3914 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1293 Number of atoms = 3914 Number of groups = 1298 Number of bonds = 3907 Number of angles = 1397 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1295 Number of HB donors = 2568 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1293 Number of atoms = 3914 Number of groups = 1298 Number of bonds = 3907 Number of angles = 1397 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1295 Number of HB donors = 2568 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.968" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1293" Evaluating: 1293-7 Parameter: NUMWAT <- "1286" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1286" Comparing "1081" and "1286". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.968" Parameter: BOX -> "33.968" Parameter: BOX -> "33.968" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.96800 B = 33.96800 C = 33.96800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9226 2 1 -1 0 -1 3.4746 3 1 -1 1 -1 4.1217 4 1 0 -1 -1 3.5480 5 1 0 0 -1 1.4837 6 1 0 1 -1 2.7595 7 1 -1 -1 0 2.7787 8 1 -1 0 0 2.1779 9 1 -1 1 0 3.8934 10 1 0 -1 0 1.1908 11 1 0 1 0 1.1908 12 1 -1 -1 1 3.3958 13 1 -1 0 1 3.4853 14 1 -1 1 1 4.1647 15 1 0 -1 1 2.7595 16 1 0 0 1 1.4837 17 1 0 1 1 3.5480 18 1 1 1 1 6.9226 19 1 1 0 1 3.4746 20 1 1 -1 1 4.1217 21 1 1 1 0 2.7787 22 1 1 0 0 2.1779 23 1 1 -1 0 3.8934 24 1 1 1 -1 3.3958 25 1 1 0 -1 3.4853 26 1 1 -1 -1 4.1647 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3840 atoms have been selected out of 3914 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 399 133 133 0.00 2 C002 has 702 234 234 0.00 3 C003 has 105 35 35 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 513 171 171 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1784 593 593 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1698 566 566 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 123 41 41 0.70 Total of13318 atoms and 4431 groups and 4426 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3914 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1293 Number of atoms = 3914 Number of groups = 1298 Number of bonds = 3907 Number of angles = 1397 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1295 Number of HB donors = 2568 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1293 Number of atoms = 3914 Number of groups = 1298 Number of bonds = 3907 Number of angles = 1397 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1295 Number of HB donors = 2568 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.966" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1293" Evaluating: 1293-7 Parameter: NUMWAT <- "1286" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1286" Comparing "1081" and "1286". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.966" Parameter: BOX -> "33.966" Parameter: BOX -> "33.966" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.96600 B = 33.96600 C = 33.96600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9205 2 1 -1 0 -1 3.4718 3 1 -1 1 -1 4.1183 4 1 0 -1 -1 3.5452 5 1 0 0 -1 1.4818 6 1 0 1 -1 2.7568 7 1 -1 -1 0 2.7760 8 1 -1 0 0 2.1760 9 1 -1 1 0 3.8914 10 1 0 -1 0 1.1907 11 1 0 1 0 1.1907 12 1 -1 -1 1 3.3924 13 1 -1 0 1 3.4825 14 1 -1 1 1 4.1619 15 1 0 -1 1 2.7568 16 1 0 0 1 1.4818 17 1 0 1 1 3.5452 18 1 1 1 1 6.9205 19 1 1 0 1 3.4718 20 1 1 -1 1 4.1183 21 1 1 1 0 2.7760 22 1 1 0 0 2.1760 23 1 1 -1 0 3.8914 24 1 1 1 -1 3.3924 25 1 1 0 -1 3.4825 26 1 1 -1 -1 4.1619 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3840 atoms have been selected out of 3914 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 399 133 133 0.00 2 C002 has 702 234 234 0.00 3 C003 has 105 35 35 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 513 171 171 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1784 593 593 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1698 566 566 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 123 41 41 0.70 Total of13318 atoms and 4431 groups and 4426 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3914 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1293 Number of atoms = 3914 Number of groups = 1298 Number of bonds = 3907 Number of angles = 1397 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1295 Number of HB donors = 2568 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1293 Number of atoms = 3914 Number of groups = 1298 Number of bonds = 3907 Number of angles = 1397 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1295 Number of HB donors = 2568 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.964" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1293" Evaluating: 1293-7 Parameter: NUMWAT <- "1286" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1286" Comparing "1081" and "1286". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.964" Parameter: BOX -> "33.964" Parameter: BOX -> "33.964" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.96400 B = 33.96400 C = 33.96400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9183 2 1 -1 0 -1 3.4691 3 1 -1 1 -1 4.1149 4 1 0 -1 -1 3.5425 5 1 0 0 -1 1.4799 6 1 0 1 -1 2.7541 7 1 -1 -1 0 2.7733 8 1 -1 0 0 2.1741 9 1 -1 1 0 3.8893 10 1 0 -1 0 1.1906 11 1 0 1 0 1.1906 12 1 -1 -1 1 3.3889 13 1 -1 0 1 3.4798 14 1 -1 1 1 4.1590 15 1 0 -1 1 2.7541 16 1 0 0 1 1.4799 17 1 0 1 1 3.5425 18 1 1 1 1 6.9183 19 1 1 0 1 3.4691 20 1 1 -1 1 4.1149 21 1 1 1 0 2.7733 22 1 1 0 0 2.1741 23 1 1 -1 0 3.8893 24 1 1 1 -1 3.3889 25 1 1 0 -1 3.4798 26 1 1 -1 -1 4.1590 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3840 atoms have been selected out of 3914 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 399 133 133 0.00 2 C002 has 702 234 234 0.00 3 C003 has 105 35 35 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 513 171 171 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1784 593 593 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1698 566 566 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 123 41 41 0.70 Total of13318 atoms and 4431 groups and 4426 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3914 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1293 Number of atoms = 3914 Number of groups = 1298 Number of bonds = 3907 Number of angles = 1397 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1295 Number of HB donors = 2568 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1293 Number of atoms = 3914 Number of groups = 1298 Number of bonds = 3907 Number of angles = 1397 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1295 Number of HB donors = 2568 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.962" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1293" Evaluating: 1293-7 Parameter: NUMWAT <- "1286" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1286" Comparing "1081" and "1286". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.962" Parameter: BOX -> "33.962" Parameter: BOX -> "33.962" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.96200 B = 33.96200 C = 33.96200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9162 2 1 -1 0 -1 3.4663 3 1 -1 1 -1 4.1114 4 1 0 -1 -1 3.5397 5 1 0 0 -1 1.4781 6 1 0 1 -1 2.7513 7 1 -1 -1 0 2.7706 8 1 -1 0 0 2.1721 9 1 -1 1 0 3.8873 10 1 0 -1 0 1.1905 11 1 0 1 0 1.1905 12 1 -1 -1 1 3.3855 13 1 -1 0 1 3.4770 14 1 -1 1 1 4.1562 15 1 0 -1 1 2.7513 16 1 0 0 1 1.4781 17 1 0 1 1 3.5397 18 1 1 1 1 6.9162 19 1 1 0 1 3.4663 20 1 1 -1 1 4.1114 21 1 1 1 0 2.7706 22 1 1 0 0 2.1721 23 1 1 -1 0 3.8873 24 1 1 1 -1 3.3855 25 1 1 0 -1 3.4770 26 1 1 -1 -1 4.1562 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3840 atoms have been selected out of 3914 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 647 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 402 134 134 0.00 2 C002 has 705 235 235 0.00 3 C003 has 105 35 35 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 513 171 171 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1784 593 593 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1698 566 566 0.00 12 C012 has 117 39 39 0.00 13 C013 has 468 156 156 0.00 14 C014 has 126 42 42 0.70 Total of13324 atoms and 4433 groups and 4428 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3914 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1292 Number of atoms = 3911 Number of groups = 1297 Number of bonds = 3904 Number of angles = 1396 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1294 Number of HB donors = 2566 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1292 Number of atoms = 3911 Number of groups = 1297 Number of bonds = 3904 Number of angles = 1396 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1294 Number of HB donors = 2566 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.96" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1292" Evaluating: 1292-7 Parameter: NUMWAT <- "1285" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1285" Comparing "1081" and "1285". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.96" Parameter: BOX -> "33.96" Parameter: BOX -> "33.96" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.96000 B = 33.96000 C = 33.96000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9140 2 1 -1 0 -1 3.4635 3 1 -1 1 -1 4.1080 4 1 0 -1 -1 3.5370 5 1 0 0 -1 1.4762 6 1 0 1 -1 2.7486 7 1 -1 -1 0 2.7679 8 1 -1 0 0 2.1702 9 1 -1 1 0 3.8853 10 1 0 -1 0 1.1904 11 1 0 1 0 1.1904 12 1 -1 -1 1 3.3820 13 1 -1 0 1 3.4743 14 1 -1 1 1 4.1534 15 1 0 -1 1 2.7486 16 1 0 0 1 1.4762 17 1 0 1 1 3.5370 18 1 1 1 1 6.9140 19 1 1 0 1 3.4635 20 1 1 -1 1 4.1080 21 1 1 1 0 2.7679 22 1 1 0 0 2.1702 23 1 1 -1 0 3.8853 24 1 1 1 -1 3.3820 25 1 1 0 -1 3.4743 26 1 1 -1 -1 4.1534 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3837 atoms have been selected out of 3911 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 402 134 134 0.00 2 C002 has 702 234 234 0.00 3 C003 has 105 35 35 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 513 171 171 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1784 593 593 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1695 565 565 0.00 12 C012 has 117 39 39 0.00 13 C013 has 468 156 156 0.00 14 C014 has 126 42 42 0.69 Total of13309 atoms and 4428 groups and 4423 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3911 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1292 Number of atoms = 3911 Number of groups = 1297 Number of bonds = 3904 Number of angles = 1396 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1294 Number of HB donors = 2566 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1292 Number of atoms = 3911 Number of groups = 1297 Number of bonds = 3904 Number of angles = 1396 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1294 Number of HB donors = 2566 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.958" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1292" Evaluating: 1292-7 Parameter: NUMWAT <- "1285" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1285" Comparing "1081" and "1285". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.958" Parameter: BOX -> "33.958" Parameter: BOX -> "33.958" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.95800 B = 33.95800 C = 33.95800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9119 2 1 -1 0 -1 3.4608 3 1 -1 1 -1 4.1046 4 1 0 -1 -1 3.5342 5 1 0 0 -1 1.4743 6 1 0 1 -1 2.7459 7 1 -1 -1 0 2.7652 8 1 -1 0 0 2.1683 9 1 -1 1 0 3.8833 10 1 0 -1 0 1.1903 11 1 0 1 0 1.1903 12 1 -1 -1 1 3.3786 13 1 -1 0 1 3.4715 14 1 -1 1 1 4.1506 15 1 0 -1 1 2.7459 16 1 0 0 1 1.4743 17 1 0 1 1 3.5342 18 1 1 1 1 6.9119 19 1 1 0 1 3.4608 20 1 1 -1 1 4.1046 21 1 1 1 0 2.7652 22 1 1 0 0 2.1683 23 1 1 -1 0 3.8833 24 1 1 1 -1 3.3786 25 1 1 0 -1 3.4715 26 1 1 -1 -1 4.1506 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3837 atoms have been selected out of 3911 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 402 134 134 0.00 2 C002 has 702 234 234 0.00 3 C003 has 105 35 35 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 513 171 171 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1784 593 593 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1695 565 565 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.69 Total of13315 atoms and 4430 groups and 4425 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3911 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1292 Number of atoms = 3911 Number of groups = 1297 Number of bonds = 3904 Number of angles = 1396 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1294 Number of HB donors = 2566 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1292 Number of atoms = 3911 Number of groups = 1297 Number of bonds = 3904 Number of angles = 1396 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1294 Number of HB donors = 2566 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.956" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1292" Evaluating: 1292-7 Parameter: NUMWAT <- "1285" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1285" Comparing "1081" and "1285". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.956" Parameter: BOX -> "33.956" Parameter: BOX -> "33.956" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.95600 B = 33.95600 C = 33.95600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9097 2 1 -1 0 -1 3.4580 3 1 -1 1 -1 4.1011 4 1 0 -1 -1 3.5315 5 1 0 0 -1 1.4725 6 1 0 1 -1 2.7432 7 1 -1 -1 0 2.7624 8 1 -1 0 0 2.1664 9 1 -1 1 0 3.8813 10 1 0 -1 0 1.1902 11 1 0 1 0 1.1902 12 1 -1 -1 1 3.3751 13 1 -1 0 1 3.4688 14 1 -1 1 1 4.1478 15 1 0 -1 1 2.7432 16 1 0 0 1 1.4725 17 1 0 1 1 3.5315 18 1 1 1 1 6.9097 19 1 1 0 1 3.4580 20 1 1 -1 1 4.1011 21 1 1 1 0 2.7624 22 1 1 0 0 2.1664 23 1 1 -1 0 3.8813 24 1 1 1 -1 3.3751 25 1 1 0 -1 3.4688 26 1 1 -1 -1 4.1478 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3837 atoms have been selected out of 3911 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 402 134 134 0.00 2 C002 has 702 234 234 0.00 3 C003 has 105 35 35 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 513 171 171 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1695 565 565 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.69 Total of13318 atoms and 4431 groups and 4426 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3911 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1292 Number of atoms = 3911 Number of groups = 1297 Number of bonds = 3904 Number of angles = 1396 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1294 Number of HB donors = 2566 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1292 Number of atoms = 3911 Number of groups = 1297 Number of bonds = 3904 Number of angles = 1396 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1294 Number of HB donors = 2566 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.954" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1292" Evaluating: 1292-7 Parameter: NUMWAT <- "1285" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1285" Comparing "1081" and "1285". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.954" Parameter: BOX -> "33.954" Parameter: BOX -> "33.954" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.95400 B = 33.95400 C = 33.95400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9076 2 1 -1 0 -1 3.4553 3 1 -1 1 -1 4.0977 4 1 0 -1 -1 3.5287 5 1 0 0 -1 1.4706 6 1 0 1 -1 2.7405 7 1 -1 -1 0 2.7597 8 1 -1 0 0 2.1645 9 1 -1 1 0 3.8793 10 1 0 -1 0 1.1901 11 1 0 1 0 1.1901 12 1 -1 -1 1 3.3717 13 1 -1 0 1 3.4660 14 1 -1 1 1 4.1450 15 1 0 -1 1 2.7405 16 1 0 0 1 1.4706 17 1 0 1 1 3.5287 18 1 1 1 1 6.9076 19 1 1 0 1 3.4553 20 1 1 -1 1 4.0977 21 1 1 1 0 2.7597 22 1 1 0 0 2.1645 23 1 1 -1 0 3.8793 24 1 1 1 -1 3.3717 25 1 1 0 -1 3.4660 26 1 1 -1 -1 4.1450 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3837 atoms have been selected out of 3911 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 402 134 134 0.00 2 C002 has 702 234 234 0.00 3 C003 has 105 35 35 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1635 545 545 0.00 6 C006 has 513 171 171 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1695 565 565 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.69 Total of13318 atoms and 4431 groups and 4426 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3911 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1292 Number of atoms = 3911 Number of groups = 1297 Number of bonds = 3904 Number of angles = 1396 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1294 Number of HB donors = 2566 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1292 Number of atoms = 3911 Number of groups = 1297 Number of bonds = 3904 Number of angles = 1396 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1294 Number of HB donors = 2566 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.952" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1292" Evaluating: 1292-7 Parameter: NUMWAT <- "1285" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1285" Comparing "1081" and "1285". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.952" Parameter: BOX -> "33.952" Parameter: BOX -> "33.952" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.95200 B = 33.95200 C = 33.95200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9055 2 1 -1 0 -1 3.4525 3 1 -1 1 -1 4.0943 4 1 0 -1 -1 3.5260 5 1 0 0 -1 1.4687 6 1 0 1 -1 2.7378 7 1 -1 -1 0 2.7570 8 1 -1 0 0 2.1626 9 1 -1 1 0 3.8773 10 1 0 -1 0 1.1901 11 1 0 1 0 1.1901 12 1 -1 -1 1 3.3683 13 1 -1 0 1 3.4632 14 1 -1 1 1 4.1422 15 1 0 -1 1 2.7378 16 1 0 0 1 1.4687 17 1 0 1 1 3.5260 18 1 1 1 1 6.9055 19 1 1 0 1 3.4525 20 1 1 -1 1 4.0943 21 1 1 1 0 2.7570 22 1 1 0 0 2.1626 23 1 1 -1 0 3.8773 24 1 1 1 -1 3.3683 25 1 1 0 -1 3.4632 26 1 1 -1 -1 4.1422 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3837 atoms have been selected out of 3911 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 402 134 134 0.00 2 C002 has 702 234 234 0.00 3 C003 has 105 35 35 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 513 171 171 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1695 565 565 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.69 Total of13321 atoms and 4432 groups and 4427 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3911 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1292 Number of atoms = 3911 Number of groups = 1297 Number of bonds = 3904 Number of angles = 1396 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1294 Number of HB donors = 2566 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1292 Number of atoms = 3911 Number of groups = 1297 Number of bonds = 3904 Number of angles = 1396 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1294 Number of HB donors = 2566 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.95" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1292" Evaluating: 1292-7 Parameter: NUMWAT <- "1285" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1285" Comparing "1081" and "1285". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.95" Parameter: BOX -> "33.95" Parameter: BOX -> "33.95" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.95000 B = 33.95000 C = 33.95000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9033 2 1 -1 0 -1 3.4497 3 1 -1 1 -1 4.0909 4 1 0 -1 -1 3.5232 5 1 0 0 -1 1.4669 6 1 0 1 -1 2.7350 7 1 -1 -1 0 2.7543 8 1 -1 0 0 2.1607 9 1 -1 1 0 3.8753 10 1 0 -1 0 1.1900 11 1 0 1 0 1.1900 12 1 -1 -1 1 3.3648 13 1 -1 0 1 3.4605 14 1 -1 1 1 4.1393 15 1 0 -1 1 2.7350 16 1 0 0 1 1.4669 17 1 0 1 1 3.5232 18 1 1 1 1 6.9033 19 1 1 0 1 3.4497 20 1 1 -1 1 4.0909 21 1 1 1 0 2.7543 22 1 1 0 0 2.1607 23 1 1 -1 0 3.8753 24 1 1 1 -1 3.3648 25 1 1 0 -1 3.4605 26 1 1 -1 -1 4.1393 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3837 atoms have been selected out of 3911 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 402 134 134 0.00 2 C002 has 702 234 234 0.00 3 C003 has 105 35 35 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1638 546 546 0.00 6 C006 has 513 171 171 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1698 566 566 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.68 Total of13327 atoms and 4434 groups and 4429 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3911 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1292 Number of atoms = 3911 Number of groups = 1297 Number of bonds = 3904 Number of angles = 1396 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1294 Number of HB donors = 2566 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1292 Number of atoms = 3911 Number of groups = 1297 Number of bonds = 3904 Number of angles = 1396 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1294 Number of HB donors = 2566 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.948" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1292" Evaluating: 1292-7 Parameter: NUMWAT <- "1285" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1285" Comparing "1081" and "1285". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.948" Parameter: BOX -> "33.948" Parameter: BOX -> "33.948" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.94800 B = 33.94800 C = 33.94800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.9012 2 1 -1 0 -1 3.4470 3 1 -1 1 -1 4.0874 4 1 0 -1 -1 3.5205 5 1 0 0 -1 1.4650 6 1 0 1 -1 2.7323 7 1 -1 -1 0 2.7516 8 1 -1 0 0 2.1587 9 1 -1 1 0 3.8733 10 1 0 -1 0 1.1899 11 1 0 1 0 1.1899 12 1 -1 -1 1 3.3614 13 1 -1 0 1 3.4577 14 1 -1 1 1 4.1365 15 1 0 -1 1 2.7323 16 1 0 0 1 1.4650 17 1 0 1 1 3.5205 18 1 1 1 1 6.9012 19 1 1 0 1 3.4470 20 1 1 -1 1 4.0874 21 1 1 1 0 2.7516 22 1 1 0 0 2.1587 23 1 1 -1 0 3.8733 24 1 1 1 -1 3.3614 25 1 1 0 -1 3.4577 26 1 1 -1 -1 4.1365 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3837 atoms have been selected out of 3911 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 405 135 135 0.00 2 C002 has 702 234 234 0.00 3 C003 has 105 35 35 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 513 171 171 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1698 566 566 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.68 Total of13333 atoms and 4436 groups and 4431 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3911 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1292 Number of atoms = 3911 Number of groups = 1297 Number of bonds = 3904 Number of angles = 1396 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1294 Number of HB donors = 2566 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1292 Number of atoms = 3911 Number of groups = 1297 Number of bonds = 3904 Number of angles = 1396 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1294 Number of HB donors = 2566 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.946" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1292" Evaluating: 1292-7 Parameter: NUMWAT <- "1285" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1285" Comparing "1081" and "1285". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.946" Parameter: BOX -> "33.946" Parameter: BOX -> "33.946" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.94600 B = 33.94600 C = 33.94600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8990 2 1 -1 0 -1 3.4442 3 1 -1 1 -1 4.0840 4 1 0 -1 -1 3.5177 5 1 0 0 -1 1.4631 6 1 0 1 -1 2.7296 7 1 -1 -1 0 2.7489 8 1 -1 0 0 2.1568 9 1 -1 1 0 3.8713 10 1 0 -1 0 1.1898 11 1 0 1 0 1.1898 12 1 -1 -1 1 3.3579 13 1 -1 0 1 3.4550 14 1 -1 1 1 4.1337 15 1 0 -1 1 2.7296 16 1 0 0 1 1.4631 17 1 0 1 1 3.5177 18 1 1 1 1 6.8990 19 1 1 0 1 3.4442 20 1 1 -1 1 4.0840 21 1 1 1 0 2.7489 22 1 1 0 0 2.1568 23 1 1 -1 0 3.8713 24 1 1 1 -1 3.3579 25 1 1 0 -1 3.4550 26 1 1 -1 -1 4.1337 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3837 atoms have been selected out of 3911 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 405 135 135 0.00 2 C002 has 702 234 234 0.00 3 C003 has 105 35 35 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1647 549 549 0.00 6 C006 has 513 171 171 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1698 566 566 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.68 Total of13342 atoms and 4439 groups and 4434 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3911 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1292 Number of atoms = 3911 Number of groups = 1297 Number of bonds = 3904 Number of angles = 1396 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1294 Number of HB donors = 2566 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1292 Number of atoms = 3911 Number of groups = 1297 Number of bonds = 3904 Number of angles = 1396 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1294 Number of HB donors = 2566 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.944" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1292" Evaluating: 1292-7 Parameter: NUMWAT <- "1285" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1285" Comparing "1081" and "1285". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.944" Parameter: BOX -> "33.944" Parameter: BOX -> "33.944" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.94400 B = 33.94400 C = 33.94400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8969 2 1 -1 0 -1 3.4415 3 1 -1 1 -1 4.0806 4 1 0 -1 -1 3.5149 5 1 0 0 -1 1.4613 6 1 0 1 -1 2.7269 7 1 -1 -1 0 2.7462 8 1 -1 0 0 2.1549 9 1 -1 1 0 3.8693 10 1 0 -1 0 1.1897 11 1 0 1 0 1.1897 12 1 -1 -1 1 3.3545 13 1 -1 0 1 3.4522 14 1 -1 1 1 4.1309 15 1 0 -1 1 2.7269 16 1 0 0 1 1.4613 17 1 0 1 1 3.5149 18 1 1 1 1 6.8969 19 1 1 0 1 3.4415 20 1 1 -1 1 4.0806 21 1 1 1 0 2.7462 22 1 1 0 0 2.1549 23 1 1 -1 0 3.8693 24 1 1 1 -1 3.3545 25 1 1 0 -1 3.4522 26 1 1 -1 -1 4.1309 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3837 atoms have been selected out of 3911 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 405 135 135 0.00 2 C002 has 705 235 235 0.00 3 C003 has 105 35 35 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1650 550 550 0.00 6 C006 has 513 171 171 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1698 566 566 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.68 Total of13348 atoms and 4441 groups and 4436 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3911 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1292 Number of atoms = 3911 Number of groups = 1297 Number of bonds = 3904 Number of angles = 1396 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1294 Number of HB donors = 2566 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1292 Number of atoms = 3911 Number of groups = 1297 Number of bonds = 3904 Number of angles = 1396 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1294 Number of HB donors = 2566 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.942" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1292" Evaluating: 1292-7 Parameter: NUMWAT <- "1285" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1285" Comparing "1081" and "1285". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.942" Parameter: BOX -> "33.942" Parameter: BOX -> "33.942" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.94200 B = 33.94200 C = 33.94200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8948 2 1 -1 0 -1 3.4387 3 1 -1 1 -1 4.0771 4 1 0 -1 -1 3.5122 5 1 0 0 -1 1.4594 6 1 0 1 -1 2.7242 7 1 -1 -1 0 2.7435 8 1 -1 0 0 2.1530 9 1 -1 1 0 3.8673 10 1 0 -1 0 1.1897 11 1 0 1 0 1.1897 12 1 -1 -1 1 3.3510 13 1 -1 0 1 3.4495 14 1 -1 1 1 4.1281 15 1 0 -1 1 2.7242 16 1 0 0 1 1.4594 17 1 0 1 1 3.5122 18 1 1 1 1 6.8948 19 1 1 0 1 3.4387 20 1 1 -1 1 4.0771 21 1 1 1 0 2.7435 22 1 1 0 0 2.1530 23 1 1 -1 0 3.8673 24 1 1 1 -1 3.3510 25 1 1 0 -1 3.4495 26 1 1 -1 -1 4.1281 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3837 atoms have been selected out of 3911 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1230 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 402 134 134 0.00 2 C002 has 702 234 234 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1650 550 550 0.00 6 C006 has 513 171 171 0.00 7 C007 has 744 248 248 0.00 8 C008 has 1790 595 595 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1698 566 566 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 126 42 42 0.79 Total of13348 atoms and 4441 groups and 4436 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3911 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1291 Number of atoms = 3908 Number of groups = 1296 Number of bonds = 3901 Number of angles = 1395 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1293 Number of HB donors = 2564 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1291 Number of atoms = 3908 Number of groups = 1296 Number of bonds = 3901 Number of angles = 1395 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1293 Number of HB donors = 2564 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.94" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1291" Evaluating: 1291-7 Parameter: NUMWAT <- "1284" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1284" Comparing "1081" and "1284". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.94" Parameter: BOX -> "33.94" Parameter: BOX -> "33.94" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.94000 B = 33.94000 C = 33.94000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8926 2 1 -1 0 -1 3.4360 3 1 -1 1 -1 4.0737 4 1 0 -1 -1 3.5094 5 1 0 0 -1 1.4576 6 1 0 1 -1 2.7215 7 1 -1 -1 0 2.7407 8 1 -1 0 0 2.1511 9 1 -1 1 0 3.8653 10 1 0 -1 0 1.1896 11 1 0 1 0 1.1896 12 1 -1 -1 1 3.3476 13 1 -1 0 1 3.4467 14 1 -1 1 1 4.1253 15 1 0 -1 1 2.7215 16 1 0 0 1 1.4576 17 1 0 1 1 3.5094 18 1 1 1 1 6.8926 19 1 1 0 1 3.4360 20 1 1 -1 1 4.0737 21 1 1 1 0 2.7407 22 1 1 0 0 2.1511 23 1 1 -1 0 3.8653 24 1 1 1 -1 3.3476 25 1 1 0 -1 3.4467 26 1 1 -1 -1 4.1253 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3834 atoms have been selected out of 3908 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 402 134 134 0.00 2 C002 has 702 234 234 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1647 549 549 0.00 6 C006 has 513 171 171 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1695 565 565 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.79 Total of13330 atoms and 4435 groups and 4430 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3908 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1291 Number of atoms = 3908 Number of groups = 1296 Number of bonds = 3901 Number of angles = 1395 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1293 Number of HB donors = 2564 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1291 Number of atoms = 3908 Number of groups = 1296 Number of bonds = 3901 Number of angles = 1395 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1293 Number of HB donors = 2564 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.938" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1291" Evaluating: 1291-7 Parameter: NUMWAT <- "1284" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1284" Comparing "1081" and "1284". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.938" Parameter: BOX -> "33.938" Parameter: BOX -> "33.938" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.93800 B = 33.93800 C = 33.93800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8905 2 1 -1 0 -1 3.4332 3 1 -1 1 -1 4.0703 4 1 0 -1 -1 3.5067 5 1 0 0 -1 1.4557 6 1 0 1 -1 2.7187 7 1 -1 -1 0 2.7380 8 1 -1 0 0 2.1492 9 1 -1 1 0 3.8633 10 1 0 -1 0 1.1895 11 1 0 1 0 1.1895 12 1 -1 -1 1 3.3441 13 1 -1 0 1 3.4439 14 1 -1 1 1 4.1225 15 1 0 -1 1 2.7187 16 1 0 0 1 1.4557 17 1 0 1 1 3.5067 18 1 1 1 1 6.8905 19 1 1 0 1 3.4332 20 1 1 -1 1 4.0703 21 1 1 1 0 2.7380 22 1 1 0 0 2.1492 23 1 1 -1 0 3.8633 24 1 1 1 -1 3.3441 25 1 1 0 -1 3.4439 26 1 1 -1 -1 4.1225 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3834 atoms have been selected out of 3908 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 405 135 135 0.00 2 C002 has 702 234 234 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1650 550 550 0.00 6 C006 has 513 171 171 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1698 566 566 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.78 Total of13339 atoms and 4438 groups and 4433 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3908 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1291 Number of atoms = 3908 Number of groups = 1296 Number of bonds = 3901 Number of angles = 1395 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1293 Number of HB donors = 2564 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1291 Number of atoms = 3908 Number of groups = 1296 Number of bonds = 3901 Number of angles = 1395 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1293 Number of HB donors = 2564 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.936" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1291" Evaluating: 1291-7 Parameter: NUMWAT <- "1284" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1284" Comparing "1081" and "1284". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.936" Parameter: BOX -> "33.936" Parameter: BOX -> "33.936" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.93600 B = 33.93600 C = 33.93600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8883 2 1 -1 0 -1 3.4304 3 1 -1 1 -1 4.0668 4 1 0 -1 -1 3.5039 5 1 0 0 -1 1.4538 6 1 0 1 -1 2.7160 7 1 -1 -1 0 2.7353 8 1 -1 0 0 2.1473 9 1 -1 1 0 3.8613 10 1 0 -1 0 1.1895 11 1 0 1 0 1.1895 12 1 -1 -1 1 3.3407 13 1 -1 0 1 3.4412 14 1 -1 1 1 4.1197 15 1 0 -1 1 2.7160 16 1 0 0 1 1.4538 17 1 0 1 1 3.5039 18 1 1 1 1 6.8883 19 1 1 0 1 3.4304 20 1 1 -1 1 4.0668 21 1 1 1 0 2.7353 22 1 1 0 0 2.1473 23 1 1 -1 0 3.8613 24 1 1 1 -1 3.3407 25 1 1 0 -1 3.4412 26 1 1 -1 -1 4.1197 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3834 atoms have been selected out of 3908 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 405 135 135 0.00 2 C002 has 702 234 234 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1650 550 550 0.00 6 C006 has 513 171 171 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 507 169 169 0.00 10 C010 has 1698 566 566 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.78 Total of13342 atoms and 4439 groups and 4434 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3908 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1291 Number of atoms = 3908 Number of groups = 1296 Number of bonds = 3901 Number of angles = 1395 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1293 Number of HB donors = 2564 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1291 Number of atoms = 3908 Number of groups = 1296 Number of bonds = 3901 Number of angles = 1395 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1293 Number of HB donors = 2564 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.934" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1291" Evaluating: 1291-7 Parameter: NUMWAT <- "1284" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1284" Comparing "1081" and "1284". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.934" Parameter: BOX -> "33.934" Parameter: BOX -> "33.934" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.93400 B = 33.93400 C = 33.93400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8862 2 1 -1 0 -1 3.4277 3 1 -1 1 -1 4.0634 4 1 0 -1 -1 3.5012 5 1 0 0 -1 1.4520 6 1 0 1 -1 2.7133 7 1 -1 -1 0 2.7326 8 1 -1 0 0 2.1454 9 1 -1 1 0 3.8593 10 1 0 -1 0 1.1894 11 1 0 1 0 1.1894 12 1 -1 -1 1 3.3372 13 1 -1 0 1 3.4384 14 1 -1 1 1 4.1169 15 1 0 -1 1 2.7133 16 1 0 0 1 1.4520 17 1 0 1 1 3.5012 18 1 1 1 1 6.8862 19 1 1 0 1 3.4277 20 1 1 -1 1 4.0634 21 1 1 1 0 2.7326 22 1 1 0 0 2.1454 23 1 1 -1 0 3.8593 24 1 1 1 -1 3.3372 25 1 1 0 -1 3.4384 26 1 1 -1 -1 4.1169 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3834 atoms have been selected out of 3908 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 405 135 135 0.00 2 C002 has 702 234 234 0.00 3 C003 has 105 35 35 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1650 550 550 0.00 6 C006 has 513 171 171 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 507 169 169 0.00 10 C010 has 1698 566 566 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.78 Total of13345 atoms and 4440 groups and 4435 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3908 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1291 Number of atoms = 3908 Number of groups = 1296 Number of bonds = 3901 Number of angles = 1395 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1293 Number of HB donors = 2564 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1291 Number of atoms = 3908 Number of groups = 1296 Number of bonds = 3901 Number of angles = 1395 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1293 Number of HB donors = 2564 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.932" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1291" Evaluating: 1291-7 Parameter: NUMWAT <- "1284" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1284" Comparing "1081" and "1284". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.932" Parameter: BOX -> "33.932" Parameter: BOX -> "33.932" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.93200 B = 33.93200 C = 33.93200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8841 2 1 -1 0 -1 3.4249 3 1 -1 1 -1 4.0600 4 1 0 -1 -1 3.4984 5 1 0 0 -1 1.4501 6 1 0 1 -1 2.7106 7 1 -1 -1 0 2.7299 8 1 -1 0 0 2.1435 9 1 -1 1 0 3.8573 10 1 0 -1 0 1.1894 11 1 0 1 0 1.1894 12 1 -1 -1 1 3.3338 13 1 -1 0 1 3.4357 14 1 -1 1 1 4.1141 15 1 0 -1 1 2.7106 16 1 0 0 1 1.4501 17 1 0 1 1 3.4984 18 1 1 1 1 6.8841 19 1 1 0 1 3.4249 20 1 1 -1 1 4.0600 21 1 1 1 0 2.7299 22 1 1 0 0 2.1435 23 1 1 -1 0 3.8573 24 1 1 1 -1 3.3338 25 1 1 0 -1 3.4357 26 1 1 -1 -1 4.1141 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3834 atoms have been selected out of 3908 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 405 135 135 0.00 2 C002 has 702 234 234 0.00 3 C003 has 105 35 35 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1650 550 550 0.00 6 C006 has 513 171 171 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 507 169 169 0.00 10 C010 has 1698 566 566 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.78 Total of13345 atoms and 4440 groups and 4435 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3908 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1291 Number of atoms = 3908 Number of groups = 1296 Number of bonds = 3901 Number of angles = 1395 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1293 Number of HB donors = 2564 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1291 Number of atoms = 3908 Number of groups = 1296 Number of bonds = 3901 Number of angles = 1395 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1293 Number of HB donors = 2564 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.93" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1291" Evaluating: 1291-7 Parameter: NUMWAT <- "1284" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1284" Comparing "1081" and "1284". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.93" Parameter: BOX -> "33.93" Parameter: BOX -> "33.93" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.93000 B = 33.93000 C = 33.93000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8820 2 1 -1 0 -1 3.4222 3 1 -1 1 -1 4.0566 4 1 0 -1 -1 3.4957 5 1 0 0 -1 1.4482 6 1 0 1 -1 2.7079 7 1 -1 -1 0 2.7272 8 1 -1 0 0 2.1415 9 1 -1 1 0 3.8553 10 1 0 -1 0 1.1893 11 1 0 1 0 1.1893 12 1 -1 -1 1 3.3303 13 1 -1 0 1 3.4329 14 1 -1 1 1 4.1113 15 1 0 -1 1 2.7079 16 1 0 0 1 1.4482 17 1 0 1 1 3.4957 18 1 1 1 1 6.8820 19 1 1 0 1 3.4222 20 1 1 -1 1 4.0566 21 1 1 1 0 2.7272 22 1 1 0 0 2.1415 23 1 1 -1 0 3.8553 24 1 1 1 -1 3.3303 25 1 1 0 -1 3.4329 26 1 1 -1 -1 4.1113 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3834 atoms have been selected out of 3908 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 946 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 408 136 136 0.00 2 C002 has 702 234 234 0.00 3 C003 has 102 34 34 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1650 550 550 0.00 6 C006 has 510 170 170 0.00 7 C007 has 744 248 248 0.00 8 C008 has 1787 594 594 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1698 566 566 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.78 Total of13345 atoms and 4440 groups and 4435 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3908 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1290 Number of atoms = 3905 Number of groups = 1295 Number of bonds = 3898 Number of angles = 1394 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1292 Number of HB donors = 2562 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1290 Number of atoms = 3905 Number of groups = 1295 Number of bonds = 3898 Number of angles = 1394 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1292 Number of HB donors = 2562 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.928" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1290" Evaluating: 1290-7 Parameter: NUMWAT <- "1283" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1283" Comparing "1081" and "1283". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.928" Parameter: BOX -> "33.928" Parameter: BOX -> "33.928" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.92800 B = 33.92800 C = 33.92800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8798 2 1 -1 0 -1 3.4194 3 1 -1 1 -1 4.0531 4 1 0 -1 -1 3.4929 5 1 0 0 -1 1.4464 6 1 0 1 -1 2.7052 7 1 -1 -1 0 2.7245 8 1 -1 0 0 2.1396 9 1 -1 1 0 3.8533 10 1 0 -1 0 1.1893 11 1 0 1 0 1.1893 12 1 -1 -1 1 3.3269 13 1 -1 0 1 3.4302 14 1 -1 1 1 4.1085 15 1 0 -1 1 2.7052 16 1 0 0 1 1.4464 17 1 0 1 1 3.4929 18 1 1 1 1 6.8798 19 1 1 0 1 3.4194 20 1 1 -1 1 4.0531 21 1 1 1 0 2.7245 22 1 1 0 0 2.1396 23 1 1 -1 0 3.8533 24 1 1 1 -1 3.3269 25 1 1 0 -1 3.4302 26 1 1 -1 -1 4.1085 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3831 atoms have been selected out of 3905 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 405 135 135 0.00 2 C002 has 699 233 233 0.00 3 C003 has 102 34 34 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1647 549 549 0.00 6 C006 has 510 170 170 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1784 593 593 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1695 565 565 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.77 Total of13321 atoms and 4432 groups and 4427 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3905 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1290 Number of atoms = 3905 Number of groups = 1295 Number of bonds = 3898 Number of angles = 1394 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1292 Number of HB donors = 2562 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1290 Number of atoms = 3905 Number of groups = 1295 Number of bonds = 3898 Number of angles = 1394 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1292 Number of HB donors = 2562 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.926" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1290" Evaluating: 1290-7 Parameter: NUMWAT <- "1283" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1283" Comparing "1081" and "1283". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.926" Parameter: BOX -> "33.926" Parameter: BOX -> "33.926" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.92600 B = 33.92600 C = 33.92600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8777 2 1 -1 0 -1 3.4167 3 1 -1 1 -1 4.0497 4 1 0 -1 -1 3.4902 5 1 0 0 -1 1.4445 6 1 0 1 -1 2.7024 7 1 -1 -1 0 2.7218 8 1 -1 0 0 2.1377 9 1 -1 1 0 3.8513 10 1 0 -1 0 1.1892 11 1 0 1 0 1.1892 12 1 -1 -1 1 3.3235 13 1 -1 0 1 3.4274 14 1 -1 1 1 4.1057 15 1 0 -1 1 2.7024 16 1 0 0 1 1.4445 17 1 0 1 1 3.4902 18 1 1 1 1 6.8777 19 1 1 0 1 3.4167 20 1 1 -1 1 4.0497 21 1 1 1 0 2.7218 22 1 1 0 0 2.1377 23 1 1 -1 0 3.8513 24 1 1 1 -1 3.3235 25 1 1 0 -1 3.4274 26 1 1 -1 -1 4.1057 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3831 atoms have been selected out of 3905 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 405 135 135 0.00 2 C002 has 699 233 233 0.00 3 C003 has 102 34 34 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1647 549 549 0.00 6 C006 has 510 170 170 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1784 593 593 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1695 565 565 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.77 Total of13321 atoms and 4432 groups and 4427 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3905 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1290 Number of atoms = 3905 Number of groups = 1295 Number of bonds = 3898 Number of angles = 1394 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1292 Number of HB donors = 2562 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1290 Number of atoms = 3905 Number of groups = 1295 Number of bonds = 3898 Number of angles = 1394 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1292 Number of HB donors = 2562 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.924" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1290" Evaluating: 1290-7 Parameter: NUMWAT <- "1283" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1283" Comparing "1081" and "1283". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.924" Parameter: BOX -> "33.924" Parameter: BOX -> "33.924" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.92400 B = 33.92400 C = 33.92400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8756 2 1 -1 0 -1 3.4139 3 1 -1 1 -1 4.0463 4 1 0 -1 -1 3.4874 5 1 0 0 -1 1.4427 6 1 0 1 -1 2.6997 7 1 -1 -1 0 2.7191 8 1 -1 0 0 2.1358 9 1 -1 1 0 3.8493 10 1 0 -1 0 1.1892 11 1 0 1 0 1.1892 12 1 -1 -1 1 3.3200 13 1 -1 0 1 3.4247 14 1 -1 1 1 4.1029 15 1 0 -1 1 2.6997 16 1 0 0 1 1.4427 17 1 0 1 1 3.4874 18 1 1 1 1 6.8756 19 1 1 0 1 3.4139 20 1 1 -1 1 4.0463 21 1 1 1 0 2.7191 22 1 1 0 0 2.1358 23 1 1 -1 0 3.8493 24 1 1 1 -1 3.3200 25 1 1 0 -1 3.4247 26 1 1 -1 -1 4.1029 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3831 atoms have been selected out of 3905 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 405 135 135 0.00 2 C002 has 699 233 233 0.00 3 C003 has 102 34 34 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1647 549 549 0.00 6 C006 has 510 170 170 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1784 593 593 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1695 565 565 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.77 Total of13321 atoms and 4432 groups and 4427 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3905 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1290 Number of atoms = 3905 Number of groups = 1295 Number of bonds = 3898 Number of angles = 1394 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1292 Number of HB donors = 2562 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1290 Number of atoms = 3905 Number of groups = 1295 Number of bonds = 3898 Number of angles = 1394 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1292 Number of HB donors = 2562 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.922" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1290" Evaluating: 1290-7 Parameter: NUMWAT <- "1283" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1283" Comparing "1081" and "1283". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.922" Parameter: BOX -> "33.922" Parameter: BOX -> "33.922" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.92200 B = 33.92200 C = 33.92200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8734 2 1 -1 0 -1 3.4111 3 1 -1 1 -1 4.0428 4 1 0 -1 -1 3.4847 5 1 0 0 -1 1.4408 6 1 0 1 -1 2.6970 7 1 -1 -1 0 2.7164 8 1 -1 0 0 2.1339 9 1 -1 1 0 3.8473 10 1 0 -1 0 1.1892 11 1 0 1 0 1.1892 12 1 -1 -1 1 3.3166 13 1 -1 0 1 3.4219 14 1 -1 1 1 4.1001 15 1 0 -1 1 2.6970 16 1 0 0 1 1.4408 17 1 0 1 1 3.4847 18 1 1 1 1 6.8734 19 1 1 0 1 3.4111 20 1 1 -1 1 4.0428 21 1 1 1 0 2.7164 22 1 1 0 0 2.1339 23 1 1 -1 0 3.8473 24 1 1 1 -1 3.3166 25 1 1 0 -1 3.4219 26 1 1 -1 -1 4.1001 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3831 atoms have been selected out of 3905 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 405 135 135 0.00 2 C002 has 699 233 233 0.00 3 C003 has 102 34 34 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1650 550 550 0.00 6 C006 has 510 170 170 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1784 593 593 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1695 565 565 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.77 Total of13324 atoms and 4433 groups and 4428 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3905 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1290 Number of atoms = 3905 Number of groups = 1295 Number of bonds = 3898 Number of angles = 1394 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1292 Number of HB donors = 2562 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1290 Number of atoms = 3905 Number of groups = 1295 Number of bonds = 3898 Number of angles = 1394 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1292 Number of HB donors = 2562 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.92" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1290" Evaluating: 1290-7 Parameter: NUMWAT <- "1283" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1283" Comparing "1081" and "1283". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.92" Parameter: BOX -> "33.92" Parameter: BOX -> "33.92" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.92000 B = 33.92000 C = 33.92000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8713 2 1 -1 0 -1 3.4084 3 1 -1 1 -1 4.0394 4 1 0 -1 -1 3.4819 5 1 0 0 -1 1.4390 6 1 0 1 -1 2.6943 7 1 -1 -1 0 2.7137 8 1 -1 0 0 2.1320 9 1 -1 1 0 3.8453 10 1 0 -1 0 1.1891 11 1 0 1 0 1.1891 12 1 -1 -1 1 3.3131 13 1 -1 0 1 3.4191 14 1 -1 1 1 4.0973 15 1 0 -1 1 2.6943 16 1 0 0 1 1.4390 17 1 0 1 1 3.4819 18 1 1 1 1 6.8713 19 1 1 0 1 3.4084 20 1 1 -1 1 4.0394 21 1 1 1 0 2.7137 22 1 1 0 0 2.1320 23 1 1 -1 0 3.8453 24 1 1 1 -1 3.3131 25 1 1 0 -1 3.4191 26 1 1 -1 -1 4.0973 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3831 atoms have been selected out of 3905 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 405 135 135 0.00 2 C002 has 699 233 233 0.00 3 C003 has 102 34 34 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1650 550 550 0.00 6 C006 has 510 170 170 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1784 593 593 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1695 565 565 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.77 Total of13324 atoms and 4433 groups and 4428 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3905 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1290 Number of atoms = 3905 Number of groups = 1295 Number of bonds = 3898 Number of angles = 1394 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1292 Number of HB donors = 2562 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1290 Number of atoms = 3905 Number of groups = 1295 Number of bonds = 3898 Number of angles = 1394 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1292 Number of HB donors = 2562 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.918" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1290" Evaluating: 1290-7 Parameter: NUMWAT <- "1283" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1283" Comparing "1081" and "1283". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.918" Parameter: BOX -> "33.918" Parameter: BOX -> "33.918" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.91800 B = 33.91800 C = 33.91800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8692 2 1 -1 0 -1 3.4056 3 1 -1 1 -1 4.0360 4 1 0 -1 -1 3.4792 5 1 0 0 -1 1.4371 6 1 0 1 -1 2.6916 7 1 -1 -1 0 2.7109 8 1 -1 0 0 2.1301 9 1 -1 1 0 3.8434 10 1 0 -1 0 1.1891 11 1 0 1 0 1.1891 12 1 -1 -1 1 3.3097 13 1 -1 0 1 3.4164 14 1 -1 1 1 4.0945 15 1 0 -1 1 2.6916 16 1 0 0 1 1.4371 17 1 0 1 1 3.4792 18 1 1 1 1 6.8692 19 1 1 0 1 3.4056 20 1 1 -1 1 4.0360 21 1 1 1 0 2.7109 22 1 1 0 0 2.1301 23 1 1 -1 0 3.8434 24 1 1 1 -1 3.3097 25 1 1 0 -1 3.4164 26 1 1 -1 -1 4.0945 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3831 atoms have been selected out of 3905 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 266 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 405 135 135 0.00 2 C002 has 699 233 233 0.00 3 C003 has 102 34 34 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1650 550 550 0.00 6 C006 has 510 170 170 0.00 7 C007 has 744 248 248 0.00 8 C008 has 1784 593 593 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1695 565 565 0.00 12 C012 has 120 40 40 0.00 13 C013 has 471 157 157 0.00 14 C014 has 123 41 41 0.70 Total of13324 atoms and 4433 groups and 4428 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3905 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1289 Number of atoms = 3902 Number of groups = 1294 Number of bonds = 3895 Number of angles = 1393 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1291 Number of HB donors = 2560 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1289 Number of atoms = 3902 Number of groups = 1294 Number of bonds = 3895 Number of angles = 1393 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1291 Number of HB donors = 2560 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.916" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1289" Evaluating: 1289-7 Parameter: NUMWAT <- "1282" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1282" Comparing "1081" and "1282". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.916" Parameter: BOX -> "33.916" Parameter: BOX -> "33.916" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.91600 B = 33.91600 C = 33.91600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8671 2 1 -1 0 -1 3.4029 3 1 -1 1 -1 4.0325 4 1 0 -1 -1 3.4764 5 1 0 0 -1 1.4352 6 1 0 1 -1 2.6889 7 1 -1 -1 0 2.7082 8 1 -1 0 0 2.1282 9 1 -1 1 0 3.8414 10 1 0 -1 0 1.1891 11 1 0 1 0 1.1891 12 1 -1 -1 1 3.3062 13 1 -1 0 1 3.4136 14 1 -1 1 1 4.0917 15 1 0 -1 1 2.6889 16 1 0 0 1 1.4352 17 1 0 1 1 3.4764 18 1 1 1 1 6.8671 19 1 1 0 1 3.4029 20 1 1 -1 1 4.0325 21 1 1 1 0 2.7082 22 1 1 0 0 2.1282 23 1 1 -1 0 3.8414 24 1 1 1 -1 3.3062 25 1 1 0 -1 3.4136 26 1 1 -1 -1 4.0917 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3828 atoms have been selected out of 3902 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 405 135 135 0.00 2 C002 has 699 233 233 0.00 3 C003 has 102 34 34 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1650 550 550 0.00 6 C006 has 510 170 170 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1781 592 592 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1692 564 564 0.00 12 C012 has 117 39 39 0.00 13 C013 has 468 156 156 0.00 14 C014 has 123 41 41 0.76 Total of13306 atoms and 4427 groups and 4422 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3902 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1289 Number of atoms = 3902 Number of groups = 1294 Number of bonds = 3895 Number of angles = 1393 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1291 Number of HB donors = 2560 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1289 Number of atoms = 3902 Number of groups = 1294 Number of bonds = 3895 Number of angles = 1393 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1291 Number of HB donors = 2560 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.914" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1289" Evaluating: 1289-7 Parameter: NUMWAT <- "1282" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1282" Comparing "1081" and "1282". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.914" Parameter: BOX -> "33.914" Parameter: BOX -> "33.914" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.91400 B = 33.91400 C = 33.91400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8649 2 1 -1 0 -1 3.4001 3 1 -1 1 -1 4.0291 4 1 0 -1 -1 3.4737 5 1 0 0 -1 1.4334 6 1 0 1 -1 2.6862 7 1 -1 -1 0 2.7055 8 1 -1 0 0 2.1263 9 1 -1 1 0 3.8394 10 1 0 -1 0 1.1891 11 1 0 1 0 1.1891 12 1 -1 -1 1 3.3028 13 1 -1 0 1 3.4109 14 1 -1 1 1 4.0889 15 1 0 -1 1 2.6862 16 1 0 0 1 1.4334 17 1 0 1 1 3.4737 18 1 1 1 1 6.8649 19 1 1 0 1 3.4001 20 1 1 -1 1 4.0291 21 1 1 1 0 2.7055 22 1 1 0 0 2.1263 23 1 1 -1 0 3.8394 24 1 1 1 -1 3.3028 25 1 1 0 -1 3.4109 26 1 1 -1 -1 4.0889 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3828 atoms have been selected out of 3902 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 405 135 135 0.00 2 C002 has 699 233 233 0.00 3 C003 has 102 34 34 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1650 550 550 0.00 6 C006 has 510 170 170 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1781 592 592 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1692 564 564 0.00 12 C012 has 117 39 39 0.00 13 C013 has 468 156 156 0.00 14 C014 has 123 41 41 0.76 Total of13306 atoms and 4427 groups and 4422 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3902 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1289 Number of atoms = 3902 Number of groups = 1294 Number of bonds = 3895 Number of angles = 1393 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1291 Number of HB donors = 2560 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1289 Number of atoms = 3902 Number of groups = 1294 Number of bonds = 3895 Number of angles = 1393 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1291 Number of HB donors = 2560 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.912" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1289" Evaluating: 1289-7 Parameter: NUMWAT <- "1282" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1282" Comparing "1081" and "1282". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.912" Parameter: BOX -> "33.912" Parameter: BOX -> "33.912" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.91200 B = 33.91200 C = 33.91200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8628 2 1 -1 0 -1 3.3974 3 1 -1 1 -1 4.0257 4 1 0 -1 -1 3.4709 5 1 0 0 -1 1.4315 6 1 0 1 -1 2.6835 7 1 -1 -1 0 2.7028 8 1 -1 0 0 2.1244 9 1 -1 1 0 3.8374 10 1 0 -1 0 1.1890 11 1 0 1 0 1.1890 12 1 -1 -1 1 3.2993 13 1 -1 0 1 3.4081 14 1 -1 1 1 4.0861 15 1 0 -1 1 2.6835 16 1 0 0 1 1.4315 17 1 0 1 1 3.4709 18 1 1 1 1 6.8628 19 1 1 0 1 3.3974 20 1 1 -1 1 4.0257 21 1 1 1 0 2.7028 22 1 1 0 0 2.1244 23 1 1 -1 0 3.8374 24 1 1 1 -1 3.2993 25 1 1 0 -1 3.4081 26 1 1 -1 -1 4.0861 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3828 atoms have been selected out of 3902 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 405 135 135 0.00 2 C002 has 699 233 233 0.00 3 C003 has 102 34 34 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1650 550 550 0.00 6 C006 has 510 170 170 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1781 592 592 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1692 564 564 0.00 12 C012 has 117 39 39 0.00 13 C013 has 468 156 156 0.00 14 C014 has 123 41 41 0.76 Total of13306 atoms and 4427 groups and 4422 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3902 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1289 Number of atoms = 3902 Number of groups = 1294 Number of bonds = 3895 Number of angles = 1393 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1291 Number of HB donors = 2560 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1289 Number of atoms = 3902 Number of groups = 1294 Number of bonds = 3895 Number of angles = 1393 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1291 Number of HB donors = 2560 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.91" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1289" Evaluating: 1289-7 Parameter: NUMWAT <- "1282" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1282" Comparing "1081" and "1282". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.91" Parameter: BOX -> "33.91" Parameter: BOX -> "33.91" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.91000 B = 33.91000 C = 33.91000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8607 2 1 -1 0 -1 3.3946 3 1 -1 1 -1 4.0223 4 1 0 -1 -1 3.4682 5 1 0 0 -1 1.4297 6 1 0 1 -1 2.6807 7 1 -1 -1 0 2.7001 8 1 -1 0 0 2.1224 9 1 -1 1 0 3.8354 10 1 0 -1 0 1.1890 11 1 0 1 0 1.1890 12 1 -1 -1 1 3.2959 13 1 -1 0 1 3.4054 14 1 -1 1 1 4.0833 15 1 0 -1 1 2.6807 16 1 0 0 1 1.4297 17 1 0 1 1 3.4682 18 1 1 1 1 6.8607 19 1 1 0 1 3.3946 20 1 1 -1 1 4.0223 21 1 1 1 0 2.7001 22 1 1 0 0 2.1224 23 1 1 -1 0 3.8354 24 1 1 1 -1 3.2959 25 1 1 0 -1 3.4054 26 1 1 -1 -1 4.0833 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3828 atoms have been selected out of 3902 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 405 135 135 0.00 2 C002 has 699 233 233 0.00 3 C003 has 102 34 34 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1650 550 550 0.00 6 C006 has 510 170 170 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1781 592 592 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1692 564 564 0.00 12 C012 has 117 39 39 0.00 13 C013 has 468 156 156 0.00 14 C014 has 123 41 41 0.76 Total of13306 atoms and 4427 groups and 4422 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3902 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1289 Number of atoms = 3902 Number of groups = 1294 Number of bonds = 3895 Number of angles = 1393 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1291 Number of HB donors = 2560 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1289 Number of atoms = 3902 Number of groups = 1294 Number of bonds = 3895 Number of angles = 1393 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1291 Number of HB donors = 2560 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.908" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1289" Evaluating: 1289-7 Parameter: NUMWAT <- "1282" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1282" Comparing "1081" and "1282". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.908" Parameter: BOX -> "33.908" Parameter: BOX -> "33.908" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.90800 B = 33.90800 C = 33.90800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8586 2 1 -1 0 -1 3.3919 3 1 -1 1 -1 4.0188 4 1 0 -1 -1 3.4654 5 1 0 0 -1 1.4278 6 1 0 1 -1 2.6780 7 1 -1 -1 0 2.6974 8 1 -1 0 0 2.1205 9 1 -1 1 0 3.8334 10 1 0 -1 0 1.1890 11 1 0 1 0 1.1890 12 1 -1 -1 1 3.2924 13 1 -1 0 1 3.4026 14 1 -1 1 1 4.0805 15 1 0 -1 1 2.6780 16 1 0 0 1 1.4278 17 1 0 1 1 3.4654 18 1 1 1 1 6.8586 19 1 1 0 1 3.3919 20 1 1 -1 1 4.0188 21 1 1 1 0 2.6974 22 1 1 0 0 2.1205 23 1 1 -1 0 3.8334 24 1 1 1 -1 3.2924 25 1 1 0 -1 3.4026 26 1 1 -1 -1 4.0805 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3828 atoms have been selected out of 3902 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 412 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 405 135 135 0.00 2 C002 has 699 233 233 0.00 3 C003 has 102 34 34 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1647 549 549 0.00 6 C006 has 513 171 171 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1781 592 592 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1689 563 563 0.00 12 C012 has 117 39 39 0.00 13 C013 has 468 156 156 0.00 14 C014 has 123 41 41 0.71 Total of13306 atoms and 4427 groups and 4422 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3902 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1288 Number of atoms = 3899 Number of groups = 1293 Number of bonds = 3892 Number of angles = 1392 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1290 Number of HB donors = 2558 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1288 Number of atoms = 3899 Number of groups = 1293 Number of bonds = 3892 Number of angles = 1392 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1290 Number of HB donors = 2558 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.906" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1288" Evaluating: 1288-7 Parameter: NUMWAT <- "1281" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1281" Comparing "1081" and "1281". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.906" Parameter: BOX -> "33.906" Parameter: BOX -> "33.906" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.90600 B = 33.90600 C = 33.90600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8565 2 1 -1 0 -1 3.3891 3 1 -1 1 -1 4.0154 4 1 0 -1 -1 3.4627 5 1 0 0 -1 1.4260 6 1 0 1 -1 2.6753 7 1 -1 -1 0 2.6947 8 1 -1 0 0 2.1186 9 1 -1 1 0 3.8315 10 1 0 -1 0 1.1890 11 1 0 1 0 1.1890 12 1 -1 -1 1 3.2890 13 1 -1 0 1 3.3999 14 1 -1 1 1 4.0778 15 1 0 -1 1 2.6753 16 1 0 0 1 1.4260 17 1 0 1 1 3.4627 18 1 1 1 1 6.8565 19 1 1 0 1 3.3891 20 1 1 -1 1 4.0154 21 1 1 1 0 2.6947 22 1 1 0 0 2.1186 23 1 1 -1 0 3.8315 24 1 1 1 -1 3.2890 25 1 1 0 -1 3.3999 26 1 1 -1 -1 4.0778 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3825 atoms have been selected out of 3899 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 405 135 135 0.00 2 C002 has 699 233 233 0.00 3 C003 has 102 34 34 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 513 171 171 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1781 592 592 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1689 563 563 0.00 12 C012 has 117 39 39 0.00 13 C013 has 468 156 156 0.00 14 C014 has 123 41 41 0.75 Total of13297 atoms and 4424 groups and 4419 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3899 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1288 Number of atoms = 3899 Number of groups = 1293 Number of bonds = 3892 Number of angles = 1392 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1290 Number of HB donors = 2558 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1288 Number of atoms = 3899 Number of groups = 1293 Number of bonds = 3892 Number of angles = 1392 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1290 Number of HB donors = 2558 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.904" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1288" Evaluating: 1288-7 Parameter: NUMWAT <- "1281" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1281" Comparing "1081" and "1281". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.904" Parameter: BOX -> "33.904" Parameter: BOX -> "33.904" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.90400 B = 33.90400 C = 33.90400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8543 2 1 -1 0 -1 3.3863 3 1 -1 1 -1 4.0120 4 1 0 -1 -1 3.4599 5 1 0 0 -1 1.4241 6 1 0 1 -1 2.6726 7 1 -1 -1 0 2.6920 8 1 -1 0 0 2.1167 9 1 -1 1 0 3.8295 10 1 0 -1 0 1.1890 11 1 0 1 0 1.1890 12 1 -1 -1 1 3.2856 13 1 -1 0 1 3.3971 14 1 -1 1 1 4.0750 15 1 0 -1 1 2.6726 16 1 0 0 1 1.4241 17 1 0 1 1 3.4599 18 1 1 1 1 6.8543 19 1 1 0 1 3.3863 20 1 1 -1 1 4.0120 21 1 1 1 0 2.6920 22 1 1 0 0 2.1167 23 1 1 -1 0 3.8295 24 1 1 1 -1 3.2856 25 1 1 0 -1 3.3971 26 1 1 -1 -1 4.0750 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3825 atoms have been selected out of 3899 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1110 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 405 135 135 0.00 2 C002 has 699 233 233 0.00 3 C003 has 102 34 34 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1644 548 548 0.00 6 C006 has 519 173 173 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1781 592 592 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1689 563 563 0.00 12 C012 has 120 40 40 0.00 13 C013 has 468 156 156 0.00 14 C014 has 123 41 41 0.75 Total of13303 atoms and 4426 groups and 4421 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3899 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1287 Number of atoms = 3896 Number of groups = 1292 Number of bonds = 3889 Number of angles = 1391 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1289 Number of HB donors = 2556 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1287 Number of atoms = 3896 Number of groups = 1292 Number of bonds = 3889 Number of angles = 1391 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1289 Number of HB donors = 2556 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.902" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1287" Evaluating: 1287-7 Parameter: NUMWAT <- "1280" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1280" Comparing "1081" and "1280". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.902" Parameter: BOX -> "33.902" Parameter: BOX -> "33.902" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.90200 B = 33.90200 C = 33.90200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8522 2 1 -1 0 -1 3.3836 3 1 -1 1 -1 4.0085 4 1 0 -1 -1 3.4572 5 1 0 0 -1 1.4222 6 1 0 1 -1 2.6699 7 1 -1 -1 0 2.6893 8 1 -1 0 0 2.1148 9 1 -1 1 0 3.8275 10 1 0 -1 0 1.1890 11 1 0 1 0 1.1890 12 1 -1 -1 1 3.2821 13 1 -1 0 1 3.3944 14 1 -1 1 1 4.0722 15 1 0 -1 1 2.6699 16 1 0 0 1 1.4222 17 1 0 1 1 3.4572 18 1 1 1 1 6.8522 19 1 1 0 1 3.3836 20 1 1 -1 1 4.0085 21 1 1 1 0 2.6893 22 1 1 0 0 2.1148 23 1 1 -1 0 3.8275 24 1 1 1 -1 3.2821 25 1 1 0 -1 3.3944 26 1 1 -1 -1 4.0722 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3822 atoms have been selected out of 3896 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 670 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 408 136 136 0.00 2 C002 has 702 234 234 0.00 3 C003 has 102 34 34 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1641 547 547 0.00 6 C006 has 516 172 172 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1781 592 592 0.00 9 C009 has 507 169 169 0.00 10 C010 has 1689 563 563 0.00 12 C012 has 120 40 40 0.00 13 C013 has 468 156 156 0.00 14 C014 has 123 41 41 0.75 Total of13306 atoms and 4427 groups and 4422 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3896 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1286 Number of atoms = 3893 Number of groups = 1291 Number of bonds = 3886 Number of angles = 1390 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1288 Number of HB donors = 2554 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1286 Number of atoms = 3893 Number of groups = 1291 Number of bonds = 3886 Number of angles = 1390 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1288 Number of HB donors = 2554 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.9" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1286" Evaluating: 1286-7 Parameter: NUMWAT <- "1279" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1279" Comparing "1081" and "1279". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.9" Parameter: BOX -> "33.9" Parameter: BOX -> "33.9" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.90000 B = 33.90000 C = 33.90000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8501 2 1 -1 0 -1 3.3808 3 1 -1 1 -1 4.0051 4 1 0 -1 -1 3.4544 5 1 0 0 -1 1.4204 6 1 0 1 -1 2.6672 7 1 -1 -1 0 2.6866 8 1 -1 0 0 2.1129 9 1 -1 1 0 3.8255 10 1 0 -1 0 1.1890 11 1 0 1 0 1.1890 12 1 -1 -1 1 3.2787 13 1 -1 0 1 3.3916 14 1 -1 1 1 4.0694 15 1 0 -1 1 2.6672 16 1 0 0 1 1.4204 17 1 0 1 1 3.4544 18 1 1 1 1 6.8501 19 1 1 0 1 3.3808 20 1 1 -1 1 4.0051 21 1 1 1 0 2.6866 22 1 1 0 0 2.1129 23 1 1 -1 0 3.8255 24 1 1 1 -1 3.2787 25 1 1 0 -1 3.3916 26 1 1 -1 -1 4.0694 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3819 atoms have been selected out of 3893 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 630 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 411 137 137 0.00 2 C002 has 702 234 234 0.00 3 C003 has 102 34 34 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1632 544 544 0.00 6 C006 has 516 172 172 0.00 7 C007 has 744 248 248 0.00 8 C008 has 1778 591 591 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1689 563 563 0.00 12 C012 has 117 39 39 0.00 13 C013 has 465 155 155 0.00 14 C014 has 123 41 41 0.75 Total of13291 atoms and 4422 groups and 4417 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3893 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.898" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1285" Evaluating: 1285-7 Parameter: NUMWAT <- "1278" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1278" Comparing "1081" and "1278". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.898" Parameter: BOX -> "33.898" Parameter: BOX -> "33.898" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.89800 B = 33.89800 C = 33.89800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8480 2 1 -1 0 -1 3.3781 3 1 -1 1 -1 4.0017 4 1 0 -1 -1 3.4517 5 1 0 0 -1 1.4185 6 1 0 1 -1 2.6645 7 1 -1 -1 0 2.6839 8 1 -1 0 0 2.1110 9 1 -1 1 0 3.8235 10 1 0 -1 0 1.1890 11 1 0 1 0 1.1890 12 1 -1 -1 1 3.2752 13 1 -1 0 1 3.3888 14 1 -1 1 1 4.0666 15 1 0 -1 1 2.6645 16 1 0 0 1 1.4185 17 1 0 1 1 3.4517 18 1 1 1 1 6.8480 19 1 1 0 1 3.3781 20 1 1 -1 1 4.0017 21 1 1 1 0 2.6839 22 1 1 0 0 2.1110 23 1 1 -1 0 3.8235 24 1 1 1 -1 3.2752 25 1 1 0 -1 3.3888 26 1 1 -1 -1 4.0666 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3816 atoms have been selected out of 3890 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 408 136 136 0.00 2 C002 has 699 233 233 0.00 3 C003 has 102 34 34 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1629 543 543 0.00 6 C006 has 516 172 172 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1686 562 562 0.00 12 C012 has 117 39 39 0.00 13 C013 has 465 155 155 0.00 14 C014 has 123 41 41 0.74 Total of13267 atoms and 4414 groups and 4409 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3890 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.896" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1285" Evaluating: 1285-7 Parameter: NUMWAT <- "1278" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1278" Comparing "1081" and "1278". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.896" Parameter: BOX -> "33.896" Parameter: BOX -> "33.896" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.89600 B = 33.89600 C = 33.89600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8459 2 1 -1 0 -1 3.3753 3 1 -1 1 -1 3.9983 4 1 0 -1 -1 3.4489 5 1 0 0 -1 1.4167 6 1 0 1 -1 2.6618 7 1 -1 -1 0 2.6812 8 1 -1 0 0 2.1091 9 1 -1 1 0 3.8216 10 1 0 -1 0 1.1890 11 1 0 1 0 1.1890 12 1 -1 -1 1 3.2718 13 1 -1 0 1 3.3861 14 1 -1 1 1 4.0638 15 1 0 -1 1 2.6618 16 1 0 0 1 1.4167 17 1 0 1 1 3.4489 18 1 1 1 1 6.8459 19 1 1 0 1 3.3753 20 1 1 -1 1 3.9983 21 1 1 1 0 2.6812 22 1 1 0 0 2.1091 23 1 1 -1 0 3.8216 24 1 1 1 -1 3.2718 25 1 1 0 -1 3.3861 26 1 1 -1 -1 4.0638 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3816 atoms have been selected out of 3890 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 408 136 136 0.00 2 C002 has 699 233 233 0.00 3 C003 has 102 34 34 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1629 543 543 0.00 6 C006 has 516 172 172 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1686 562 562 0.00 12 C012 has 117 39 39 0.00 13 C013 has 465 155 155 0.00 14 C014 has 123 41 41 0.74 Total of13267 atoms and 4414 groups and 4409 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3890 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.894" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1285" Evaluating: 1285-7 Parameter: NUMWAT <- "1278" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1278" Comparing "1081" and "1278". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.894" Parameter: BOX -> "33.894" Parameter: BOX -> "33.894" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.89400 B = 33.89400 C = 33.89400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8438 2 1 -1 0 -1 3.3726 3 1 -1 1 -1 3.9948 4 1 0 -1 -1 3.4462 5 1 0 0 -1 1.4148 6 1 0 1 -1 2.6590 7 1 -1 -1 0 2.6785 8 1 -1 0 0 2.1072 9 1 -1 1 0 3.8196 10 1 0 -1 0 1.1890 11 1 0 1 0 1.1890 12 1 -1 -1 1 3.2683 13 1 -1 0 1 3.3833 14 1 -1 1 1 4.0610 15 1 0 -1 1 2.6590 16 1 0 0 1 1.4148 17 1 0 1 1 3.4462 18 1 1 1 1 6.8438 19 1 1 0 1 3.3726 20 1 1 -1 1 3.9948 21 1 1 1 0 2.6785 22 1 1 0 0 2.1072 23 1 1 -1 0 3.8196 24 1 1 1 -1 3.2683 25 1 1 0 -1 3.3833 26 1 1 -1 -1 4.0610 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3816 atoms have been selected out of 3890 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 408 136 136 0.00 2 C002 has 699 233 233 0.00 3 C003 has 102 34 34 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1629 543 543 0.00 6 C006 has 516 172 172 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1686 562 562 0.00 12 C012 has 117 39 39 0.00 13 C013 has 465 155 155 0.00 14 C014 has 123 41 41 0.74 Total of13267 atoms and 4414 groups and 4409 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3890 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.892" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1285" Evaluating: 1285-7 Parameter: NUMWAT <- "1278" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1278" Comparing "1081" and "1278". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.892" Parameter: BOX -> "33.892" Parameter: BOX -> "33.892" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.89200 B = 33.89200 C = 33.89200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8417 2 1 -1 0 -1 3.3698 3 1 -1 1 -1 3.9914 4 1 0 -1 -1 3.4434 5 1 0 0 -1 1.4130 6 1 0 1 -1 2.6563 7 1 -1 -1 0 2.6758 8 1 -1 0 0 2.1053 9 1 -1 1 0 3.8176 10 1 0 -1 0 1.1890 11 1 0 1 0 1.1890 12 1 -1 -1 1 3.2649 13 1 -1 0 1 3.3806 14 1 -1 1 1 4.0583 15 1 0 -1 1 2.6563 16 1 0 0 1 1.4130 17 1 0 1 1 3.4434 18 1 1 1 1 6.8417 19 1 1 0 1 3.3698 20 1 1 -1 1 3.9914 21 1 1 1 0 2.6758 22 1 1 0 0 2.1053 23 1 1 -1 0 3.8176 24 1 1 1 -1 3.2649 25 1 1 0 -1 3.3806 26 1 1 -1 -1 4.0583 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3816 atoms have been selected out of 3890 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 408 136 136 0.00 2 C002 has 699 233 233 0.00 3 C003 has 102 34 34 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1629 543 543 0.00 6 C006 has 516 172 172 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1686 562 562 0.00 12 C012 has 117 39 39 0.00 13 C013 has 465 155 155 0.00 14 C014 has 123 41 41 0.74 Total of13267 atoms and 4414 groups and 4409 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3890 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.89" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1285" Evaluating: 1285-7 Parameter: NUMWAT <- "1278" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1278" Comparing "1081" and "1278". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.89" Parameter: BOX -> "33.89" Parameter: BOX -> "33.89" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.89000 B = 33.89000 C = 33.89000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8395 2 1 -1 0 -1 3.3671 3 1 -1 1 -1 3.9880 4 1 0 -1 -1 3.4407 5 1 0 0 -1 1.4111 6 1 0 1 -1 2.6536 7 1 -1 -1 0 2.6731 8 1 -1 0 0 2.1034 9 1 -1 1 0 3.8156 10 1 0 -1 0 1.1891 11 1 0 1 0 1.1891 12 1 -1 -1 1 3.2614 13 1 -1 0 1 3.3778 14 1 -1 1 1 4.0555 15 1 0 -1 1 2.6536 16 1 0 0 1 1.4111 17 1 0 1 1 3.4407 18 1 1 1 1 6.8395 19 1 1 0 1 3.3671 20 1 1 -1 1 3.9880 21 1 1 1 0 2.6731 22 1 1 0 0 2.1034 23 1 1 -1 0 3.8156 24 1 1 1 -1 3.2614 25 1 1 0 -1 3.3778 26 1 1 -1 -1 4.0555 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3816 atoms have been selected out of 3890 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 408 136 136 0.00 2 C002 has 699 233 233 0.00 3 C003 has 102 34 34 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1629 543 543 0.00 6 C006 has 519 173 173 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1686 562 562 0.00 12 C012 has 117 39 39 0.00 13 C013 has 465 155 155 0.00 14 C014 has 123 41 41 0.74 Total of13270 atoms and 4415 groups and 4410 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3890 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.888" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1285" Evaluating: 1285-7 Parameter: NUMWAT <- "1278" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1278" Comparing "1081" and "1278". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.888" Parameter: BOX -> "33.888" Parameter: BOX -> "33.888" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.88800 B = 33.88800 C = 33.88800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8374 2 1 -1 0 -1 3.3643 3 1 -1 1 -1 3.9845 4 1 0 -1 -1 3.4379 5 1 0 0 -1 1.4093 6 1 0 1 -1 2.6509 7 1 -1 -1 0 2.6704 8 1 -1 0 0 2.1015 9 1 -1 1 0 3.8137 10 1 0 -1 0 1.1891 11 1 0 1 0 1.1891 12 1 -1 -1 1 3.2580 13 1 -1 0 1 3.3751 14 1 -1 1 1 4.0527 15 1 0 -1 1 2.6509 16 1 0 0 1 1.4093 17 1 0 1 1 3.4379 18 1 1 1 1 6.8374 19 1 1 0 1 3.3643 20 1 1 -1 1 3.9845 21 1 1 1 0 2.6704 22 1 1 0 0 2.1015 23 1 1 -1 0 3.8137 24 1 1 1 -1 3.2580 25 1 1 0 -1 3.3751 26 1 1 -1 -1 4.0527 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3816 atoms have been selected out of 3890 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 408 136 136 0.00 2 C002 has 699 233 233 0.00 3 C003 has 102 34 34 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1629 543 543 0.00 6 C006 has 519 173 173 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1686 562 562 0.00 12 C012 has 117 39 39 0.00 13 C013 has 465 155 155 0.00 14 C014 has 123 41 41 0.73 Total of13270 atoms and 4415 groups and 4410 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3890 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.886" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1285" Evaluating: 1285-7 Parameter: NUMWAT <- "1278" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1278" Comparing "1081" and "1278". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.886" Parameter: BOX -> "33.886" Parameter: BOX -> "33.886" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.88600 B = 33.88600 C = 33.88600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8353 2 1 -1 0 -1 3.3616 3 1 -1 1 -1 3.9811 4 1 0 -1 -1 3.4352 5 1 0 0 -1 1.4074 6 1 0 1 -1 2.6482 7 1 -1 -1 0 2.6676 8 1 -1 0 0 2.0996 9 1 -1 1 0 3.8117 10 1 0 -1 0 1.1891 11 1 0 1 0 1.1891 12 1 -1 -1 1 3.2545 13 1 -1 0 1 3.3723 14 1 -1 1 1 4.0499 15 1 0 -1 1 2.6482 16 1 0 0 1 1.4074 17 1 0 1 1 3.4352 18 1 1 1 1 6.8353 19 1 1 0 1 3.3616 20 1 1 -1 1 3.9811 21 1 1 1 0 2.6676 22 1 1 0 0 2.0996 23 1 1 -1 0 3.8117 24 1 1 1 -1 3.2545 25 1 1 0 -1 3.3723 26 1 1 -1 -1 4.0499 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3816 atoms have been selected out of 3890 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 408 136 136 0.00 2 C002 has 699 233 233 0.00 3 C003 has 102 34 34 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1629 543 543 0.00 6 C006 has 519 173 173 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1686 562 562 0.00 12 C012 has 117 39 39 0.00 13 C013 has 465 155 155 0.00 14 C014 has 123 41 41 0.73 Total of13273 atoms and 4416 groups and 4411 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3890 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.884" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1285" Evaluating: 1285-7 Parameter: NUMWAT <- "1278" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1278" Comparing "1081" and "1278". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.884" Parameter: BOX -> "33.884" Parameter: BOX -> "33.884" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.88400 B = 33.88400 C = 33.88400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8332 2 1 -1 0 -1 3.3588 3 1 -1 1 -1 3.9777 4 1 0 -1 -1 3.4324 5 1 0 0 -1 1.4056 6 1 0 1 -1 2.6455 7 1 -1 -1 0 2.6649 8 1 -1 0 0 2.0976 9 1 -1 1 0 3.8097 10 1 0 -1 0 1.1891 11 1 0 1 0 1.1891 12 1 -1 -1 1 3.2511 13 1 -1 0 1 3.3696 14 1 -1 1 1 4.0471 15 1 0 -1 1 2.6455 16 1 0 0 1 1.4056 17 1 0 1 1 3.4324 18 1 1 1 1 6.8332 19 1 1 0 1 3.3588 20 1 1 -1 1 3.9777 21 1 1 1 0 2.6649 22 1 1 0 0 2.0976 23 1 1 -1 0 3.8097 24 1 1 1 -1 3.2511 25 1 1 0 -1 3.3696 26 1 1 -1 -1 4.0471 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3816 atoms have been selected out of 3890 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 408 136 136 0.00 2 C002 has 699 233 233 0.00 3 C003 has 105 35 35 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1629 543 543 0.00 6 C006 has 519 173 173 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1686 562 562 0.00 12 C012 has 117 39 39 0.00 13 C013 has 465 155 155 0.00 14 C014 has 123 41 41 0.73 Total of13276 atoms and 4417 groups and 4412 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3890 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.882" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1285" Evaluating: 1285-7 Parameter: NUMWAT <- "1278" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1278" Comparing "1081" and "1278". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.882" Parameter: BOX -> "33.882" Parameter: BOX -> "33.882" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.88200 B = 33.88200 C = 33.88200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8311 2 1 -1 0 -1 3.3560 3 1 -1 1 -1 3.9743 4 1 0 -1 -1 3.4297 5 1 0 0 -1 1.4037 6 1 0 1 -1 2.6428 7 1 -1 -1 0 2.6622 8 1 -1 0 0 2.0957 9 1 -1 1 0 3.8078 10 1 0 -1 0 1.1892 11 1 0 1 0 1.1892 12 1 -1 -1 1 3.2477 13 1 -1 0 1 3.3668 14 1 -1 1 1 4.0444 15 1 0 -1 1 2.6428 16 1 0 0 1 1.4037 17 1 0 1 1 3.4297 18 1 1 1 1 6.8311 19 1 1 0 1 3.3560 20 1 1 -1 1 3.9743 21 1 1 1 0 2.6622 22 1 1 0 0 2.0957 23 1 1 -1 0 3.8078 24 1 1 1 -1 3.2477 25 1 1 0 -1 3.3668 26 1 1 -1 -1 4.0444 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3816 atoms have been selected out of 3890 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 408 136 136 0.00 2 C002 has 699 233 233 0.00 3 C003 has 105 35 35 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1629 543 543 0.00 6 C006 has 519 173 173 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1686 562 562 0.00 12 C012 has 117 39 39 0.00 13 C013 has 465 155 155 0.00 14 C014 has 123 41 41 0.73 Total of13279 atoms and 4418 groups and 4413 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3890 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.88" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1285" Evaluating: 1285-7 Parameter: NUMWAT <- "1278" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1278" Comparing "1081" and "1278". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.88" Parameter: BOX -> "33.88" Parameter: BOX -> "33.88" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.88000 B = 33.88000 C = 33.88000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8290 2 1 -1 0 -1 3.3533 3 1 -1 1 -1 3.9708 4 1 0 -1 -1 3.4269 5 1 0 0 -1 1.4019 6 1 0 1 -1 2.6401 7 1 -1 -1 0 2.6595 8 1 -1 0 0 2.0938 9 1 -1 1 0 3.8058 10 1 0 -1 0 1.1892 11 1 0 1 0 1.1892 12 1 -1 -1 1 3.2442 13 1 -1 0 1 3.3641 14 1 -1 1 1 4.0416 15 1 0 -1 1 2.6401 16 1 0 0 1 1.4019 17 1 0 1 1 3.4269 18 1 1 1 1 6.8290 19 1 1 0 1 3.3533 20 1 1 -1 1 3.9708 21 1 1 1 0 2.6595 22 1 1 0 0 2.0938 23 1 1 -1 0 3.8058 24 1 1 1 -1 3.2442 25 1 1 0 -1 3.3641 26 1 1 -1 -1 4.0416 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3816 atoms have been selected out of 3890 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 408 136 136 0.00 2 C002 has 699 233 233 0.00 3 C003 has 105 35 35 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1629 543 543 0.00 6 C006 has 522 174 174 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1686 562 562 0.00 12 C012 has 117 39 39 0.00 13 C013 has 465 155 155 0.00 14 C014 has 123 41 41 0.73 Total of13282 atoms and 4419 groups and 4414 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3890 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.878" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1285" Evaluating: 1285-7 Parameter: NUMWAT <- "1278" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1278" Comparing "1081" and "1278". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.878" Parameter: BOX -> "33.878" Parameter: BOX -> "33.878" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.87800 B = 33.87800 C = 33.87800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8269 2 1 -1 0 -1 3.3505 3 1 -1 1 -1 3.9674 4 1 0 -1 -1 3.4242 5 1 0 0 -1 1.4000 6 1 0 1 -1 2.6374 7 1 -1 -1 0 2.6568 8 1 -1 0 0 2.0919 9 1 -1 1 0 3.8038 10 1 0 -1 0 1.1893 11 1 0 1 0 1.1893 12 1 -1 -1 1 3.2408 13 1 -1 0 1 3.3613 14 1 -1 1 1 4.0388 15 1 0 -1 1 2.6374 16 1 0 0 1 1.4000 17 1 0 1 1 3.4242 18 1 1 1 1 6.8269 19 1 1 0 1 3.3505 20 1 1 -1 1 3.9674 21 1 1 1 0 2.6568 22 1 1 0 0 2.0919 23 1 1 -1 0 3.8038 24 1 1 1 -1 3.2408 25 1 1 0 -1 3.3613 26 1 1 -1 -1 4.0388 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3816 atoms have been selected out of 3890 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 408 136 136 0.00 2 C002 has 699 233 233 0.00 3 C003 has 105 35 35 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1629 543 543 0.00 6 C006 has 522 174 174 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1689 563 563 0.00 12 C012 has 117 39 39 0.00 13 C013 has 465 155 155 0.00 14 C014 has 123 41 41 0.72 Total of13285 atoms and 4420 groups and 4415 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3890 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.876" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1285" Evaluating: 1285-7 Parameter: NUMWAT <- "1278" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1278" Comparing "1081" and "1278". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.876" Parameter: BOX -> "33.876" Parameter: BOX -> "33.876" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.87600 B = 33.87600 C = 33.87600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8248 2 1 -1 0 -1 3.3478 3 1 -1 1 -1 3.9640 4 1 0 -1 -1 3.4214 5 1 0 0 -1 1.3982 6 1 0 1 -1 2.6347 7 1 -1 -1 0 2.6541 8 1 -1 0 0 2.0900 9 1 -1 1 0 3.8019 10 1 0 -1 0 1.1893 11 1 0 1 0 1.1893 12 1 -1 -1 1 3.2373 13 1 -1 0 1 3.3586 14 1 -1 1 1 4.0360 15 1 0 -1 1 2.6347 16 1 0 0 1 1.3982 17 1 0 1 1 3.4214 18 1 1 1 1 6.8248 19 1 1 0 1 3.3478 20 1 1 -1 1 3.9640 21 1 1 1 0 2.6541 22 1 1 0 0 2.0900 23 1 1 -1 0 3.8019 24 1 1 1 -1 3.2373 25 1 1 0 -1 3.3586 26 1 1 -1 -1 4.0360 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3816 atoms have been selected out of 3890 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 408 136 136 0.00 2 C002 has 702 234 234 0.00 3 C003 has 105 35 35 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1629 543 543 0.00 6 C006 has 522 174 174 0.00 7 C007 has 744 248 248 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1689 563 563 0.00 12 C012 has 117 39 39 0.00 13 C013 has 465 155 155 0.00 14 C014 has 123 41 41 0.72 Total of13291 atoms and 4422 groups and 4417 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3890 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.874" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1285" Evaluating: 1285-7 Parameter: NUMWAT <- "1278" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1278" Comparing "1081" and "1278". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.874" Parameter: BOX -> "33.874" Parameter: BOX -> "33.874" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.87400 B = 33.87400 C = 33.87400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8227 2 1 -1 0 -1 3.3450 3 1 -1 1 -1 3.9605 4 1 0 -1 -1 3.4187 5 1 0 0 -1 1.3963 6 1 0 1 -1 2.6320 7 1 -1 -1 0 2.6514 8 1 -1 0 0 2.0881 9 1 -1 1 0 3.7999 10 1 0 -1 0 1.1893 11 1 0 1 0 1.1893 12 1 -1 -1 1 3.2339 13 1 -1 0 1 3.3558 14 1 -1 1 1 4.0333 15 1 0 -1 1 2.6320 16 1 0 0 1 1.3963 17 1 0 1 1 3.4187 18 1 1 1 1 6.8227 19 1 1 0 1 3.3450 20 1 1 -1 1 3.9605 21 1 1 1 0 2.6514 22 1 1 0 0 2.0881 23 1 1 -1 0 3.7999 24 1 1 1 -1 3.2339 25 1 1 0 -1 3.3558 26 1 1 -1 -1 4.0333 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3816 atoms have been selected out of 3890 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 408 136 136 0.00 2 C002 has 702 234 234 0.00 3 C003 has 105 35 35 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1629 543 543 0.00 6 C006 has 522 174 174 0.00 7 C007 has 744 248 248 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1689 563 563 0.00 12 C012 has 117 39 39 0.00 13 C013 has 468 156 156 0.00 14 C014 has 123 41 41 0.72 Total of13294 atoms and 4423 groups and 4418 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3890 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.872" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1285" Evaluating: 1285-7 Parameter: NUMWAT <- "1278" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1278" Comparing "1081" and "1278". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.872" Parameter: BOX -> "33.872" Parameter: BOX -> "33.872" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.87200 B = 33.87200 C = 33.87200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8206 2 1 -1 0 -1 3.3423 3 1 -1 1 -1 3.9571 4 1 0 -1 -1 3.4160 5 1 0 0 -1 1.3945 6 1 0 1 -1 2.6292 7 1 -1 -1 0 2.6487 8 1 -1 0 0 2.0862 9 1 -1 1 0 3.7979 10 1 0 -1 0 1.1894 11 1 0 1 0 1.1894 12 1 -1 -1 1 3.2304 13 1 -1 0 1 3.3531 14 1 -1 1 1 4.0305 15 1 0 -1 1 2.6292 16 1 0 0 1 1.3945 17 1 0 1 1 3.4160 18 1 1 1 1 6.8206 19 1 1 0 1 3.3423 20 1 1 -1 1 3.9571 21 1 1 1 0 2.6487 22 1 1 0 0 2.0862 23 1 1 -1 0 3.7979 24 1 1 1 -1 3.2304 25 1 1 0 -1 3.3531 26 1 1 -1 -1 4.0305 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3816 atoms have been selected out of 3890 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 408 136 136 0.00 2 C002 has 702 234 234 0.00 3 C003 has 105 35 35 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1629 543 543 0.00 6 C006 has 525 175 175 0.00 7 C007 has 744 248 248 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1689 563 563 0.00 12 C012 has 117 39 39 0.00 13 C013 has 468 156 156 0.00 14 C014 has 123 41 41 0.72 Total of13297 atoms and 4424 groups and 4419 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3890 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.87" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1285" Evaluating: 1285-7 Parameter: NUMWAT <- "1278" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1278" Comparing "1081" and "1278". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.87" Parameter: BOX -> "33.87" Parameter: BOX -> "33.87" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.87000 B = 33.87000 C = 33.87000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8185 2 1 -1 0 -1 3.3395 3 1 -1 1 -1 3.9537 4 1 0 -1 -1 3.4132 5 1 0 0 -1 1.3926 6 1 0 1 -1 2.6265 7 1 -1 -1 0 2.6460 8 1 -1 0 0 2.0843 9 1 -1 1 0 3.7960 10 1 0 -1 0 1.1894 11 1 0 1 0 1.1894 12 1 -1 -1 1 3.2270 13 1 -1 0 1 3.3503 14 1 -1 1 1 4.0277 15 1 0 -1 1 2.6265 16 1 0 0 1 1.3926 17 1 0 1 1 3.4132 18 1 1 1 1 6.8185 19 1 1 0 1 3.3395 20 1 1 -1 1 3.9537 21 1 1 1 0 2.6460 22 1 1 0 0 2.0843 23 1 1 -1 0 3.7960 24 1 1 1 -1 3.2270 25 1 1 0 -1 3.3503 26 1 1 -1 -1 4.0277 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3816 atoms have been selected out of 3890 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 408 136 136 0.00 2 C002 has 702 234 234 0.00 3 C003 has 105 35 35 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1629 543 543 0.00 6 C006 has 525 175 175 0.00 7 C007 has 744 248 248 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1689 563 563 0.00 12 C012 has 117 39 39 0.00 13 C013 has 468 156 156 0.00 14 C014 has 123 41 41 0.72 Total of13297 atoms and 4424 groups and 4419 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3890 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.868" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1285" Evaluating: 1285-7 Parameter: NUMWAT <- "1278" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1278" Comparing "1081" and "1278". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.868" Parameter: BOX -> "33.868" Parameter: BOX -> "33.868" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.86800 B = 33.86800 C = 33.86800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8164 2 1 -1 0 -1 3.3368 3 1 -1 1 -1 3.9503 4 1 0 -1 -1 3.4105 5 1 0 0 -1 1.3908 6 1 0 1 -1 2.6238 7 1 -1 -1 0 2.6433 8 1 -1 0 0 2.0824 9 1 -1 1 0 3.7940 10 1 0 -1 0 1.1895 11 1 0 1 0 1.1895 12 1 -1 -1 1 3.2235 13 1 -1 0 1 3.3476 14 1 -1 1 1 4.0250 15 1 0 -1 1 2.6238 16 1 0 0 1 1.3908 17 1 0 1 1 3.4105 18 1 1 1 1 6.8164 19 1 1 0 1 3.3368 20 1 1 -1 1 3.9503 21 1 1 1 0 2.6433 22 1 1 0 0 2.0824 23 1 1 -1 0 3.7940 24 1 1 1 -1 3.2235 25 1 1 0 -1 3.3476 26 1 1 -1 -1 4.0250 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3816 atoms have been selected out of 3890 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 408 136 136 0.00 2 C002 has 702 234 234 0.00 3 C003 has 105 35 35 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1629 543 543 0.00 6 C006 has 525 175 175 0.00 7 C007 has 744 248 248 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1689 563 563 0.00 12 C012 has 117 39 39 0.00 13 C013 has 468 156 156 0.00 14 C014 has 123 41 41 0.71 Total of13297 atoms and 4424 groups and 4419 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3890 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.866" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1285" Evaluating: 1285-7 Parameter: NUMWAT <- "1278" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1278" Comparing "1081" and "1278". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.866" Parameter: BOX -> "33.866" Parameter: BOX -> "33.866" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.86600 B = 33.86600 C = 33.86600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8143 2 1 -1 0 -1 3.3340 3 1 -1 1 -1 3.9468 4 1 0 -1 -1 3.4077 5 1 0 0 -1 1.3889 6 1 0 1 -1 2.6211 7 1 -1 -1 0 2.6406 8 1 -1 0 0 2.0805 9 1 -1 1 0 3.7921 10 1 0 -1 0 1.1896 11 1 0 1 0 1.1896 12 1 -1 -1 1 3.2201 13 1 -1 0 1 3.3448 14 1 -1 1 1 4.0222 15 1 0 -1 1 2.6211 16 1 0 0 1 1.3889 17 1 0 1 1 3.4077 18 1 1 1 1 6.8143 19 1 1 0 1 3.3340 20 1 1 -1 1 3.9468 21 1 1 1 0 2.6406 22 1 1 0 0 2.0805 23 1 1 -1 0 3.7921 24 1 1 1 -1 3.2201 25 1 1 0 -1 3.3448 26 1 1 -1 -1 4.0222 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3816 atoms have been selected out of 3890 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 408 136 136 0.00 2 C002 has 705 235 235 0.00 3 C003 has 105 35 35 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1629 543 543 0.00 6 C006 has 525 175 175 0.00 7 C007 has 747 249 249 0.00 8 C008 has 1778 591 591 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1689 563 563 0.00 12 C012 has 117 39 39 0.00 13 C013 has 468 156 156 0.00 14 C014 has 123 41 41 0.71 Total of13306 atoms and 4427 groups and 4422 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3890 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1285 Number of atoms = 3890 Number of groups = 1290 Number of bonds = 3883 Number of angles = 1389 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1287 Number of HB donors = 2552 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.864" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1285" Evaluating: 1285-7 Parameter: NUMWAT <- "1278" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1278" Comparing "1081" and "1278". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.864" Parameter: BOX -> "33.864" Parameter: BOX -> "33.864" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.86400 B = 33.86400 C = 33.86400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8122 2 1 -1 0 -1 3.3313 3 1 -1 1 -1 3.9434 4 1 0 -1 -1 3.4050 5 1 0 0 -1 1.3871 6 1 0 1 -1 2.6184 7 1 -1 -1 0 2.6379 8 1 -1 0 0 2.0786 9 1 -1 1 0 3.7901 10 1 0 -1 0 1.1896 11 1 0 1 0 1.1896 12 1 -1 -1 1 3.2167 13 1 -1 0 1 3.3421 14 1 -1 1 1 4.0194 15 1 0 -1 1 2.6184 16 1 0 0 1 1.3871 17 1 0 1 1 3.4050 18 1 1 1 1 6.8122 19 1 1 0 1 3.3313 20 1 1 -1 1 3.9434 21 1 1 1 0 2.6379 22 1 1 0 0 2.0786 23 1 1 -1 0 3.7901 24 1 1 1 -1 3.2167 25 1 1 0 -1 3.3421 26 1 1 -1 -1 4.0194 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3816 atoms have been selected out of 3890 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 768 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 408 136 136 0.00 2 C002 has 711 237 237 0.00 3 C003 has 108 36 36 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1629 543 543 0.00 6 C006 has 525 175 175 0.00 7 C007 has 747 249 249 0.00 8 C008 has 1781 592 592 0.00 9 C009 has 507 169 169 0.00 10 C010 has 1689 563 563 0.00 12 C012 has 117 39 39 0.00 13 C013 has 468 156 156 0.00 14 C014 has 123 41 41 0.71 Total of13321 atoms and 4432 groups and 4427 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3890 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1284 Number of atoms = 3887 Number of groups = 1289 Number of bonds = 3880 Number of angles = 1388 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1286 Number of HB donors = 2550 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1284 Number of atoms = 3887 Number of groups = 1289 Number of bonds = 3880 Number of angles = 1388 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1286 Number of HB donors = 2550 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.862" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1284" Evaluating: 1284-7 Parameter: NUMWAT <- "1277" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1277" Comparing "1081" and "1277". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.862" Parameter: BOX -> "33.862" Parameter: BOX -> "33.862" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.86200 B = 33.86200 C = 33.86200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8101 2 1 -1 0 -1 3.3285 3 1 -1 1 -1 3.9400 4 1 0 -1 -1 3.4022 5 1 0 0 -1 1.3852 6 1 0 1 -1 2.6157 7 1 -1 -1 0 2.6352 8 1 -1 0 0 2.0767 9 1 -1 1 0 3.7881 10 1 0 -1 0 1.1897 11 1 0 1 0 1.1897 12 1 -1 -1 1 3.2132 13 1 -1 0 1 3.3393 14 1 -1 1 1 4.0167 15 1 0 -1 1 2.6157 16 1 0 0 1 1.3852 17 1 0 1 1 3.4022 18 1 1 1 1 6.8101 19 1 1 0 1 3.3285 20 1 1 -1 1 3.9400 21 1 1 1 0 2.6352 22 1 1 0 0 2.0767 23 1 1 -1 0 3.7881 24 1 1 1 -1 3.2132 25 1 1 0 -1 3.3393 26 1 1 -1 -1 4.0167 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3813 atoms have been selected out of 3887 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 408 136 136 0.00 2 C002 has 708 236 236 0.00 3 C003 has 105 35 35 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1626 542 542 0.00 6 C006 has 522 174 174 0.00 7 C007 has 747 249 249 0.00 8 C008 has 1778 591 591 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1689 563 563 0.00 12 C012 has 117 39 39 0.00 13 C013 has 468 156 156 0.00 14 C014 has 123 41 41 0.71 Total of13300 atoms and 4425 groups and 4420 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3887 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1284 Number of atoms = 3887 Number of groups = 1289 Number of bonds = 3880 Number of angles = 1388 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1286 Number of HB donors = 2550 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1284 Number of atoms = 3887 Number of groups = 1289 Number of bonds = 3880 Number of angles = 1388 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1286 Number of HB donors = 2550 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.86" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1284" Evaluating: 1284-7 Parameter: NUMWAT <- "1277" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1277" Comparing "1081" and "1277". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.86" Parameter: BOX -> "33.86" Parameter: BOX -> "33.86" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.86000 B = 33.86000 C = 33.86000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8080 2 1 -1 0 -1 3.3258 3 1 -1 1 -1 3.9365 4 1 0 -1 -1 3.3995 5 1 0 0 -1 1.3834 6 1 0 1 -1 2.6130 7 1 -1 -1 0 2.6325 8 1 -1 0 0 2.0748 9 1 -1 1 0 3.7862 10 1 0 -1 0 1.1898 11 1 0 1 0 1.1898 12 1 -1 -1 1 3.2098 13 1 -1 0 1 3.3366 14 1 -1 1 1 4.0139 15 1 0 -1 1 2.6130 16 1 0 0 1 1.3834 17 1 0 1 1 3.3995 18 1 1 1 1 6.8080 19 1 1 0 1 3.3258 20 1 1 -1 1 3.9365 21 1 1 1 0 2.6325 22 1 1 0 0 2.0748 23 1 1 -1 0 3.7862 24 1 1 1 -1 3.2098 25 1 1 0 -1 3.3366 26 1 1 -1 -1 4.0139 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3813 atoms have been selected out of 3887 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 411 137 137 0.00 2 C002 has 708 236 236 0.00 3 C003 has 105 35 35 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1626 542 542 0.00 6 C006 has 522 174 174 0.00 7 C007 has 747 249 249 0.00 8 C008 has 1778 591 591 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1689 563 563 0.00 12 C012 has 117 39 39 0.00 13 C013 has 468 156 156 0.00 14 C014 has 123 41 41 0.71 Total of13303 atoms and 4426 groups and 4421 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3887 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1284 Number of atoms = 3887 Number of groups = 1289 Number of bonds = 3880 Number of angles = 1388 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1286 Number of HB donors = 2550 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1284 Number of atoms = 3887 Number of groups = 1289 Number of bonds = 3880 Number of angles = 1388 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1286 Number of HB donors = 2550 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.858" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1284" Evaluating: 1284-7 Parameter: NUMWAT <- "1277" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1277" Comparing "1081" and "1277". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.858" Parameter: BOX -> "33.858" Parameter: BOX -> "33.858" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.85800 B = 33.85800 C = 33.85800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8059 2 1 -1 0 -1 3.3230 3 1 -1 1 -1 3.9331 4 1 0 -1 -1 3.3967 5 1 0 0 -1 1.3815 6 1 0 1 -1 2.6103 7 1 -1 -1 0 2.6298 8 1 -1 0 0 2.0729 9 1 -1 1 0 3.7842 10 1 0 -1 0 1.1898 11 1 0 1 0 1.1898 12 1 -1 -1 1 3.2063 13 1 -1 0 1 3.3338 14 1 -1 1 1 4.0111 15 1 0 -1 1 2.6103 16 1 0 0 1 1.3815 17 1 0 1 1 3.3967 18 1 1 1 1 6.8059 19 1 1 0 1 3.3230 20 1 1 -1 1 3.9331 21 1 1 1 0 2.6298 22 1 1 0 0 2.0729 23 1 1 -1 0 3.7842 24 1 1 1 -1 3.2063 25 1 1 0 -1 3.3338 26 1 1 -1 -1 4.0111 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3813 atoms have been selected out of 3887 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 411 137 137 0.00 2 C002 has 708 236 236 0.00 3 C003 has 105 35 35 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1629 543 543 0.00 6 C006 has 522 174 174 0.00 7 C007 has 747 249 249 0.00 8 C008 has 1778 591 591 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1689 563 563 0.00 12 C012 has 117 39 39 0.00 13 C013 has 468 156 156 0.00 14 C014 has 123 41 41 0.70 Total of13306 atoms and 4427 groups and 4422 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3887 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1284 Number of atoms = 3887 Number of groups = 1289 Number of bonds = 3880 Number of angles = 1388 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1286 Number of HB donors = 2550 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1284 Number of atoms = 3887 Number of groups = 1289 Number of bonds = 3880 Number of angles = 1388 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1286 Number of HB donors = 2550 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.856" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1284" Evaluating: 1284-7 Parameter: NUMWAT <- "1277" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1277" Comparing "1081" and "1277". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.856" Parameter: BOX -> "33.856" Parameter: BOX -> "33.856" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.85600 B = 33.85600 C = 33.85600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8039 2 1 -1 0 -1 3.3203 3 1 -1 1 -1 3.9297 4 1 0 -1 -1 3.3940 5 1 0 0 -1 1.3797 6 1 0 1 -1 2.6076 7 1 -1 -1 0 2.6271 8 1 -1 0 0 2.0710 9 1 -1 1 0 3.7823 10 1 0 -1 0 1.1899 11 1 0 1 0 1.1899 12 1 -1 -1 1 3.2029 13 1 -1 0 1 3.3311 14 1 -1 1 1 4.0084 15 1 0 -1 1 2.6076 16 1 0 0 1 1.3797 17 1 0 1 1 3.3940 18 1 1 1 1 6.8039 19 1 1 0 1 3.3203 20 1 1 -1 1 3.9297 21 1 1 1 0 2.6271 22 1 1 0 0 2.0710 23 1 1 -1 0 3.7823 24 1 1 1 -1 3.2029 25 1 1 0 -1 3.3311 26 1 1 -1 -1 4.0084 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3813 atoms have been selected out of 3887 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 411 137 137 0.00 2 C002 has 708 236 236 0.00 3 C003 has 105 35 35 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1629 543 543 0.00 6 C006 has 522 174 174 0.00 7 C007 has 747 249 249 0.00 8 C008 has 1778 591 591 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1689 563 563 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 123 41 41 0.70 Total of13309 atoms and 4428 groups and 4423 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3887 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1284 Number of atoms = 3887 Number of groups = 1289 Number of bonds = 3880 Number of angles = 1388 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1286 Number of HB donors = 2550 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1284 Number of atoms = 3887 Number of groups = 1289 Number of bonds = 3880 Number of angles = 1388 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1286 Number of HB donors = 2550 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.854" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1284" Evaluating: 1284-7 Parameter: NUMWAT <- "1277" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1277" Comparing "1081" and "1277". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.854" Parameter: BOX -> "33.854" Parameter: BOX -> "33.854" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.85400 B = 33.85400 C = 33.85400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8018 2 1 -1 0 -1 3.3175 3 1 -1 1 -1 3.9263 4 1 0 -1 -1 3.3912 5 1 0 0 -1 1.3778 6 1 0 1 -1 2.6049 7 1 -1 -1 0 2.6244 8 1 -1 0 0 2.0691 9 1 -1 1 0 3.7803 10 1 0 -1 0 1.1900 11 1 0 1 0 1.1900 12 1 -1 -1 1 3.1994 13 1 -1 0 1 3.3283 14 1 -1 1 1 4.0056 15 1 0 -1 1 2.6049 16 1 0 0 1 1.3778 17 1 0 1 1 3.3912 18 1 1 1 1 6.8018 19 1 1 0 1 3.3175 20 1 1 -1 1 3.9263 21 1 1 1 0 2.6244 22 1 1 0 0 2.0691 23 1 1 -1 0 3.7803 24 1 1 1 -1 3.1994 25 1 1 0 -1 3.3283 26 1 1 -1 -1 4.0056 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3813 atoms have been selected out of 3887 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 411 137 137 0.00 2 C002 has 708 236 236 0.00 3 C003 has 105 35 35 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1629 543 543 0.00 6 C006 has 525 175 175 0.00 7 C007 has 747 249 249 0.00 8 C008 has 1778 591 591 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1689 563 563 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 123 41 41 0.70 Total of13312 atoms and 4429 groups and 4424 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3887 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1284 Number of atoms = 3887 Number of groups = 1289 Number of bonds = 3880 Number of angles = 1388 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1286 Number of HB donors = 2550 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1284 Number of atoms = 3887 Number of groups = 1289 Number of bonds = 3880 Number of angles = 1388 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1286 Number of HB donors = 2550 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.852" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1284" Evaluating: 1284-7 Parameter: NUMWAT <- "1277" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1277" Comparing "1081" and "1277". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.852" Parameter: BOX -> "33.852" Parameter: BOX -> "33.852" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.85200 B = 33.85200 C = 33.85200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7997 2 1 -1 0 -1 3.3148 3 1 -1 1 -1 3.9228 4 1 0 -1 -1 3.3885 5 1 0 0 -1 1.3760 6 1 0 1 -1 2.6022 7 1 -1 -1 0 2.6217 8 1 -1 0 0 2.0672 9 1 -1 1 0 3.7784 10 1 0 -1 0 1.1901 11 1 0 1 0 1.1901 12 1 -1 -1 1 3.1960 13 1 -1 0 1 3.3255 14 1 -1 1 1 4.0028 15 1 0 -1 1 2.6022 16 1 0 0 1 1.3760 17 1 0 1 1 3.3885 18 1 1 1 1 6.7997 19 1 1 0 1 3.3148 20 1 1 -1 1 3.9228 21 1 1 1 0 2.6217 22 1 1 0 0 2.0672 23 1 1 -1 0 3.7784 24 1 1 1 -1 3.1960 25 1 1 0 -1 3.3255 26 1 1 -1 -1 4.0028 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3813 atoms have been selected out of 3887 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 475 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 411 137 137 0.00 2 C002 has 708 236 236 0.00 3 C003 has 105 35 35 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1629 543 543 0.00 6 C006 has 525 175 175 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1781 592 592 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1692 564 564 0.00 12 C012 has 123 41 41 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 0.70 Total of13330 atoms and 4435 groups and 4430 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3887 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1283 Number of atoms = 3884 Number of groups = 1288 Number of bonds = 3877 Number of angles = 1387 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1285 Number of HB donors = 2548 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1283 Number of atoms = 3884 Number of groups = 1288 Number of bonds = 3877 Number of angles = 1387 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1285 Number of HB donors = 2548 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.85" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1283" Evaluating: 1283-7 Parameter: NUMWAT <- "1276" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1276" Comparing "1081" and "1276". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.85" Parameter: BOX -> "33.85" Parameter: BOX -> "33.85" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.85000 B = 33.85000 C = 33.85000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7976 2 1 -1 0 -1 3.3120 3 1 -1 1 -1 3.9194 4 1 0 -1 -1 3.3857 5 1 0 0 -1 1.3742 6 1 0 1 -1 2.5995 7 1 -1 -1 0 2.6190 8 1 -1 0 0 2.0653 9 1 -1 1 0 3.7764 10 1 0 -1 0 1.1901 11 1 0 1 0 1.1901 12 1 -1 -1 1 3.1925 13 1 -1 0 1 3.3228 14 1 -1 1 1 4.0001 15 1 0 -1 1 2.5995 16 1 0 0 1 1.3742 17 1 0 1 1 3.3857 18 1 1 1 1 6.7976 19 1 1 0 1 3.3120 20 1 1 -1 1 3.9194 21 1 1 1 0 2.6190 22 1 1 0 0 2.0653 23 1 1 -1 0 3.7764 24 1 1 1 -1 3.1925 25 1 1 0 -1 3.3228 26 1 1 -1 -1 4.0001 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3810 atoms have been selected out of 3884 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 411 137 137 0.00 2 C002 has 708 236 236 0.00 3 C003 has 105 35 35 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1629 543 543 0.00 6 C006 has 525 175 175 0.00 7 C007 has 747 249 249 0.00 8 C008 has 1778 591 591 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1689 563 563 0.00 12 C012 has 120 40 40 0.00 13 C013 has 471 157 157 0.00 14 C014 has 123 41 41 0.70 Total of13312 atoms and 4429 groups and 4424 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3884 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1283 Number of atoms = 3884 Number of groups = 1288 Number of bonds = 3877 Number of angles = 1387 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1285 Number of HB donors = 2548 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1283 Number of atoms = 3884 Number of groups = 1288 Number of bonds = 3877 Number of angles = 1387 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1285 Number of HB donors = 2548 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.848" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1283" Evaluating: 1283-7 Parameter: NUMWAT <- "1276" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1276" Comparing "1081" and "1276". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.848" Parameter: BOX -> "33.848" Parameter: BOX -> "33.848" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.84800 B = 33.84800 C = 33.84800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7955 2 1 -1 0 -1 3.3093 3 1 -1 1 -1 3.9160 4 1 0 -1 -1 3.3830 5 1 0 0 -1 1.3723 6 1 0 1 -1 2.5968 7 1 -1 -1 0 2.6163 8 1 -1 0 0 2.0634 9 1 -1 1 0 3.7745 10 1 0 -1 0 1.1902 11 1 0 1 0 1.1902 12 1 -1 -1 1 3.1891 13 1 -1 0 1 3.3200 14 1 -1 1 1 3.9973 15 1 0 -1 1 2.5968 16 1 0 0 1 1.3723 17 1 0 1 1 3.3830 18 1 1 1 1 6.7955 19 1 1 0 1 3.3093 20 1 1 -1 1 3.9160 21 1 1 1 0 2.6163 22 1 1 0 0 2.0634 23 1 1 -1 0 3.7745 24 1 1 1 -1 3.1891 25 1 1 0 -1 3.3200 26 1 1 -1 -1 3.9973 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3810 atoms have been selected out of 3884 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 599 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 411 137 137 0.00 2 C002 has 708 236 236 0.00 3 C003 has 105 35 35 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1629 543 543 0.00 6 C006 has 525 175 175 0.00 7 C007 has 744 248 248 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1689 563 563 0.00 12 C012 has 120 40 40 0.00 13 C013 has 468 156 156 0.00 14 C014 has 126 42 42 0.69 Total of13306 atoms and 4427 groups and 4422 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3884 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1282 Number of atoms = 3881 Number of groups = 1287 Number of bonds = 3874 Number of angles = 1386 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1284 Number of HB donors = 2546 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1282 Number of atoms = 3881 Number of groups = 1287 Number of bonds = 3874 Number of angles = 1386 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1284 Number of HB donors = 2546 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.846" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1282" Evaluating: 1282-7 Parameter: NUMWAT <- "1275" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1275" Comparing "1081" and "1275". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.846" Parameter: BOX -> "33.846" Parameter: BOX -> "33.846" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.84600 B = 33.84600 C = 33.84600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7934 2 1 -1 0 -1 3.3065 3 1 -1 1 -1 3.9126 4 1 0 -1 -1 3.3802 5 1 0 0 -1 1.3705 6 1 0 1 -1 2.5941 7 1 -1 -1 0 2.6136 8 1 -1 0 0 2.0614 9 1 -1 1 0 3.7725 10 1 0 -1 0 1.1903 11 1 0 1 0 1.1903 12 1 -1 -1 1 3.1857 13 1 -1 0 1 3.3173 14 1 -1 1 1 3.9946 15 1 0 -1 1 2.5941 16 1 0 0 1 1.3705 17 1 0 1 1 3.3802 18 1 1 1 1 6.7934 19 1 1 0 1 3.3065 20 1 1 -1 1 3.9126 21 1 1 1 0 2.6136 22 1 1 0 0 2.0614 23 1 1 -1 0 3.7725 24 1 1 1 -1 3.1857 25 1 1 0 -1 3.3173 26 1 1 -1 -1 3.9946 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3807 atoms have been selected out of 3881 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 411 137 137 0.00 2 C002 has 708 236 236 0.00 3 C003 has 105 35 35 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1629 543 543 0.00 6 C006 has 525 175 175 0.00 7 C007 has 744 248 248 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1686 562 562 0.00 12 C012 has 120 40 40 0.00 13 C013 has 468 156 156 0.00 14 C014 has 126 42 42 0.69 Total of13300 atoms and 4425 groups and 4420 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3881 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1282 Number of atoms = 3881 Number of groups = 1287 Number of bonds = 3874 Number of angles = 1386 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1284 Number of HB donors = 2546 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1282 Number of atoms = 3881 Number of groups = 1287 Number of bonds = 3874 Number of angles = 1386 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1284 Number of HB donors = 2546 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.844" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1282" Evaluating: 1282-7 Parameter: NUMWAT <- "1275" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1275" Comparing "1081" and "1275". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.844" Parameter: BOX -> "33.844" Parameter: BOX -> "33.844" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.84400 B = 33.84400 C = 33.84400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7913 2 1 -1 0 -1 3.3038 3 1 -1 1 -1 3.9091 4 1 0 -1 -1 3.3775 5 1 0 0 -1 1.3686 6 1 0 1 -1 2.5914 7 1 -1 -1 0 2.6109 8 1 -1 0 0 2.0595 9 1 -1 1 0 3.7706 10 1 0 -1 0 1.1904 11 1 0 1 0 1.1904 12 1 -1 -1 1 3.1822 13 1 -1 0 1 3.3145 14 1 -1 1 1 3.9918 15 1 0 -1 1 2.5914 16 1 0 0 1 1.3686 17 1 0 1 1 3.3775 18 1 1 1 1 6.7913 19 1 1 0 1 3.3038 20 1 1 -1 1 3.9091 21 1 1 1 0 2.6109 22 1 1 0 0 2.0595 23 1 1 -1 0 3.7706 24 1 1 1 -1 3.1822 25 1 1 0 -1 3.3145 26 1 1 -1 -1 3.9918 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3807 atoms have been selected out of 3881 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 323 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 411 137 137 0.00 2 C002 has 708 236 236 0.00 3 C003 has 105 35 35 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1632 544 544 0.00 6 C006 has 525 175 175 0.00 7 C007 has 744 248 248 0.00 8 C008 has 1772 589 589 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1686 562 562 0.00 12 C012 has 120 40 40 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.69 Total of13300 atoms and 4425 groups and 4420 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3881 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1281 Number of atoms = 3878 Number of groups = 1286 Number of bonds = 3871 Number of angles = 1385 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1283 Number of HB donors = 2544 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1281 Number of atoms = 3878 Number of groups = 1286 Number of bonds = 3871 Number of angles = 1385 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1283 Number of HB donors = 2544 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.842" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1281" Evaluating: 1281-7 Parameter: NUMWAT <- "1274" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1274" Comparing "1081" and "1274". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.842" Parameter: BOX -> "33.842" Parameter: BOX -> "33.842" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.84200 B = 33.84200 C = 33.84200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7893 2 1 -1 0 -1 3.3010 3 1 -1 1 -1 3.9057 4 1 0 -1 -1 3.3748 5 1 0 0 -1 1.3668 6 1 0 1 -1 2.5887 7 1 -1 -1 0 2.6082 8 1 -1 0 0 2.0576 9 1 -1 1 0 3.7686 10 1 0 -1 0 1.1905 11 1 0 1 0 1.1905 12 1 -1 -1 1 3.1788 13 1 -1 0 1 3.3118 14 1 -1 1 1 3.9891 15 1 0 -1 1 2.5887 16 1 0 0 1 1.3668 17 1 0 1 1 3.3748 18 1 1 1 1 6.7893 19 1 1 0 1 3.3010 20 1 1 -1 1 3.9057 21 1 1 1 0 2.6082 22 1 1 0 0 2.0576 23 1 1 -1 0 3.7686 24 1 1 1 -1 3.1788 25 1 1 0 -1 3.3118 26 1 1 -1 -1 3.9891 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3804 atoms have been selected out of 3878 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 318 OPERATED ON BY TRANSFORMATION C016 RESIDUE 629 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 417 139 139 0.00 2 C002 has 714 238 238 0.00 3 C003 has 108 36 36 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1629 543 543 0.00 6 C006 has 516 172 172 0.00 7 C007 has 744 248 248 0.00 8 C008 has 1772 589 589 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1686 562 562 0.00 12 C012 has 117 39 39 0.00 13 C013 has 465 155 155 0.00 14 C014 has 123 41 41 0.69 Total of13282 atoms and 4419 groups and 4414 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3878 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1279 Number of atoms = 3872 Number of groups = 1284 Number of bonds = 3865 Number of angles = 1383 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1281 Number of HB donors = 2540 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1279 Number of atoms = 3872 Number of groups = 1284 Number of bonds = 3865 Number of angles = 1383 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1281 Number of HB donors = 2540 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.84" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1279" Evaluating: 1279-7 Parameter: NUMWAT <- "1272" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1272" Comparing "1081" and "1272". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.84" Parameter: BOX -> "33.84" Parameter: BOX -> "33.84" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.84000 B = 33.84000 C = 33.84000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7872 2 1 -1 0 -1 3.2982 3 1 -1 1 -1 3.9023 4 1 0 -1 -1 3.3720 5 1 0 0 -1 1.3649 6 1 0 1 -1 2.5860 7 1 -1 -1 0 2.6055 8 1 -1 0 0 2.0557 9 1 -1 1 0 3.7667 10 1 0 -1 0 1.1906 11 1 0 1 0 1.1906 12 1 -1 -1 1 3.1753 13 1 -1 0 1 3.3090 14 1 -1 1 1 3.9863 15 1 0 -1 1 2.5860 16 1 0 0 1 1.3649 17 1 0 1 1 3.3720 18 1 1 1 1 6.7872 19 1 1 0 1 3.2982 20 1 1 -1 1 3.9023 21 1 1 1 0 2.6055 22 1 1 0 0 2.0557 23 1 1 -1 0 3.7667 24 1 1 1 -1 3.1753 25 1 1 0 -1 3.3090 26 1 1 -1 -1 3.9863 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3798 atoms have been selected out of 3872 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 417 139 139 0.00 2 C002 has 708 236 236 0.00 3 C003 has 105 35 35 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1623 541 541 0.00 6 C006 has 513 171 171 0.00 7 C007 has 744 248 248 0.00 8 C008 has 1766 587 587 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1683 561 561 0.00 12 C012 has 117 39 39 0.00 13 C013 has 465 155 155 0.00 14 C014 has 126 42 42 0.69 Total of13246 atoms and 4407 groups and 4402 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3872 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1279 Number of atoms = 3872 Number of groups = 1284 Number of bonds = 3865 Number of angles = 1383 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1281 Number of HB donors = 2540 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1279 Number of atoms = 3872 Number of groups = 1284 Number of bonds = 3865 Number of angles = 1383 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1281 Number of HB donors = 2540 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.838" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1279" Evaluating: 1279-7 Parameter: NUMWAT <- "1272" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1272" Comparing "1081" and "1272". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.838" Parameter: BOX -> "33.838" Parameter: BOX -> "33.838" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.83800 B = 33.83800 C = 33.83800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7851 2 1 -1 0 -1 3.2955 3 1 -1 1 -1 3.8988 4 1 0 -1 -1 3.3693 5 1 0 0 -1 1.3631 6 1 0 1 -1 2.5832 7 1 -1 -1 0 2.6028 8 1 -1 0 0 2.0538 9 1 -1 1 0 3.7647 10 1 0 -1 0 1.1907 11 1 0 1 0 1.1907 12 1 -1 -1 1 3.1719 13 1 -1 0 1 3.3063 14 1 -1 1 1 3.9836 15 1 0 -1 1 2.5832 16 1 0 0 1 1.3631 17 1 0 1 1 3.3693 18 1 1 1 1 6.7851 19 1 1 0 1 3.2955 20 1 1 -1 1 3.8988 21 1 1 1 0 2.6028 22 1 1 0 0 2.0538 23 1 1 -1 0 3.7647 24 1 1 1 -1 3.1719 25 1 1 0 -1 3.3063 26 1 1 -1 -1 3.9836 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3798 atoms have been selected out of 3872 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 174 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 417 139 139 0.00 2 C002 has 711 237 237 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1623 541 541 0.00 6 C006 has 516 172 172 0.00 7 C007 has 747 249 249 0.00 8 C008 has 1766 587 587 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1683 561 561 0.00 12 C012 has 117 39 39 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.68 Total of13252 atoms and 4409 groups and 4404 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3872 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.836" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1278" Evaluating: 1278-7 Parameter: NUMWAT <- "1271" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1271" Comparing "1081" and "1271". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.836" Parameter: BOX -> "33.836" Parameter: BOX -> "33.836" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.83600 B = 33.83600 C = 33.83600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7830 2 1 -1 0 -1 3.2927 3 1 -1 1 -1 3.8954 4 1 0 -1 -1 3.3665 5 1 0 0 -1 1.3613 6 1 0 1 -1 2.5805 7 1 -1 -1 0 2.6001 8 1 -1 0 0 2.0519 9 1 -1 1 0 3.7628 10 1 0 -1 0 1.1908 11 1 0 1 0 1.1908 12 1 -1 -1 1 3.1684 13 1 -1 0 1 3.3035 14 1 -1 1 1 3.9808 15 1 0 -1 1 2.5805 16 1 0 0 1 1.3613 17 1 0 1 1 3.3665 18 1 1 1 1 6.7830 19 1 1 0 1 3.2927 20 1 1 -1 1 3.8954 21 1 1 1 0 2.6001 22 1 1 0 0 2.0519 23 1 1 -1 0 3.7628 24 1 1 1 -1 3.1684 25 1 1 0 -1 3.3035 26 1 1 -1 -1 3.9808 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3795 atoms have been selected out of 3869 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 417 139 139 0.00 2 C002 has 708 236 236 0.00 3 C003 has 105 35 35 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1623 541 541 0.00 6 C006 has 513 171 171 0.00 7 C007 has 747 249 249 0.00 8 C008 has 1763 586 586 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1683 561 561 0.00 12 C012 has 117 39 39 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.68 Total of13234 atoms and 4403 groups and 4398 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3869 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.834" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1278" Evaluating: 1278-7 Parameter: NUMWAT <- "1271" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1271" Comparing "1081" and "1271". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.834" Parameter: BOX -> "33.834" Parameter: BOX -> "33.834" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.83400 B = 33.83400 C = 33.83400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7809 2 1 -1 0 -1 3.2900 3 1 -1 1 -1 3.8920 4 1 0 -1 -1 3.3638 5 1 0 0 -1 1.3594 6 1 0 1 -1 2.5778 7 1 -1 -1 0 2.5974 8 1 -1 0 0 2.0500 9 1 -1 1 0 3.7608 10 1 0 -1 0 1.1910 11 1 0 1 0 1.1910 12 1 -1 -1 1 3.1650 13 1 -1 0 1 3.3008 14 1 -1 1 1 3.9780 15 1 0 -1 1 2.5778 16 1 0 0 1 1.3594 17 1 0 1 1 3.3638 18 1 1 1 1 6.7809 19 1 1 0 1 3.2900 20 1 1 -1 1 3.8920 21 1 1 1 0 2.5974 22 1 1 0 0 2.0500 23 1 1 -1 0 3.7608 24 1 1 1 -1 3.1650 25 1 1 0 -1 3.3008 26 1 1 -1 -1 3.9780 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3795 atoms have been selected out of 3869 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 417 139 139 0.00 2 C002 has 708 236 236 0.00 3 C003 has 105 35 35 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1623 541 541 0.00 6 C006 has 513 171 171 0.00 7 C007 has 747 249 249 0.00 8 C008 has 1763 586 586 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1683 561 561 0.00 12 C012 has 117 39 39 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.68 Total of13234 atoms and 4403 groups and 4398 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3869 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.832" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1278" Evaluating: 1278-7 Parameter: NUMWAT <- "1271" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1271" Comparing "1081" and "1271". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.832" Parameter: BOX -> "33.832" Parameter: BOX -> "33.832" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.83200 B = 33.83200 C = 33.83200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7789 2 1 -1 0 -1 3.2872 3 1 -1 1 -1 3.8886 4 1 0 -1 -1 3.3610 5 1 0 0 -1 1.3576 6 1 0 1 -1 2.5751 7 1 -1 -1 0 2.5947 8 1 -1 0 0 2.0481 9 1 -1 1 0 3.7589 10 1 0 -1 0 1.1911 11 1 0 1 0 1.1911 12 1 -1 -1 1 3.1616 13 1 -1 0 1 3.2980 14 1 -1 1 1 3.9753 15 1 0 -1 1 2.5751 16 1 0 0 1 1.3576 17 1 0 1 1 3.3610 18 1 1 1 1 6.7789 19 1 1 0 1 3.2872 20 1 1 -1 1 3.8886 21 1 1 1 0 2.5947 22 1 1 0 0 2.0481 23 1 1 -1 0 3.7589 24 1 1 1 -1 3.1616 25 1 1 0 -1 3.2980 26 1 1 -1 -1 3.9753 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3795 atoms have been selected out of 3869 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 417 139 139 0.00 2 C002 has 708 236 236 0.00 3 C003 has 105 35 35 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1623 541 541 0.00 6 C006 has 513 171 171 0.00 7 C007 has 747 249 249 0.00 8 C008 has 1766 587 587 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1683 561 561 0.00 12 C012 has 120 40 40 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.68 Total of13240 atoms and 4405 groups and 4400 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3869 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.83" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1278" Evaluating: 1278-7 Parameter: NUMWAT <- "1271" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1271" Comparing "1081" and "1271". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.83" Parameter: BOX -> "33.83" Parameter: BOX -> "33.83" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.83000 B = 33.83000 C = 33.83000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7768 2 1 -1 0 -1 3.2845 3 1 -1 1 -1 3.8851 4 1 0 -1 -1 3.3583 5 1 0 0 -1 1.3557 6 1 0 1 -1 2.5724 7 1 -1 -1 0 2.5920 8 1 -1 0 0 2.0462 9 1 -1 1 0 3.7570 10 1 0 -1 0 1.1912 11 1 0 1 0 1.1912 12 1 -1 -1 1 3.1581 13 1 -1 0 1 3.2953 14 1 -1 1 1 3.9726 15 1 0 -1 1 2.5724 16 1 0 0 1 1.3557 17 1 0 1 1 3.3583 18 1 1 1 1 6.7768 19 1 1 0 1 3.2845 20 1 1 -1 1 3.8851 21 1 1 1 0 2.5920 22 1 1 0 0 2.0462 23 1 1 -1 0 3.7570 24 1 1 1 -1 3.1581 25 1 1 0 -1 3.2953 26 1 1 -1 -1 3.9726 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3795 atoms have been selected out of 3869 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 417 139 139 0.00 2 C002 has 711 237 237 0.00 3 C003 has 105 35 35 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1623 541 541 0.00 6 C006 has 513 171 171 0.00 7 C007 has 747 249 249 0.00 8 C008 has 1769 588 588 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1683 561 561 0.00 12 C012 has 120 40 40 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.68 Total of13246 atoms and 4407 groups and 4402 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3869 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.828" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1278" Evaluating: 1278-7 Parameter: NUMWAT <- "1271" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1271" Comparing "1081" and "1271". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.828" Parameter: BOX -> "33.828" Parameter: BOX -> "33.828" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.82800 B = 33.82800 C = 33.82800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7747 2 1 -1 0 -1 3.2817 3 1 -1 1 -1 3.8817 4 1 0 -1 -1 3.3555 5 1 0 0 -1 1.3539 6 1 0 1 -1 2.5697 7 1 -1 -1 0 2.5893 8 1 -1 0 0 2.0443 9 1 -1 1 0 3.7550 10 1 0 -1 0 1.1913 11 1 0 1 0 1.1913 12 1 -1 -1 1 3.1547 13 1 -1 0 1 3.2925 14 1 -1 1 1 3.9698 15 1 0 -1 1 2.5697 16 1 0 0 1 1.3539 17 1 0 1 1 3.3555 18 1 1 1 1 6.7747 19 1 1 0 1 3.2817 20 1 1 -1 1 3.8817 21 1 1 1 0 2.5893 22 1 1 0 0 2.0443 23 1 1 -1 0 3.7550 24 1 1 1 -1 3.1547 25 1 1 0 -1 3.2925 26 1 1 -1 -1 3.9698 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3795 atoms have been selected out of 3869 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 417 139 139 0.00 2 C002 has 711 237 237 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1626 542 542 0.00 6 C006 has 513 171 171 0.00 7 C007 has 747 249 249 0.00 8 C008 has 1769 588 588 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1683 561 561 0.00 12 C012 has 120 40 40 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.67 Total of13252 atoms and 4409 groups and 4404 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3869 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.826" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1278" Evaluating: 1278-7 Parameter: NUMWAT <- "1271" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1271" Comparing "1081" and "1271". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.826" Parameter: BOX -> "33.826" Parameter: BOX -> "33.826" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.82600 B = 33.82600 C = 33.82600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7726 2 1 -1 0 -1 3.2790 3 1 -1 1 -1 3.8783 4 1 0 -1 -1 3.3528 5 1 0 0 -1 1.3521 6 1 0 1 -1 2.5670 7 1 -1 -1 0 2.5866 8 1 -1 0 0 2.0424 9 1 -1 1 0 3.7531 10 1 0 -1 0 1.1914 11 1 0 1 0 1.1914 12 1 -1 -1 1 3.1512 13 1 -1 0 1 3.2898 14 1 -1 1 1 3.9671 15 1 0 -1 1 2.5670 16 1 0 0 1 1.3521 17 1 0 1 1 3.3528 18 1 1 1 1 6.7726 19 1 1 0 1 3.2790 20 1 1 -1 1 3.8783 21 1 1 1 0 2.5866 22 1 1 0 0 2.0424 23 1 1 -1 0 3.7531 24 1 1 1 -1 3.1512 25 1 1 0 -1 3.2898 26 1 1 -1 -1 3.9671 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3795 atoms have been selected out of 3869 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 417 139 139 0.00 2 C002 has 711 237 237 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1626 542 542 0.00 6 C006 has 513 171 171 0.00 7 C007 has 747 249 249 0.00 8 C008 has 1769 588 588 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1683 561 561 0.00 12 C012 has 120 40 40 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.67 Total of13252 atoms and 4409 groups and 4404 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3869 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.824" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1278" Evaluating: 1278-7 Parameter: NUMWAT <- "1271" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1271" Comparing "1081" and "1271". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.824" Parameter: BOX -> "33.824" Parameter: BOX -> "33.824" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.82400 B = 33.82400 C = 33.82400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7706 2 1 -1 0 -1 3.2762 3 1 -1 1 -1 3.8749 4 1 0 -1 -1 3.3500 5 1 0 0 -1 1.3502 6 1 0 1 -1 2.5643 7 1 -1 -1 0 2.5839 8 1 -1 0 0 2.0405 9 1 -1 1 0 3.7512 10 1 0 -1 0 1.1916 11 1 0 1 0 1.1916 12 1 -1 -1 1 3.1478 13 1 -1 0 1 3.2871 14 1 -1 1 1 3.9643 15 1 0 -1 1 2.5643 16 1 0 0 1 1.3502 17 1 0 1 1 3.3500 18 1 1 1 1 6.7706 19 1 1 0 1 3.2762 20 1 1 -1 1 3.8749 21 1 1 1 0 2.5839 22 1 1 0 0 2.0405 23 1 1 -1 0 3.7512 24 1 1 1 -1 3.1478 25 1 1 0 -1 3.2871 26 1 1 -1 -1 3.9643 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3795 atoms have been selected out of 3869 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 417 139 139 0.00 2 C002 has 711 237 237 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1626 542 542 0.00 6 C006 has 513 171 171 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1769 588 588 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1683 561 561 0.00 12 C012 has 120 40 40 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.67 Total of13255 atoms and 4410 groups and 4405 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3869 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.822" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1278" Evaluating: 1278-7 Parameter: NUMWAT <- "1271" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1271" Comparing "1081" and "1271". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.822" Parameter: BOX -> "33.822" Parameter: BOX -> "33.822" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.82200 B = 33.82200 C = 33.82200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7685 2 1 -1 0 -1 3.2735 3 1 -1 1 -1 3.8714 4 1 0 -1 -1 3.3473 5 1 0 0 -1 1.3484 6 1 0 1 -1 2.5616 7 1 -1 -1 0 2.5813 8 1 -1 0 0 2.0386 9 1 -1 1 0 3.7492 10 1 0 -1 0 1.1917 11 1 0 1 0 1.1917 12 1 -1 -1 1 3.1443 13 1 -1 0 1 3.2843 14 1 -1 1 1 3.9616 15 1 0 -1 1 2.5616 16 1 0 0 1 1.3484 17 1 0 1 1 3.3473 18 1 1 1 1 6.7685 19 1 1 0 1 3.2735 20 1 1 -1 1 3.8714 21 1 1 1 0 2.5813 22 1 1 0 0 2.0386 23 1 1 -1 0 3.7492 24 1 1 1 -1 3.1443 25 1 1 0 -1 3.2843 26 1 1 -1 -1 3.9616 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3795 atoms have been selected out of 3869 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 417 139 139 0.00 2 C002 has 711 237 237 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1626 542 542 0.00 6 C006 has 513 171 171 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1772 589 589 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1683 561 561 0.00 12 C012 has 120 40 40 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.67 Total of13258 atoms and 4411 groups and 4406 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3869 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.82" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1278" Evaluating: 1278-7 Parameter: NUMWAT <- "1271" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1271" Comparing "1081" and "1271". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.82" Parameter: BOX -> "33.82" Parameter: BOX -> "33.82" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.82000 B = 33.82000 C = 33.82000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7664 2 1 -1 0 -1 3.2707 3 1 -1 1 -1 3.8680 4 1 0 -1 -1 3.3446 5 1 0 0 -1 1.3466 6 1 0 1 -1 2.5589 7 1 -1 -1 0 2.5786 8 1 -1 0 0 2.0367 9 1 -1 1 0 3.7473 10 1 0 -1 0 1.1918 11 1 0 1 0 1.1918 12 1 -1 -1 1 3.1409 13 1 -1 0 1 3.2816 14 1 -1 1 1 3.9588 15 1 0 -1 1 2.5589 16 1 0 0 1 1.3466 17 1 0 1 1 3.3446 18 1 1 1 1 6.7664 19 1 1 0 1 3.2707 20 1 1 -1 1 3.8680 21 1 1 1 0 2.5786 22 1 1 0 0 2.0367 23 1 1 -1 0 3.7473 24 1 1 1 -1 3.1409 25 1 1 0 -1 3.2816 26 1 1 -1 -1 3.9588 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3795 atoms have been selected out of 3869 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 417 139 139 0.00 2 C002 has 711 237 237 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1626 542 542 0.00 6 C006 has 513 171 171 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1683 561 561 0.00 12 C012 has 120 40 40 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.67 Total of13261 atoms and 4412 groups and 4407 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3869 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.818" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1278" Evaluating: 1278-7 Parameter: NUMWAT <- "1271" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1271" Comparing "1081" and "1271". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.818" Parameter: BOX -> "33.818" Parameter: BOX -> "33.818" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.81800 B = 33.81800 C = 33.81800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7643 2 1 -1 0 -1 3.2680 3 1 -1 1 -1 3.8646 4 1 0 -1 -1 3.3418 5 1 0 0 -1 1.3447 6 1 0 1 -1 2.5562 7 1 -1 -1 0 2.5759 8 1 -1 0 0 2.0348 9 1 -1 1 0 3.7454 10 1 0 -1 0 1.1920 11 1 0 1 0 1.1920 12 1 -1 -1 1 3.1374 13 1 -1 0 1 3.2788 14 1 -1 1 1 3.9561 15 1 0 -1 1 2.5562 16 1 0 0 1 1.3447 17 1 0 1 1 3.3418 18 1 1 1 1 6.7643 19 1 1 0 1 3.2680 20 1 1 -1 1 3.8646 21 1 1 1 0 2.5759 22 1 1 0 0 2.0348 23 1 1 -1 0 3.7454 24 1 1 1 -1 3.1374 25 1 1 0 -1 3.2788 26 1 1 -1 -1 3.9561 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3795 atoms have been selected out of 3869 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 417 139 139 0.00 2 C002 has 711 237 237 0.00 3 C003 has 111 37 37 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1626 542 542 0.00 6 C006 has 516 172 172 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1683 561 561 0.00 12 C012 has 120 40 40 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.66 Total of13267 atoms and 4414 groups and 4409 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3869 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.816" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1278" Evaluating: 1278-7 Parameter: NUMWAT <- "1271" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1271" Comparing "1081" and "1271". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.816" Parameter: BOX -> "33.816" Parameter: BOX -> "33.816" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.81600 B = 33.81600 C = 33.81600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7623 2 1 -1 0 -1 3.2652 3 1 -1 1 -1 3.8612 4 1 0 -1 -1 3.3391 5 1 0 0 -1 1.3429 6 1 0 1 -1 2.5535 7 1 -1 -1 0 2.5732 8 1 -1 0 0 2.0329 9 1 -1 1 0 3.7434 10 1 0 -1 0 1.1921 11 1 0 1 0 1.1921 12 1 -1 -1 1 3.1340 13 1 -1 0 1 3.2761 14 1 -1 1 1 3.9533 15 1 0 -1 1 2.5535 16 1 0 0 1 1.3429 17 1 0 1 1 3.3391 18 1 1 1 1 6.7623 19 1 1 0 1 3.2652 20 1 1 -1 1 3.8612 21 1 1 1 0 2.5732 22 1 1 0 0 2.0329 23 1 1 -1 0 3.7434 24 1 1 1 -1 3.1340 25 1 1 0 -1 3.2761 26 1 1 -1 -1 3.9533 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3795 atoms have been selected out of 3869 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 417 139 139 0.00 2 C002 has 714 238 238 0.00 3 C003 has 111 37 37 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1626 542 542 0.00 6 C006 has 516 172 172 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1683 561 561 0.00 12 C012 has 120 40 40 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.66 Total of13270 atoms and 4415 groups and 4410 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3869 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.814" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1278" Evaluating: 1278-7 Parameter: NUMWAT <- "1271" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1271" Comparing "1081" and "1271". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.814" Parameter: BOX -> "33.814" Parameter: BOX -> "33.814" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.81400 B = 33.81400 C = 33.81400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7602 2 1 -1 0 -1 3.2625 3 1 -1 1 -1 3.8577 4 1 0 -1 -1 3.3363 5 1 0 0 -1 1.3410 6 1 0 1 -1 2.5508 7 1 -1 -1 0 2.5705 8 1 -1 0 0 2.0310 9 1 -1 1 0 3.7415 10 1 0 -1 0 1.1923 11 1 0 1 0 1.1923 12 1 -1 -1 1 3.1306 13 1 -1 0 1 3.2733 14 1 -1 1 1 3.9506 15 1 0 -1 1 2.5508 16 1 0 0 1 1.3410 17 1 0 1 1 3.3363 18 1 1 1 1 6.7602 19 1 1 0 1 3.2625 20 1 1 -1 1 3.8577 21 1 1 1 0 2.5705 22 1 1 0 0 2.0310 23 1 1 -1 0 3.7415 24 1 1 1 -1 3.1306 25 1 1 0 -1 3.2733 26 1 1 -1 -1 3.9506 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3795 atoms have been selected out of 3869 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 417 139 139 0.00 2 C002 has 714 238 238 0.00 3 C003 has 111 37 37 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1626 542 542 0.00 6 C006 has 516 172 172 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1683 561 561 0.00 12 C012 has 120 40 40 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.66 Total of13270 atoms and 4415 groups and 4410 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3869 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.812" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1278" Evaluating: 1278-7 Parameter: NUMWAT <- "1271" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1271" Comparing "1081" and "1271". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.812" Parameter: BOX -> "33.812" Parameter: BOX -> "33.812" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.81200 B = 33.81200 C = 33.81200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7581 2 1 -1 0 -1 3.2597 3 1 -1 1 -1 3.8543 4 1 0 -1 -1 3.3336 5 1 0 0 -1 1.3392 6 1 0 1 -1 2.5481 7 1 -1 -1 0 2.5678 8 1 -1 0 0 2.0291 9 1 -1 1 0 3.7396 10 1 0 -1 0 1.1924 11 1 0 1 0 1.1924 12 1 -1 -1 1 3.1271 13 1 -1 0 1 3.2706 14 1 -1 1 1 3.9479 15 1 0 -1 1 2.5481 16 1 0 0 1 1.3392 17 1 0 1 1 3.3336 18 1 1 1 1 6.7581 19 1 1 0 1 3.2597 20 1 1 -1 1 3.8543 21 1 1 1 0 2.5678 22 1 1 0 0 2.0291 23 1 1 -1 0 3.7396 24 1 1 1 -1 3.1271 25 1 1 0 -1 3.2706 26 1 1 -1 -1 3.9479 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3795 atoms have been selected out of 3869 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 417 139 139 0.00 2 C002 has 714 238 238 0.00 3 C003 has 111 37 37 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1626 542 542 0.00 6 C006 has 516 172 172 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1683 561 561 0.00 12 C012 has 120 40 40 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.66 Total of13270 atoms and 4415 groups and 4410 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3869 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.81" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1278" Evaluating: 1278-7 Parameter: NUMWAT <- "1271" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1271" Comparing "1081" and "1271". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.81" Parameter: BOX -> "33.81" Parameter: BOX -> "33.81" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.81000 B = 33.81000 C = 33.81000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7561 2 1 -1 0 -1 3.2570 3 1 -1 1 -1 3.8509 4 1 0 -1 -1 3.3308 5 1 0 0 -1 1.3374 6 1 0 1 -1 2.5454 7 1 -1 -1 0 2.5651 8 1 -1 0 0 2.0272 9 1 -1 1 0 3.7376 10 1 0 -1 0 1.1926 11 1 0 1 0 1.1926 12 1 -1 -1 1 3.1237 13 1 -1 0 1 3.2678 14 1 -1 1 1 3.9451 15 1 0 -1 1 2.5454 16 1 0 0 1 1.3374 17 1 0 1 1 3.3308 18 1 1 1 1 6.7561 19 1 1 0 1 3.2570 20 1 1 -1 1 3.8509 21 1 1 1 0 2.5651 22 1 1 0 0 2.0272 23 1 1 -1 0 3.7376 24 1 1 1 -1 3.1237 25 1 1 0 -1 3.2678 26 1 1 -1 -1 3.9451 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3795 atoms have been selected out of 3869 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 417 139 139 0.00 2 C002 has 714 238 238 0.00 3 C003 has 111 37 37 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1626 542 542 0.00 6 C006 has 516 172 172 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1683 561 561 0.00 12 C012 has 120 40 40 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.66 Total of13270 atoms and 4415 groups and 4410 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3869 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1278 Number of atoms = 3869 Number of groups = 1283 Number of bonds = 3862 Number of angles = 1382 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1280 Number of HB donors = 2538 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.808" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1278" Evaluating: 1278-7 Parameter: NUMWAT <- "1271" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1271" Comparing "1081" and "1271". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.808" Parameter: BOX -> "33.808" Parameter: BOX -> "33.808" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.80800 B = 33.80800 C = 33.80800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7540 2 1 -1 0 -1 3.2542 3 1 -1 1 -1 3.8475 4 1 0 -1 -1 3.3281 5 1 0 0 -1 1.3355 6 1 0 1 -1 2.5427 7 1 -1 -1 0 2.5624 8 1 -1 0 0 2.0253 9 1 -1 1 0 3.7357 10 1 0 -1 0 1.1927 11 1 0 1 0 1.1927 12 1 -1 -1 1 3.1202 13 1 -1 0 1 3.2651 14 1 -1 1 1 3.9424 15 1 0 -1 1 2.5427 16 1 0 0 1 1.3355 17 1 0 1 1 3.3281 18 1 1 1 1 6.7540 19 1 1 0 1 3.2542 20 1 1 -1 1 3.8475 21 1 1 1 0 2.5624 22 1 1 0 0 2.0253 23 1 1 -1 0 3.7357 24 1 1 1 -1 3.1202 25 1 1 0 -1 3.2651 26 1 1 -1 -1 3.9424 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3795 atoms have been selected out of 3869 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 672 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 417 139 139 0.00 2 C002 has 717 239 239 0.00 3 C003 has 114 38 38 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1626 542 542 0.00 6 C006 has 516 172 172 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1778 591 591 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1683 561 561 0.00 12 C012 has 120 40 40 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.65 Total of13282 atoms and 4419 groups and 4414 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3869 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1277 Number of atoms = 3866 Number of groups = 1282 Number of bonds = 3859 Number of angles = 1381 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1279 Number of HB donors = 2536 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1277 Number of atoms = 3866 Number of groups = 1282 Number of bonds = 3859 Number of angles = 1381 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1279 Number of HB donors = 2536 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.806" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1277" Evaluating: 1277-7 Parameter: NUMWAT <- "1270" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1270" Comparing "1081" and "1270". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.806" Parameter: BOX -> "33.806" Parameter: BOX -> "33.806" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.80600 B = 33.80600 C = 33.80600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7520 2 1 -1 0 -1 3.2515 3 1 -1 1 -1 3.8440 4 1 0 -1 -1 3.3254 5 1 0 0 -1 1.3337 6 1 0 1 -1 2.5400 7 1 -1 -1 0 2.5597 8 1 -1 0 0 2.0234 9 1 -1 1 0 3.7334 10 1 0 -1 0 1.1929 11 1 0 1 0 1.1929 12 1 -1 -1 1 3.1168 13 1 -1 0 1 3.2623 14 1 -1 1 1 3.9397 15 1 0 -1 1 2.5400 16 1 0 0 1 1.3337 17 1 0 1 1 3.3254 18 1 1 1 1 6.7520 19 1 1 0 1 3.2515 20 1 1 -1 1 3.8440 21 1 1 1 0 2.5597 22 1 1 0 0 2.0234 23 1 1 -1 0 3.7334 24 1 1 1 -1 3.1168 25 1 1 0 -1 3.2623 26 1 1 -1 -1 3.9397 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3792 atoms have been selected out of 3866 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 417 139 139 0.00 2 C002 has 714 238 238 0.00 3 C003 has 111 37 37 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1623 541 541 0.00 6 C006 has 513 171 171 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1683 561 561 0.00 12 C012 has 120 40 40 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.65 Total of13261 atoms and 4412 groups and 4407 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3866 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1277 Number of atoms = 3866 Number of groups = 1282 Number of bonds = 3859 Number of angles = 1381 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1279 Number of HB donors = 2536 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1277 Number of atoms = 3866 Number of groups = 1282 Number of bonds = 3859 Number of angles = 1381 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1279 Number of HB donors = 2536 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.804" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1277" Evaluating: 1277-7 Parameter: NUMWAT <- "1270" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1270" Comparing "1081" and "1270". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.804" Parameter: BOX -> "33.804" Parameter: BOX -> "33.804" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.80400 B = 33.80400 C = 33.80400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7499 2 1 -1 0 -1 3.2488 3 1 -1 1 -1 3.8406 4 1 0 -1 -1 3.3226 5 1 0 0 -1 1.3319 6 1 0 1 -1 2.5373 7 1 -1 -1 0 2.5570 8 1 -1 0 0 2.0215 9 1 -1 1 0 3.7305 10 1 0 -1 0 1.1930 11 1 0 1 0 1.1930 12 1 -1 -1 1 3.1133 13 1 -1 0 1 3.2596 14 1 -1 1 1 3.9369 15 1 0 -1 1 2.5373 16 1 0 0 1 1.3319 17 1 0 1 1 3.3226 18 1 1 1 1 6.7499 19 1 1 0 1 3.2488 20 1 1 -1 1 3.8406 21 1 1 1 0 2.5570 22 1 1 0 0 2.0215 23 1 1 -1 0 3.7305 24 1 1 1 -1 3.1133 25 1 1 0 -1 3.2596 26 1 1 -1 -1 3.9369 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3792 atoms have been selected out of 3866 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 417 139 139 0.00 2 C002 has 714 238 238 0.00 3 C003 has 111 37 37 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1623 541 541 0.00 6 C006 has 513 171 171 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1683 561 561 0.00 12 C012 has 120 40 40 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.65 Total of13261 atoms and 4412 groups and 4407 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3866 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1277 Number of atoms = 3866 Number of groups = 1282 Number of bonds = 3859 Number of angles = 1381 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1279 Number of HB donors = 2536 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1277 Number of atoms = 3866 Number of groups = 1282 Number of bonds = 3859 Number of angles = 1381 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1279 Number of HB donors = 2536 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.802" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1277" Evaluating: 1277-7 Parameter: NUMWAT <- "1270" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1270" Comparing "1081" and "1270". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.802" Parameter: BOX -> "33.802" Parameter: BOX -> "33.802" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.80200 B = 33.80200 C = 33.80200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7478 2 1 -1 0 -1 3.2460 3 1 -1 1 -1 3.8372 4 1 0 -1 -1 3.3199 5 1 0 0 -1 1.3300 6 1 0 1 -1 2.5346 7 1 -1 -1 0 2.5543 8 1 -1 0 0 2.0196 9 1 -1 1 0 3.7277 10 1 0 -1 0 1.1932 11 1 0 1 0 1.1932 12 1 -1 -1 1 3.1099 13 1 -1 0 1 3.2568 14 1 -1 1 1 3.9342 15 1 0 -1 1 2.5346 16 1 0 0 1 1.3300 17 1 0 1 1 3.3199 18 1 1 1 1 6.7478 19 1 1 0 1 3.2460 20 1 1 -1 1 3.8372 21 1 1 1 0 2.5543 22 1 1 0 0 2.0196 23 1 1 -1 0 3.7277 24 1 1 1 -1 3.1099 25 1 1 0 -1 3.2568 26 1 1 -1 -1 3.9342 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3792 atoms have been selected out of 3866 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 417 139 139 0.00 2 C002 has 717 239 239 0.00 3 C003 has 111 37 37 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1623 541 541 0.00 6 C006 has 513 171 171 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1683 561 561 0.00 12 C012 has 120 40 40 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.65 Total of13264 atoms and 4413 groups and 4408 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3866 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1277 Number of atoms = 3866 Number of groups = 1282 Number of bonds = 3859 Number of angles = 1381 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1279 Number of HB donors = 2536 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1277 Number of atoms = 3866 Number of groups = 1282 Number of bonds = 3859 Number of angles = 1381 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1279 Number of HB donors = 2536 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.8" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1277" Evaluating: 1277-7 Parameter: NUMWAT <- "1270" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1270" Comparing "1081" and "1270". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.8" Parameter: BOX -> "33.8" Parameter: BOX -> "33.8" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.80000 B = 33.80000 C = 33.80000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7458 2 1 -1 0 -1 3.2433 3 1 -1 1 -1 3.8337 4 1 0 -1 -1 3.3171 5 1 0 0 -1 1.3282 6 1 0 1 -1 2.5319 7 1 -1 -1 0 2.5516 8 1 -1 0 0 2.0177 9 1 -1 1 0 3.7249 10 1 0 -1 0 1.1934 11 1 0 1 0 1.1934 12 1 -1 -1 1 3.1065 13 1 -1 0 1 3.2541 14 1 -1 1 1 3.9315 15 1 0 -1 1 2.5319 16 1 0 0 1 1.3282 17 1 0 1 1 3.3171 18 1 1 1 1 6.7458 19 1 1 0 1 3.2433 20 1 1 -1 1 3.8337 21 1 1 1 0 2.5516 22 1 1 0 0 2.0177 23 1 1 -1 0 3.7249 24 1 1 1 -1 3.1065 25 1 1 0 -1 3.2541 26 1 1 -1 -1 3.9315 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3792 atoms have been selected out of 3866 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 417 139 139 0.00 2 C002 has 717 239 239 0.00 3 C003 has 111 37 37 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1623 541 541 0.00 6 C006 has 513 171 171 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1683 561 561 0.00 12 C012 has 120 40 40 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.65 Total of13264 atoms and 4413 groups and 4408 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3866 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1277 Number of atoms = 3866 Number of groups = 1282 Number of bonds = 3859 Number of angles = 1381 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1279 Number of HB donors = 2536 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1277 Number of atoms = 3866 Number of groups = 1282 Number of bonds = 3859 Number of angles = 1381 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1279 Number of HB donors = 2536 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.798" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1277" Evaluating: 1277-7 Parameter: NUMWAT <- "1270" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1270" Comparing "1081" and "1270". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.798" Parameter: BOX -> "33.798" Parameter: BOX -> "33.798" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.79800 B = 33.79800 C = 33.79800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7437 2 1 -1 0 -1 3.2405 3 1 -1 1 -1 3.8303 4 1 0 -1 -1 3.3144 5 1 0 0 -1 1.3264 6 1 0 1 -1 2.5292 7 1 -1 -1 0 2.5489 8 1 -1 0 0 2.0158 9 1 -1 1 0 3.7221 10 1 0 -1 0 1.1936 11 1 0 1 0 1.1936 12 1 -1 -1 1 3.1030 13 1 -1 0 1 3.2513 14 1 -1 1 1 3.9287 15 1 0 -1 1 2.5292 16 1 0 0 1 1.3264 17 1 0 1 1 3.3144 18 1 1 1 1 6.7437 19 1 1 0 1 3.2405 20 1 1 -1 1 3.8303 21 1 1 1 0 2.5489 22 1 1 0 0 2.0158 23 1 1 -1 0 3.7221 24 1 1 1 -1 3.1030 25 1 1 0 -1 3.2513 26 1 1 -1 -1 3.9287 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3792 atoms have been selected out of 3866 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 417 139 139 0.00 2 C002 has 717 239 239 0.00 3 C003 has 111 37 37 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1623 541 541 0.00 6 C006 has 513 171 171 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1689 563 563 0.00 12 C012 has 120 40 40 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.64 Total of13270 atoms and 4415 groups and 4410 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3866 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1277 Number of atoms = 3866 Number of groups = 1282 Number of bonds = 3859 Number of angles = 1381 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1279 Number of HB donors = 2536 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1277 Number of atoms = 3866 Number of groups = 1282 Number of bonds = 3859 Number of angles = 1381 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1279 Number of HB donors = 2536 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.796" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1277" Evaluating: 1277-7 Parameter: NUMWAT <- "1270" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1270" Comparing "1081" and "1270". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.796" Parameter: BOX -> "33.796" Parameter: BOX -> "33.796" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.79600 B = 33.79600 C = 33.79600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7417 2 1 -1 0 -1 3.2378 3 1 -1 1 -1 3.8269 4 1 0 -1 -1 3.3116 5 1 0 0 -1 1.3245 6 1 0 1 -1 2.5265 7 1 -1 -1 0 2.5462 8 1 -1 0 0 2.0139 9 1 -1 1 0 3.7192 10 1 0 -1 0 1.1937 11 1 0 1 0 1.1937 12 1 -1 -1 1 3.0996 13 1 -1 0 1 3.2486 14 1 -1 1 1 3.9260 15 1 0 -1 1 2.5265 16 1 0 0 1 1.3245 17 1 0 1 1 3.3116 18 1 1 1 1 6.7417 19 1 1 0 1 3.2378 20 1 1 -1 1 3.8269 21 1 1 1 0 2.5462 22 1 1 0 0 2.0139 23 1 1 -1 0 3.7192 24 1 1 1 -1 3.0996 25 1 1 0 -1 3.2486 26 1 1 -1 -1 3.9260 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3792 atoms have been selected out of 3866 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 717 239 239 0.00 3 C003 has 111 37 37 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1623 541 541 0.00 6 C006 has 516 172 172 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1692 564 564 0.00 12 C012 has 120 40 40 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.64 Total of13279 atoms and 4418 groups and 4413 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3866 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1277 Number of atoms = 3866 Number of groups = 1282 Number of bonds = 3859 Number of angles = 1381 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1279 Number of HB donors = 2536 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1277 Number of atoms = 3866 Number of groups = 1282 Number of bonds = 3859 Number of angles = 1381 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1279 Number of HB donors = 2536 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.794" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1277" Evaluating: 1277-7 Parameter: NUMWAT <- "1270" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1270" Comparing "1081" and "1270". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.794" Parameter: BOX -> "33.794" Parameter: BOX -> "33.794" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.79400 B = 33.79400 C = 33.79400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7396 2 1 -1 0 -1 3.2350 3 1 -1 1 -1 3.8235 4 1 0 -1 -1 3.3089 5 1 0 0 -1 1.3227 6 1 0 1 -1 2.5238 7 1 -1 -1 0 2.5435 8 1 -1 0 0 2.0120 9 1 -1 1 0 3.7164 10 1 0 -1 0 1.1939 11 1 0 1 0 1.1939 12 1 -1 -1 1 3.0961 13 1 -1 0 1 3.2458 14 1 -1 1 1 3.9233 15 1 0 -1 1 2.5238 16 1 0 0 1 1.3227 17 1 0 1 1 3.3089 18 1 1 1 1 6.7396 19 1 1 0 1 3.2350 20 1 1 -1 1 3.8235 21 1 1 1 0 2.5435 22 1 1 0 0 2.0120 23 1 1 -1 0 3.7164 24 1 1 1 -1 3.0961 25 1 1 0 -1 3.2458 26 1 1 -1 -1 3.9233 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3792 atoms have been selected out of 3866 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 717 239 239 0.00 3 C003 has 111 37 37 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1623 541 541 0.00 6 C006 has 516 172 172 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1692 564 564 0.00 12 C012 has 120 40 40 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.64 Total of13279 atoms and 4418 groups and 4413 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3866 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1277 Number of atoms = 3866 Number of groups = 1282 Number of bonds = 3859 Number of angles = 1381 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1279 Number of HB donors = 2536 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1277 Number of atoms = 3866 Number of groups = 1282 Number of bonds = 3859 Number of angles = 1381 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1279 Number of HB donors = 2536 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.792" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1277" Evaluating: 1277-7 Parameter: NUMWAT <- "1270" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1270" Comparing "1081" and "1270". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.792" Parameter: BOX -> "33.792" Parameter: BOX -> "33.792" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.79200 B = 33.79200 C = 33.79200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7376 2 1 -1 0 -1 3.2323 3 1 -1 1 -1 3.8200 4 1 0 -1 -1 3.3062 5 1 0 0 -1 1.3209 6 1 0 1 -1 2.5211 7 1 -1 -1 0 2.5409 8 1 -1 0 0 2.0101 9 1 -1 1 0 3.7136 10 1 0 -1 0 1.1941 11 1 0 1 0 1.1941 12 1 -1 -1 1 3.0927 13 1 -1 0 1 3.2431 14 1 -1 1 1 3.9205 15 1 0 -1 1 2.5211 16 1 0 0 1 1.3209 17 1 0 1 1 3.3062 18 1 1 1 1 6.7376 19 1 1 0 1 3.2323 20 1 1 -1 1 3.8200 21 1 1 1 0 2.5409 22 1 1 0 0 2.0101 23 1 1 -1 0 3.7136 24 1 1 1 -1 3.0927 25 1 1 0 -1 3.2431 26 1 1 -1 -1 3.9205 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3792 atoms have been selected out of 3866 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 717 239 239 0.00 3 C003 has 111 37 37 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1623 541 541 0.00 6 C006 has 516 172 172 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1692 564 564 0.00 12 C012 has 120 40 40 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.64 Total of13279 atoms and 4418 groups and 4413 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3866 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1277 Number of atoms = 3866 Number of groups = 1282 Number of bonds = 3859 Number of angles = 1381 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1279 Number of HB donors = 2536 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1277 Number of atoms = 3866 Number of groups = 1282 Number of bonds = 3859 Number of angles = 1381 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1279 Number of HB donors = 2536 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.79" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1277" Evaluating: 1277-7 Parameter: NUMWAT <- "1270" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1270" Comparing "1081" and "1270". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.79" Parameter: BOX -> "33.79" Parameter: BOX -> "33.79" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.79000 B = 33.79000 C = 33.79000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7355 2 1 -1 0 -1 3.2295 3 1 -1 1 -1 3.8166 4 1 0 -1 -1 3.3034 5 1 0 0 -1 1.3190 6 1 0 1 -1 2.5184 7 1 -1 -1 0 2.5382 8 1 -1 0 0 2.0082 9 1 -1 1 0 3.7108 10 1 0 -1 0 1.1943 11 1 0 1 0 1.1943 12 1 -1 -1 1 3.0892 13 1 -1 0 1 3.2403 14 1 -1 1 1 3.9178 15 1 0 -1 1 2.5184 16 1 0 0 1 1.3190 17 1 0 1 1 3.3034 18 1 1 1 1 6.7355 19 1 1 0 1 3.2295 20 1 1 -1 1 3.8166 21 1 1 1 0 2.5382 22 1 1 0 0 2.0082 23 1 1 -1 0 3.7108 24 1 1 1 -1 3.0892 25 1 1 0 -1 3.2403 26 1 1 -1 -1 3.9178 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3792 atoms have been selected out of 3866 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 637 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 717 239 239 0.00 3 C003 has 111 37 37 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1623 541 541 0.00 6 C006 has 516 172 172 0.00 7 C007 has 747 249 249 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1692 564 564 0.00 12 C012 has 117 39 39 0.00 13 C013 has 459 153 153 0.00 14 C014 has 123 41 41 0.64 Total of13270 atoms and 4415 groups and 4410 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3866 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1276 Number of atoms = 3863 Number of groups = 1281 Number of bonds = 3856 Number of angles = 1380 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1278 Number of HB donors = 2534 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1276 Number of atoms = 3863 Number of groups = 1281 Number of bonds = 3856 Number of angles = 1380 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1278 Number of HB donors = 2534 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.788" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1276" Evaluating: 1276-7 Parameter: NUMWAT <- "1269" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1269" Comparing "1081" and "1269". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.788" Parameter: BOX -> "33.788" Parameter: BOX -> "33.788" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.78800 B = 33.78800 C = 33.78800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7334 2 1 -1 0 -1 3.2268 3 1 -1 1 -1 3.8132 4 1 0 -1 -1 3.3007 5 1 0 0 -1 1.3172 6 1 0 1 -1 2.5157 7 1 -1 -1 0 2.5355 8 1 -1 0 0 2.0063 9 1 -1 1 0 3.7079 10 1 0 -1 0 1.1945 11 1 0 1 0 1.1945 12 1 -1 -1 1 3.0858 13 1 -1 0 1 3.2376 14 1 -1 1 1 3.9151 15 1 0 -1 1 2.5157 16 1 0 0 1 1.3172 17 1 0 1 1 3.3007 18 1 1 1 1 6.7334 19 1 1 0 1 3.2268 20 1 1 -1 1 3.8132 21 1 1 1 0 2.5355 22 1 1 0 0 2.0063 23 1 1 -1 0 3.7079 24 1 1 1 -1 3.0858 25 1 1 0 -1 3.2376 26 1 1 -1 -1 3.9151 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3789 atoms have been selected out of 3863 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1045 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 717 239 239 0.00 3 C003 has 111 37 37 0.00 4 C004 has 606 202 202 0.00 5 C005 has 1623 541 541 0.00 6 C006 has 519 173 173 0.00 7 C007 has 747 249 249 0.00 8 C008 has 1772 589 589 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1686 562 562 0.00 12 C012 has 117 39 39 0.00 13 C013 has 459 153 153 0.00 14 C014 has 123 41 41 0.63 Total of13258 atoms and 4411 groups and 4406 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3863 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1275 Number of atoms = 3860 Number of groups = 1280 Number of bonds = 3853 Number of angles = 1379 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1277 Number of HB donors = 2532 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1275 Number of atoms = 3860 Number of groups = 1280 Number of bonds = 3853 Number of angles = 1379 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1277 Number of HB donors = 2532 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.786" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1275" Evaluating: 1275-7 Parameter: NUMWAT <- "1268" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1268" Comparing "1081" and "1268". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.786" Parameter: BOX -> "33.786" Parameter: BOX -> "33.786" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.78600 B = 33.78600 C = 33.78600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7314 2 1 -1 0 -1 3.2240 3 1 -1 1 -1 3.8098 4 1 0 -1 -1 3.2979 5 1 0 0 -1 1.3154 6 1 0 1 -1 2.5131 7 1 -1 -1 0 2.5328 8 1 -1 0 0 2.0044 9 1 -1 1 0 3.7051 10 1 0 -1 0 1.1947 11 1 0 1 0 1.1947 12 1 -1 -1 1 3.0824 13 1 -1 0 1 3.2348 14 1 -1 1 1 3.9124 15 1 0 -1 1 2.5131 16 1 0 0 1 1.3154 17 1 0 1 1 3.2979 18 1 1 1 1 6.7314 19 1 1 0 1 3.2240 20 1 1 -1 1 3.8098 21 1 1 1 0 2.5328 22 1 1 0 0 2.0044 23 1 1 -1 0 3.7051 24 1 1 1 -1 3.0824 25 1 1 0 -1 3.2348 26 1 1 -1 -1 3.9124 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3786 atoms have been selected out of 3860 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 717 239 239 0.00 3 C003 has 111 37 37 0.00 4 C004 has 606 202 202 0.00 5 C005 has 1620 540 540 0.00 6 C006 has 516 172 172 0.00 7 C007 has 747 249 249 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1686 562 562 0.00 12 C012 has 117 39 39 0.00 13 C013 has 459 153 153 0.00 14 C014 has 123 41 41 0.63 Total of13252 atoms and 4409 groups and 4404 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3860 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1275 Number of atoms = 3860 Number of groups = 1280 Number of bonds = 3853 Number of angles = 1379 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1277 Number of HB donors = 2532 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1275 Number of atoms = 3860 Number of groups = 1280 Number of bonds = 3853 Number of angles = 1379 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1277 Number of HB donors = 2532 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.784" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1275" Evaluating: 1275-7 Parameter: NUMWAT <- "1268" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1268" Comparing "1081" and "1268". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.784" Parameter: BOX -> "33.784" Parameter: BOX -> "33.784" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.78400 B = 33.78400 C = 33.78400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7293 2 1 -1 0 -1 3.2213 3 1 -1 1 -1 3.8063 4 1 0 -1 -1 3.2952 5 1 0 0 -1 1.3136 6 1 0 1 -1 2.5104 7 1 -1 -1 0 2.5301 8 1 -1 0 0 2.0025 9 1 -1 1 0 3.7023 10 1 0 -1 0 1.1949 11 1 0 1 0 1.1949 12 1 -1 -1 1 3.0789 13 1 -1 0 1 3.2321 14 1 -1 1 1 3.9097 15 1 0 -1 1 2.5104 16 1 0 0 1 1.3136 17 1 0 1 1 3.2952 18 1 1 1 1 6.7293 19 1 1 0 1 3.2213 20 1 1 -1 1 3.8063 21 1 1 1 0 2.5301 22 1 1 0 0 2.0025 23 1 1 -1 0 3.7023 24 1 1 1 -1 3.0789 25 1 1 0 -1 3.2321 26 1 1 -1 -1 3.9097 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3786 atoms have been selected out of 3860 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 955 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 717 239 239 0.00 3 C003 has 111 37 37 0.00 4 C004 has 603 201 201 0.00 5 C005 has 1623 541 541 0.00 6 C006 has 516 172 172 0.00 7 C007 has 747 249 249 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1689 563 563 0.00 12 C012 has 117 39 39 0.00 13 C013 has 459 153 153 0.00 14 C014 has 123 41 41 0.63 Total of13255 atoms and 4410 groups and 4405 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3860 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1274 Number of atoms = 3857 Number of groups = 1279 Number of bonds = 3850 Number of angles = 1378 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1276 Number of HB donors = 2530 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1274 Number of atoms = 3857 Number of groups = 1279 Number of bonds = 3850 Number of angles = 1378 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1276 Number of HB donors = 2530 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.782" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1274" Evaluating: 1274-7 Parameter: NUMWAT <- "1267" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1267" Comparing "1081" and "1267". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.782" Parameter: BOX -> "33.782" Parameter: BOX -> "33.782" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.78200 B = 33.78200 C = 33.78200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7273 2 1 -1 0 -1 3.2185 3 1 -1 1 -1 3.8029 4 1 0 -1 -1 3.2924 5 1 0 0 -1 1.3117 6 1 0 1 -1 2.5077 7 1 -1 -1 0 2.5274 8 1 -1 0 0 2.0006 9 1 -1 1 0 3.6994 10 1 0 -1 0 1.1951 11 1 0 1 0 1.1951 12 1 -1 -1 1 3.0755 13 1 -1 0 1 3.2294 14 1 -1 1 1 3.9069 15 1 0 -1 1 2.5077 16 1 0 0 1 1.3117 17 1 0 1 1 3.2924 18 1 1 1 1 6.7273 19 1 1 0 1 3.2185 20 1 1 -1 1 3.8029 21 1 1 1 0 2.5274 22 1 1 0 0 2.0006 23 1 1 -1 0 3.6994 24 1 1 1 -1 3.0755 25 1 1 0 -1 3.2294 26 1 1 -1 -1 3.9069 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3783 atoms have been selected out of 3857 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 717 239 239 0.00 3 C003 has 111 37 37 0.00 4 C004 has 603 201 201 0.00 5 C005 has 1617 539 539 0.00 6 C006 has 516 172 172 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1686 562 562 0.00 12 C012 has 117 39 39 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.63 Total of13249 atoms and 4408 groups and 4403 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3857 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1274 Number of atoms = 3857 Number of groups = 1279 Number of bonds = 3850 Number of angles = 1378 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1276 Number of HB donors = 2530 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1274 Number of atoms = 3857 Number of groups = 1279 Number of bonds = 3850 Number of angles = 1378 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1276 Number of HB donors = 2530 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.78" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1274" Evaluating: 1274-7 Parameter: NUMWAT <- "1267" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1267" Comparing "1081" and "1267". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.78" Parameter: BOX -> "33.78" Parameter: BOX -> "33.78" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.78000 B = 33.78000 C = 33.78000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7252 2 1 -1 0 -1 3.2158 3 1 -1 1 -1 3.7995 4 1 0 -1 -1 3.2897 5 1 0 0 -1 1.3099 6 1 0 1 -1 2.5050 7 1 -1 -1 0 2.5247 8 1 -1 0 0 1.9987 9 1 -1 1 0 3.6966 10 1 0 -1 0 1.1953 11 1 0 1 0 1.1953 12 1 -1 -1 1 3.0720 13 1 -1 0 1 3.2266 14 1 -1 1 1 3.9042 15 1 0 -1 1 2.5050 16 1 0 0 1 1.3099 17 1 0 1 1 3.2897 18 1 1 1 1 6.7252 19 1 1 0 1 3.2158 20 1 1 -1 1 3.7995 21 1 1 1 0 2.5247 22 1 1 0 0 1.9987 23 1 1 -1 0 3.6966 24 1 1 1 -1 3.0720 25 1 1 0 -1 3.2266 26 1 1 -1 -1 3.9042 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3783 atoms have been selected out of 3857 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 717 239 239 0.00 3 C003 has 111 37 37 0.00 4 C004 has 603 201 201 0.00 5 C005 has 1617 539 539 0.00 6 C006 has 516 172 172 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1778 591 591 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1686 562 562 0.00 12 C012 has 117 39 39 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.63 Total of13255 atoms and 4410 groups and 4405 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3857 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1274 Number of atoms = 3857 Number of groups = 1279 Number of bonds = 3850 Number of angles = 1378 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1276 Number of HB donors = 2530 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1274 Number of atoms = 3857 Number of groups = 1279 Number of bonds = 3850 Number of angles = 1378 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1276 Number of HB donors = 2530 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.778" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1274" Evaluating: 1274-7 Parameter: NUMWAT <- "1267" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1267" Comparing "1081" and "1267". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.778" Parameter: BOX -> "33.778" Parameter: BOX -> "33.778" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.77800 B = 33.77800 C = 33.77800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7232 2 1 -1 0 -1 3.2130 3 1 -1 1 -1 3.7961 4 1 0 -1 -1 3.2870 5 1 0 0 -1 1.3081 6 1 0 1 -1 2.5023 7 1 -1 -1 0 2.5220 8 1 -1 0 0 1.9968 9 1 -1 1 0 3.6938 10 1 0 -1 0 1.1955 11 1 0 1 0 1.1955 12 1 -1 -1 1 3.0686 13 1 -1 0 1 3.2239 14 1 -1 1 1 3.9015 15 1 0 -1 1 2.5023 16 1 0 0 1 1.3081 17 1 0 1 1 3.2870 18 1 1 1 1 6.7232 19 1 1 0 1 3.2130 20 1 1 -1 1 3.7961 21 1 1 1 0 2.5220 22 1 1 0 0 1.9968 23 1 1 -1 0 3.6938 24 1 1 1 -1 3.0686 25 1 1 0 -1 3.2239 26 1 1 -1 -1 3.9015 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3783 atoms have been selected out of 3857 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 720 240 240 0.00 3 C003 has 111 37 37 0.00 4 C004 has 603 201 201 0.00 5 C005 has 1617 539 539 0.00 6 C006 has 516 172 172 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1778 591 591 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1686 562 562 0.00 12 C012 has 117 39 39 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.62 Total of13258 atoms and 4411 groups and 4406 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3857 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1274 Number of atoms = 3857 Number of groups = 1279 Number of bonds = 3850 Number of angles = 1378 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1276 Number of HB donors = 2530 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1274 Number of atoms = 3857 Number of groups = 1279 Number of bonds = 3850 Number of angles = 1378 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1276 Number of HB donors = 2530 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.776" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1274" Evaluating: 1274-7 Parameter: NUMWAT <- "1267" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1267" Comparing "1081" and "1267". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.776" Parameter: BOX -> "33.776" Parameter: BOX -> "33.776" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.77600 B = 33.77600 C = 33.77600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7212 2 1 -1 0 -1 3.2103 3 1 -1 1 -1 3.7926 4 1 0 -1 -1 3.2842 5 1 0 0 -1 1.3062 6 1 0 1 -1 2.4996 7 1 -1 -1 0 2.5193 8 1 -1 0 0 1.9949 9 1 -1 1 0 3.6910 10 1 0 -1 0 1.1957 11 1 0 1 0 1.1957 12 1 -1 -1 1 3.0651 13 1 -1 0 1 3.2211 14 1 -1 1 1 3.8988 15 1 0 -1 1 2.4996 16 1 0 0 1 1.3062 17 1 0 1 1 3.2842 18 1 1 1 1 6.7212 19 1 1 0 1 3.2103 20 1 1 -1 1 3.7926 21 1 1 1 0 2.5193 22 1 1 0 0 1.9949 23 1 1 -1 0 3.6910 24 1 1 1 -1 3.0651 25 1 1 0 -1 3.2211 26 1 1 -1 -1 3.8988 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3783 atoms have been selected out of 3857 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 720 240 240 0.00 3 C003 has 111 37 37 0.00 4 C004 has 603 201 201 0.00 5 C005 has 1617 539 539 0.00 6 C006 has 516 172 172 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1778 591 591 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1686 562 562 0.00 12 C012 has 117 39 39 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.62 Total of13258 atoms and 4411 groups and 4406 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3857 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1274 Number of atoms = 3857 Number of groups = 1279 Number of bonds = 3850 Number of angles = 1378 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1276 Number of HB donors = 2530 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1274 Number of atoms = 3857 Number of groups = 1279 Number of bonds = 3850 Number of angles = 1378 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1276 Number of HB donors = 2530 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.774" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1274" Evaluating: 1274-7 Parameter: NUMWAT <- "1267" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1267" Comparing "1081" and "1267". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.774" Parameter: BOX -> "33.774" Parameter: BOX -> "33.774" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.77400 B = 33.77400 C = 33.77400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7191 2 1 -1 0 -1 3.2075 3 1 -1 1 -1 3.7892 4 1 0 -1 -1 3.2815 5 1 0 0 -1 1.3044 6 1 0 1 -1 2.4969 7 1 -1 -1 0 2.5166 8 1 -1 0 0 1.9930 9 1 -1 1 0 3.6881 10 1 0 -1 0 1.1959 11 1 0 1 0 1.1959 12 1 -1 -1 1 3.0617 13 1 -1 0 1 3.2184 14 1 -1 1 1 3.8961 15 1 0 -1 1 2.4969 16 1 0 0 1 1.3044 17 1 0 1 1 3.2815 18 1 1 1 1 6.7191 19 1 1 0 1 3.2075 20 1 1 -1 1 3.7892 21 1 1 1 0 2.5166 22 1 1 0 0 1.9930 23 1 1 -1 0 3.6881 24 1 1 1 -1 3.0617 25 1 1 0 -1 3.2184 26 1 1 -1 -1 3.8961 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3783 atoms have been selected out of 3857 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 720 240 240 0.00 3 C003 has 111 37 37 0.00 4 C004 has 603 201 201 0.00 5 C005 has 1617 539 539 0.00 6 C006 has 516 172 172 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1778 591 591 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1686 562 562 0.00 12 C012 has 117 39 39 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.62 Total of13258 atoms and 4411 groups and 4406 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3857 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1274 Number of atoms = 3857 Number of groups = 1279 Number of bonds = 3850 Number of angles = 1378 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1276 Number of HB donors = 2530 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1274 Number of atoms = 3857 Number of groups = 1279 Number of bonds = 3850 Number of angles = 1378 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1276 Number of HB donors = 2530 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.772" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1274" Evaluating: 1274-7 Parameter: NUMWAT <- "1267" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1267" Comparing "1081" and "1267". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.772" Parameter: BOX -> "33.772" Parameter: BOX -> "33.772" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.77200 B = 33.77200 C = 33.77200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7171 2 1 -1 0 -1 3.2048 3 1 -1 1 -1 3.7858 4 1 0 -1 -1 3.2787 5 1 0 0 -1 1.3026 6 1 0 1 -1 2.4942 7 1 -1 -1 0 2.5140 8 1 -1 0 0 1.9912 9 1 -1 1 0 3.6853 10 1 0 -1 0 1.1961 11 1 0 1 0 1.1961 12 1 -1 -1 1 3.0583 13 1 -1 0 1 3.2156 14 1 -1 1 1 3.8933 15 1 0 -1 1 2.4942 16 1 0 0 1 1.3026 17 1 0 1 1 3.2787 18 1 1 1 1 6.7171 19 1 1 0 1 3.2048 20 1 1 -1 1 3.7858 21 1 1 1 0 2.5140 22 1 1 0 0 1.9912 23 1 1 -1 0 3.6853 24 1 1 1 -1 3.0583 25 1 1 0 -1 3.2156 26 1 1 -1 -1 3.8933 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3783 atoms have been selected out of 3857 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 726 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 720 240 240 0.00 3 C003 has 111 37 37 0.00 4 C004 has 606 202 202 0.00 5 C005 has 1617 539 539 0.00 6 C006 has 513 171 171 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1778 591 591 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1686 562 562 0.00 12 C012 has 117 39 39 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.62 Total of13258 atoms and 4411 groups and 4406 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3857 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1273 Number of atoms = 3854 Number of groups = 1278 Number of bonds = 3847 Number of angles = 1377 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1275 Number of HB donors = 2528 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1273 Number of atoms = 3854 Number of groups = 1278 Number of bonds = 3847 Number of angles = 1377 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1275 Number of HB donors = 2528 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.77" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1273" Evaluating: 1273-7 Parameter: NUMWAT <- "1266" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1266" Comparing "1081" and "1266". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.77" Parameter: BOX -> "33.77" Parameter: BOX -> "33.77" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.77000 B = 33.77000 C = 33.77000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7150 2 1 -1 0 -1 3.2020 3 1 -1 1 -1 3.7824 4 1 0 -1 -1 3.2760 5 1 0 0 -1 1.3008 6 1 0 1 -1 2.4915 7 1 -1 -1 0 2.5113 8 1 -1 0 0 1.9893 9 1 -1 1 0 3.6825 10 1 0 -1 0 1.1963 11 1 0 1 0 1.1963 12 1 -1 -1 1 3.0548 13 1 -1 0 1 3.2129 14 1 -1 1 1 3.8906 15 1 0 -1 1 2.4915 16 1 0 0 1 1.3008 17 1 0 1 1 3.2760 18 1 1 1 1 6.7150 19 1 1 0 1 3.2020 20 1 1 -1 1 3.7824 21 1 1 1 0 2.5113 22 1 1 0 0 1.9893 23 1 1 -1 0 3.6825 24 1 1 1 -1 3.0548 25 1 1 0 -1 3.2129 26 1 1 -1 -1 3.8906 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3780 atoms have been selected out of 3854 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 720 240 240 0.00 3 C003 has 111 37 37 0.00 4 C004 has 603 201 201 0.00 5 C005 has 1614 538 538 0.00 6 C006 has 513 171 171 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1778 591 591 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1683 561 561 0.00 12 C012 has 117 39 39 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.62 Total of13246 atoms and 4407 groups and 4402 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3854 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1273 Number of atoms = 3854 Number of groups = 1278 Number of bonds = 3847 Number of angles = 1377 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1275 Number of HB donors = 2528 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1273 Number of atoms = 3854 Number of groups = 1278 Number of bonds = 3847 Number of angles = 1377 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1275 Number of HB donors = 2528 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.768" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1273" Evaluating: 1273-7 Parameter: NUMWAT <- "1266" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1266" Comparing "1081" and "1266". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.768" Parameter: BOX -> "33.768" Parameter: BOX -> "33.768" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.76800 B = 33.76800 C = 33.76800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7130 2 1 -1 0 -1 3.1993 3 1 -1 1 -1 3.7789 4 1 0 -1 -1 3.2733 5 1 0 0 -1 1.2989 6 1 0 1 -1 2.4888 7 1 -1 -1 0 2.5086 8 1 -1 0 0 1.9874 9 1 -1 1 0 3.6796 10 1 0 -1 0 1.1965 11 1 0 1 0 1.1965 12 1 -1 -1 1 3.0514 13 1 -1 0 1 3.2101 14 1 -1 1 1 3.8879 15 1 0 -1 1 2.4888 16 1 0 0 1 1.2989 17 1 0 1 1 3.2733 18 1 1 1 1 6.7130 19 1 1 0 1 3.1993 20 1 1 -1 1 3.7789 21 1 1 1 0 2.5086 22 1 1 0 0 1.9874 23 1 1 -1 0 3.6796 24 1 1 1 -1 3.0514 25 1 1 0 -1 3.2101 26 1 1 -1 -1 3.8879 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3780 atoms have been selected out of 3854 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1118 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 417 139 139 0.00 2 C002 has 723 241 241 0.00 3 C003 has 111 37 37 0.00 4 C004 has 600 200 200 0.00 5 C005 has 1617 539 539 0.00 6 C006 has 516 172 172 0.00 7 C007 has 747 249 249 0.00 8 C008 has 1778 591 591 0.00 9 C009 has 501 167 167 0.00 10 C010 has 1683 561 561 0.00 12 C012 has 117 39 39 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.61 Total of13249 atoms and 4408 groups and 4403 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3854 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1272 Number of atoms = 3851 Number of groups = 1277 Number of bonds = 3844 Number of angles = 1376 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1274 Number of HB donors = 2526 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1272 Number of atoms = 3851 Number of groups = 1277 Number of bonds = 3844 Number of angles = 1376 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1274 Number of HB donors = 2526 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.766" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1272" Evaluating: 1272-7 Parameter: NUMWAT <- "1265" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1265" Comparing "1081" and "1265". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.766" Parameter: BOX -> "33.766" Parameter: BOX -> "33.766" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.76600 B = 33.76600 C = 33.76600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7110 2 1 -1 0 -1 3.1966 3 1 -1 1 -1 3.7755 4 1 0 -1 -1 3.2705 5 1 0 0 -1 1.2971 6 1 0 1 -1 2.4861 7 1 -1 -1 0 2.5059 8 1 -1 0 0 1.9855 9 1 -1 1 0 3.6768 10 1 0 -1 0 1.1968 11 1 0 1 0 1.1968 12 1 -1 -1 1 3.0479 13 1 -1 0 1 3.2074 14 1 -1 1 1 3.8852 15 1 0 -1 1 2.4861 16 1 0 0 1 1.2971 17 1 0 1 1 3.2705 18 1 1 1 1 6.7110 19 1 1 0 1 3.1966 20 1 1 -1 1 3.7755 21 1 1 1 0 2.5059 22 1 1 0 0 1.9855 23 1 1 -1 0 3.6768 24 1 1 1 -1 3.0479 25 1 1 0 -1 3.2074 26 1 1 -1 -1 3.8852 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3777 atoms have been selected out of 3851 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 720 240 240 0.00 3 C003 has 111 37 37 0.00 4 C004 has 600 200 200 0.00 5 C005 has 1614 538 538 0.00 6 C006 has 513 171 171 0.00 7 C007 has 747 249 249 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 498 166 166 0.00 10 C010 has 1680 560 560 0.00 12 C012 has 117 39 39 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 0.61 Total of13231 atoms and 4402 groups and 4397 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3851 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1272 Number of atoms = 3851 Number of groups = 1277 Number of bonds = 3844 Number of angles = 1376 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1274 Number of HB donors = 2526 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1272 Number of atoms = 3851 Number of groups = 1277 Number of bonds = 3844 Number of angles = 1376 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1274 Number of HB donors = 2526 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.764" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1272" Evaluating: 1272-7 Parameter: NUMWAT <- "1265" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1265" Comparing "1081" and "1265". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.764" Parameter: BOX -> "33.764" Parameter: BOX -> "33.764" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.76400 B = 33.76400 C = 33.76400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7089 2 1 -1 0 -1 3.1938 3 1 -1 1 -1 3.7721 4 1 0 -1 -1 3.2678 5 1 0 0 -1 1.2953 6 1 0 1 -1 2.4834 7 1 -1 -1 0 2.5032 8 1 -1 0 0 1.9836 9 1 -1 1 0 3.6740 10 1 0 -1 0 1.1970 11 1 0 1 0 1.1970 12 1 -1 -1 1 3.0445 13 1 -1 0 1 3.2046 14 1 -1 1 1 3.8825 15 1 0 -1 1 2.4834 16 1 0 0 1 1.2953 17 1 0 1 1 3.2678 18 1 1 1 1 6.7089 19 1 1 0 1 3.1938 20 1 1 -1 1 3.7721 21 1 1 1 0 2.5032 22 1 1 0 0 1.9836 23 1 1 -1 0 3.6740 24 1 1 1 -1 3.0445 25 1 1 0 -1 3.2046 26 1 1 -1 -1 3.8825 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3777 atoms have been selected out of 3851 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 87 OPERATED ON BY TRANSFORMATION C011 RESIDUE 237 OPERATED ON BY TRANSFORMATION C011 RESIDUE 691 OPERATED ON BY TRANSFORMATION C011 RESIDUE 861 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 423 141 141 0.00 2 C002 has 720 240 240 0.00 3 C003 has 123 41 41 0.43 4 C004 has 597 199 199 0.00 5 C005 has 1614 538 538 0.00 6 C006 has 513 171 171 0.00 7 C007 has 732 244 244 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 504 168 168 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 87 29 29 0.00 13 C013 has 462 154 154 0.00 14 C014 has 126 42 42 1.20 Total of13198 atoms and 4391 groups and 4386 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 12 atoms have been selected out of 3851 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 4 residues deleted. DELTIC: 12 bonds deleted DELTIC: 4 angles deleted DELTIC: 8 donors deleted DELTIC: 4 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1268 Number of atoms = 3839 Number of groups = 1273 Number of bonds = 3832 Number of angles = 1372 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1270 Number of HB donors = 2518 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1268 Number of atoms = 3839 Number of groups = 1273 Number of bonds = 3832 Number of angles = 1372 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1270 Number of HB donors = 2518 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.762" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1268" Evaluating: 1268-7 Parameter: NUMWAT <- "1261" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1261" Comparing "1081" and "1261". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.762" Parameter: BOX -> "33.762" Parameter: BOX -> "33.762" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.76200 B = 33.76200 C = 33.76200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7069 2 1 -1 0 -1 3.1911 3 1 -1 1 -1 6.5121 4 1 0 -1 -1 4.2929 5 1 0 0 -1 1.2935 6 1 0 1 -1 5.0932 7 1 -1 -1 0 5.2868 8 1 -1 0 0 1.9817 9 1 -1 1 0 5.9125 10 1 0 -1 0 2.5959 11 1 0 1 0 2.5959 12 1 -1 -1 1 5.2971 13 1 -1 0 1 3.6039 14 1 -1 1 1 5.9488 15 1 0 -1 1 5.0932 16 1 0 0 1 1.2935 17 1 0 1 1 4.2929 18 1 1 1 1 6.7069 19 1 1 0 1 3.1911 20 1 1 -1 1 6.5121 21 1 1 1 0 5.2868 22 1 1 0 0 1.9817 23 1 1 -1 0 5.9125 24 1 1 1 -1 5.2971 25 1 1 0 -1 3.6039 26 1 1 -1 -1 5.9488 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3765 atoms have been selected out of 3839 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 717 239 239 0.00 3 C003 has 108 36 36 0.43 4 C004 has 591 197 197 0.00 5 C005 has 1608 536 536 0.00 6 C006 has 507 169 169 0.00 7 C007 has 726 242 242 0.00 8 C008 has 1769 588 588 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 84 28 28 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 1.19 Total of13105 atoms and 4360 groups and 4355 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3839 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1268 Number of atoms = 3839 Number of groups = 1273 Number of bonds = 3832 Number of angles = 1372 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1270 Number of HB donors = 2518 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1268 Number of atoms = 3839 Number of groups = 1273 Number of bonds = 3832 Number of angles = 1372 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1270 Number of HB donors = 2518 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.76" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1268" Evaluating: 1268-7 Parameter: NUMWAT <- "1261" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1261" Comparing "1081" and "1261". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.76" Parameter: BOX -> "33.76" Parameter: BOX -> "33.76" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.76000 B = 33.76000 C = 33.76000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7048 2 1 -1 0 -1 3.1883 3 1 -1 1 -1 6.5086 4 1 0 -1 -1 4.2942 5 1 0 0 -1 1.2917 6 1 0 1 -1 5.0908 7 1 -1 -1 0 5.2841 8 1 -1 0 0 1.9798 9 1 -1 1 0 5.9105 10 1 0 -1 0 2.5939 11 1 0 1 0 2.5939 12 1 -1 -1 1 5.2939 13 1 -1 0 1 3.6015 14 1 -1 1 1 5.9460 15 1 0 -1 1 5.0908 16 1 0 0 1 1.2917 17 1 0 1 1 4.2942 18 1 1 1 1 6.7048 19 1 1 0 1 3.1883 20 1 1 -1 1 6.5086 21 1 1 1 0 5.2841 22 1 1 0 0 1.9798 23 1 1 -1 0 5.9105 24 1 1 1 -1 5.2939 25 1 1 0 -1 3.6015 26 1 1 -1 -1 5.9460 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3765 atoms have been selected out of 3839 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 342 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 717 239 239 0.00 3 C003 has 108 36 36 0.42 4 C004 has 591 197 197 0.00 5 C005 has 1608 536 536 0.00 6 C006 has 507 169 169 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1775 590 590 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 84 28 28 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 1.27 Total of13108 atoms and 4361 groups and 4356 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3839 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1267 Number of atoms = 3836 Number of groups = 1272 Number of bonds = 3829 Number of angles = 1371 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1269 Number of HB donors = 2516 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1267 Number of atoms = 3836 Number of groups = 1272 Number of bonds = 3829 Number of angles = 1371 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1269 Number of HB donors = 2516 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.758" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1267" Evaluating: 1267-7 Parameter: NUMWAT <- "1260" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1260" Comparing "1081" and "1260". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.758" Parameter: BOX -> "33.758" Parameter: BOX -> "33.758" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.75800 B = 33.75800 C = 33.75800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7028 2 1 -1 0 -1 3.1856 3 1 -1 1 -1 6.5052 4 1 0 -1 -1 4.2955 5 1 0 0 -1 1.2898 6 1 0 1 -1 5.0884 7 1 -1 -1 0 5.2814 8 1 -1 0 0 1.9779 9 1 -1 1 0 5.9085 10 1 0 -1 0 2.5919 11 1 0 1 0 2.5919 12 1 -1 -1 1 5.2907 13 1 -1 0 1 3.5991 14 1 -1 1 1 5.9432 15 1 0 -1 1 5.0884 16 1 0 0 1 1.2898 17 1 0 1 1 4.2955 18 1 1 1 1 6.7028 19 1 1 0 1 3.1856 20 1 1 -1 1 6.5052 21 1 1 1 0 5.2814 22 1 1 0 0 1.9779 23 1 1 -1 0 5.9085 24 1 1 1 -1 5.2907 25 1 1 0 -1 3.5991 26 1 1 -1 -1 5.9432 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3762 atoms have been selected out of 3836 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 717 239 239 0.00 3 C003 has 108 36 36 0.42 4 C004 has 591 197 197 0.00 5 C005 has 1608 536 536 0.00 6 C006 has 510 170 170 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1772 589 589 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 84 28 28 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 1.26 Total of13102 atoms and 4359 groups and 4354 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3836 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1267 Number of atoms = 3836 Number of groups = 1272 Number of bonds = 3829 Number of angles = 1371 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1269 Number of HB donors = 2516 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1267 Number of atoms = 3836 Number of groups = 1272 Number of bonds = 3829 Number of angles = 1371 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1269 Number of HB donors = 2516 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.756" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1267" Evaluating: 1267-7 Parameter: NUMWAT <- "1260" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1260" Comparing "1081" and "1260". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.756" Parameter: BOX -> "33.756" Parameter: BOX -> "33.756" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.75600 B = 33.75600 C = 33.75600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7008 2 1 -1 0 -1 3.1828 3 1 -1 1 -1 6.5017 4 1 0 -1 -1 4.2967 5 1 0 0 -1 1.2880 6 1 0 1 -1 5.0860 7 1 -1 -1 0 5.2787 8 1 -1 0 0 1.9760 9 1 -1 1 0 5.9064 10 1 0 -1 0 2.5899 11 1 0 1 0 2.5899 12 1 -1 -1 1 5.2875 13 1 -1 0 1 3.5968 14 1 -1 1 1 5.9403 15 1 0 -1 1 5.0860 16 1 0 0 1 1.2880 17 1 0 1 1 4.2967 18 1 1 1 1 6.7008 19 1 1 0 1 3.1828 20 1 1 -1 1 6.5017 21 1 1 1 0 5.2787 22 1 1 0 0 1.9760 23 1 1 -1 0 5.9064 24 1 1 1 -1 5.2875 25 1 1 0 -1 3.5968 26 1 1 -1 -1 5.9403 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3762 atoms have been selected out of 3836 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 717 239 239 0.00 3 C003 has 108 36 36 0.42 4 C004 has 591 197 197 0.00 5 C005 has 1608 536 536 0.00 6 C006 has 513 171 171 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1772 589 589 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 84 28 28 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 1.26 Total of13105 atoms and 4360 groups and 4355 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3836 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1267 Number of atoms = 3836 Number of groups = 1272 Number of bonds = 3829 Number of angles = 1371 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1269 Number of HB donors = 2516 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1267 Number of atoms = 3836 Number of groups = 1272 Number of bonds = 3829 Number of angles = 1371 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1269 Number of HB donors = 2516 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.754" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1267" Evaluating: 1267-7 Parameter: NUMWAT <- "1260" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1260" Comparing "1081" and "1260". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.754" Parameter: BOX -> "33.754" Parameter: BOX -> "33.754" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.75400 B = 33.75400 C = 33.75400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6987 2 1 -1 0 -1 3.1801 3 1 -1 1 -1 6.4983 4 1 0 -1 -1 4.2980 5 1 0 0 -1 1.2862 6 1 0 1 -1 5.0837 7 1 -1 -1 0 5.2760 8 1 -1 0 0 1.9741 9 1 -1 1 0 5.9044 10 1 0 -1 0 2.5879 11 1 0 1 0 2.5879 12 1 -1 -1 1 5.2843 13 1 -1 0 1 3.5944 14 1 -1 1 1 5.9375 15 1 0 -1 1 5.0837 16 1 0 0 1 1.2862 17 1 0 1 1 4.2980 18 1 1 1 1 6.6987 19 1 1 0 1 3.1801 20 1 1 -1 1 6.4983 21 1 1 1 0 5.2760 22 1 1 0 0 1.9741 23 1 1 -1 0 5.9044 24 1 1 1 -1 5.2843 25 1 1 0 -1 3.5944 26 1 1 -1 -1 5.9375 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3762 atoms have been selected out of 3836 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 717 239 239 0.00 3 C003 has 108 36 36 0.42 4 C004 has 591 197 197 0.00 5 C005 has 1608 536 536 0.00 6 C006 has 513 171 171 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1772 589 589 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 84 28 28 0.00 13 C013 has 462 154 154 0.00 14 C014 has 123 41 41 1.26 Total of13108 atoms and 4361 groups and 4356 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3836 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1267 Number of atoms = 3836 Number of groups = 1272 Number of bonds = 3829 Number of angles = 1371 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1269 Number of HB donors = 2516 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1267 Number of atoms = 3836 Number of groups = 1272 Number of bonds = 3829 Number of angles = 1371 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1269 Number of HB donors = 2516 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.752" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1267" Evaluating: 1267-7 Parameter: NUMWAT <- "1260" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1260" Comparing "1081" and "1260". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.752" Parameter: BOX -> "33.752" Parameter: BOX -> "33.752" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.75200 B = 33.75200 C = 33.75200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6967 2 1 -1 0 -1 3.1773 3 1 -1 1 -1 6.4949 4 1 0 -1 -1 4.2993 5 1 0 0 -1 1.2844 6 1 0 1 -1 5.0813 7 1 -1 -1 0 5.2733 8 1 -1 0 0 1.9722 9 1 -1 1 0 5.9023 10 1 0 -1 0 2.5859 11 1 0 1 0 2.5859 12 1 -1 -1 1 5.2811 13 1 -1 0 1 3.5921 14 1 -1 1 1 5.9346 15 1 0 -1 1 5.0813 16 1 0 0 1 1.2844 17 1 0 1 1 4.2993 18 1 1 1 1 6.6967 19 1 1 0 1 3.1773 20 1 1 -1 1 6.4949 21 1 1 1 0 5.2733 22 1 1 0 0 1.9722 23 1 1 -1 0 5.9023 24 1 1 1 -1 5.2811 25 1 1 0 -1 3.5921 26 1 1 -1 -1 5.9346 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3762 atoms have been selected out of 3836 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 717 239 239 0.00 3 C003 has 108 36 36 0.42 4 C004 has 591 197 197 0.00 5 C005 has 1608 536 536 0.00 6 C006 has 513 171 171 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1772 589 589 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 84 28 28 0.00 13 C013 has 468 156 156 0.00 14 C014 has 123 41 41 1.26 Total of13114 atoms and 4363 groups and 4358 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3836 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1267 Number of atoms = 3836 Number of groups = 1272 Number of bonds = 3829 Number of angles = 1371 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1269 Number of HB donors = 2516 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1267 Number of atoms = 3836 Number of groups = 1272 Number of bonds = 3829 Number of angles = 1371 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1269 Number of HB donors = 2516 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.75" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1267" Evaluating: 1267-7 Parameter: NUMWAT <- "1260" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1260" Comparing "1081" and "1260". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.75" Parameter: BOX -> "33.75" Parameter: BOX -> "33.75" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.75000 B = 33.75000 C = 33.75000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6947 2 1 -1 0 -1 3.1746 3 1 -1 1 -1 6.4914 4 1 0 -1 -1 4.3006 5 1 0 0 -1 1.2825 6 1 0 1 -1 5.0789 7 1 -1 -1 0 5.2706 8 1 -1 0 0 1.9703 9 1 -1 1 0 5.9003 10 1 0 -1 0 2.5839 11 1 0 1 0 2.5839 12 1 -1 -1 1 5.2779 13 1 -1 0 1 3.5897 14 1 -1 1 1 5.9318 15 1 0 -1 1 5.0789 16 1 0 0 1 1.2825 17 1 0 1 1 4.3006 18 1 1 1 1 6.6947 19 1 1 0 1 3.1746 20 1 1 -1 1 6.4914 21 1 1 1 0 5.2706 22 1 1 0 0 1.9703 23 1 1 -1 0 5.9003 24 1 1 1 -1 5.2779 25 1 1 0 -1 3.5897 26 1 1 -1 -1 5.9318 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3762 atoms have been selected out of 3836 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 423 141 141 0.00 2 C002 has 717 239 239 0.00 3 C003 has 108 36 36 0.41 4 C004 has 591 197 197 0.00 5 C005 has 1608 536 536 0.00 6 C006 has 513 171 171 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1772 589 589 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1662 554 554 0.00 12 C012 has 84 28 28 0.00 13 C013 has 468 156 156 0.00 14 C014 has 123 41 41 1.26 Total of13120 atoms and 4365 groups and 4360 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3836 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1267 Number of atoms = 3836 Number of groups = 1272 Number of bonds = 3829 Number of angles = 1371 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1269 Number of HB donors = 2516 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1267 Number of atoms = 3836 Number of groups = 1272 Number of bonds = 3829 Number of angles = 1371 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1269 Number of HB donors = 2516 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.748" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1267" Evaluating: 1267-7 Parameter: NUMWAT <- "1260" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1260" Comparing "1081" and "1260". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.748" Parameter: BOX -> "33.748" Parameter: BOX -> "33.748" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.74800 B = 33.74800 C = 33.74800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6927 2 1 -1 0 -1 3.1718 3 1 -1 1 -1 6.4880 4 1 0 -1 -1 4.3019 5 1 0 0 -1 1.2807 6 1 0 1 -1 5.0765 7 1 -1 -1 0 5.2679 8 1 -1 0 0 1.9684 9 1 -1 1 0 5.8983 10 1 0 -1 0 2.5819 11 1 0 1 0 2.5819 12 1 -1 -1 1 5.2748 13 1 -1 0 1 3.5873 14 1 -1 1 1 5.9290 15 1 0 -1 1 5.0765 16 1 0 0 1 1.2807 17 1 0 1 1 4.3019 18 1 1 1 1 6.6927 19 1 1 0 1 3.1718 20 1 1 -1 1 6.4880 21 1 1 1 0 5.2679 22 1 1 0 0 1.9684 23 1 1 -1 0 5.8983 24 1 1 1 -1 5.2748 25 1 1 0 -1 3.5873 26 1 1 -1 -1 5.9290 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3762 atoms have been selected out of 3836 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 942 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 423 141 141 0.00 2 C002 has 714 238 238 0.00 3 C003 has 105 35 35 0.41 4 C004 has 591 197 197 0.00 5 C005 has 1611 537 537 0.00 6 C006 has 510 170 170 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1772 589 589 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1662 554 554 0.00 12 C012 has 84 28 28 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.25 Total of13120 atoms and 4365 groups and 4360 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3836 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1266 Number of atoms = 3833 Number of groups = 1271 Number of bonds = 3826 Number of angles = 1370 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1268 Number of HB donors = 2514 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1266 Number of atoms = 3833 Number of groups = 1271 Number of bonds = 3826 Number of angles = 1370 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1268 Number of HB donors = 2514 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.746" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1266" Evaluating: 1266-7 Parameter: NUMWAT <- "1259" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1259" Comparing "1081" and "1259". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.746" Parameter: BOX -> "33.746" Parameter: BOX -> "33.746" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.74600 B = 33.74600 C = 33.74600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6906 2 1 -1 0 -1 3.1691 3 1 -1 1 -1 6.4845 4 1 0 -1 -1 4.3031 5 1 0 0 -1 1.2789 6 1 0 1 -1 5.0742 7 1 -1 -1 0 5.2652 8 1 -1 0 0 1.9665 9 1 -1 1 0 5.8962 10 1 0 -1 0 2.5799 11 1 0 1 0 2.5799 12 1 -1 -1 1 5.2716 13 1 -1 0 1 3.5850 14 1 -1 1 1 5.9261 15 1 0 -1 1 5.0742 16 1 0 0 1 1.2789 17 1 0 1 1 4.3031 18 1 1 1 1 6.6906 19 1 1 0 1 3.1691 20 1 1 -1 1 6.4845 21 1 1 1 0 5.2652 22 1 1 0 0 1.9665 23 1 1 -1 0 5.8962 24 1 1 1 -1 5.2716 25 1 1 0 -1 3.5850 26 1 1 -1 -1 5.9261 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3759 atoms have been selected out of 3833 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 717 239 239 0.00 3 C003 has 105 35 35 0.41 4 C004 has 591 197 197 0.00 5 C005 has 1605 535 535 0.00 6 C006 has 510 170 170 0.00 7 C007 has 726 242 242 0.00 8 C008 has 1769 588 588 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1662 554 554 0.00 12 C012 has 84 28 28 0.00 13 C013 has 468 156 156 0.00 14 C014 has 123 41 41 1.25 Total of13108 atoms and 4361 groups and 4356 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3833 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1266 Number of atoms = 3833 Number of groups = 1271 Number of bonds = 3826 Number of angles = 1370 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1268 Number of HB donors = 2514 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1266 Number of atoms = 3833 Number of groups = 1271 Number of bonds = 3826 Number of angles = 1370 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1268 Number of HB donors = 2514 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.744" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1266" Evaluating: 1266-7 Parameter: NUMWAT <- "1259" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1259" Comparing "1081" and "1259". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.744" Parameter: BOX -> "33.744" Parameter: BOX -> "33.744" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.74400 B = 33.74400 C = 33.74400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6886 2 1 -1 0 -1 3.1664 3 1 -1 1 -1 6.4811 4 1 0 -1 -1 4.3044 5 1 0 0 -1 1.2771 6 1 0 1 -1 5.0718 7 1 -1 -1 0 5.2625 8 1 -1 0 0 1.9646 9 1 -1 1 0 5.8942 10 1 0 -1 0 2.5779 11 1 0 1 0 2.5779 12 1 -1 -1 1 5.2684 13 1 -1 0 1 3.5826 14 1 -1 1 1 5.9233 15 1 0 -1 1 5.0718 16 1 0 0 1 1.2771 17 1 0 1 1 4.3044 18 1 1 1 1 6.6886 19 1 1 0 1 3.1664 20 1 1 -1 1 6.4811 21 1 1 1 0 5.2625 22 1 1 0 0 1.9646 23 1 1 -1 0 5.8942 24 1 1 1 -1 5.2684 25 1 1 0 -1 3.5826 26 1 1 -1 -1 5.9233 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3759 atoms have been selected out of 3833 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 717 239 239 0.00 3 C003 has 105 35 35 0.41 4 C004 has 591 197 197 0.00 5 C005 has 1605 535 535 0.00 6 C006 has 510 170 170 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1769 588 588 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1662 554 554 0.00 12 C012 has 84 28 28 0.00 13 C013 has 468 156 156 0.00 14 C014 has 126 42 42 1.25 Total of13114 atoms and 4363 groups and 4358 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3833 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1266 Number of atoms = 3833 Number of groups = 1271 Number of bonds = 3826 Number of angles = 1370 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1268 Number of HB donors = 2514 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1266 Number of atoms = 3833 Number of groups = 1271 Number of bonds = 3826 Number of angles = 1370 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1268 Number of HB donors = 2514 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.742" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1266" Evaluating: 1266-7 Parameter: NUMWAT <- "1259" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1259" Comparing "1081" and "1259". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.742" Parameter: BOX -> "33.742" Parameter: BOX -> "33.742" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.74200 B = 33.74200 C = 33.74200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6866 2 1 -1 0 -1 3.1636 3 1 -1 1 -1 6.4776 4 1 0 -1 -1 4.3057 5 1 0 0 -1 1.2753 6 1 0 1 -1 5.0694 7 1 -1 -1 0 5.2598 8 1 -1 0 0 1.9627 9 1 -1 1 0 5.8921 10 1 0 -1 0 2.5759 11 1 0 1 0 2.5759 12 1 -1 -1 1 5.2652 13 1 -1 0 1 3.5802 14 1 -1 1 1 5.9205 15 1 0 -1 1 5.0694 16 1 0 0 1 1.2753 17 1 0 1 1 4.3057 18 1 1 1 1 6.6866 19 1 1 0 1 3.1636 20 1 1 -1 1 6.4776 21 1 1 1 0 5.2598 22 1 1 0 0 1.9627 23 1 1 -1 0 5.8921 24 1 1 1 -1 5.2652 25 1 1 0 -1 3.5802 26 1 1 -1 -1 5.9205 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3759 atoms have been selected out of 3833 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 717 239 239 0.00 3 C003 has 105 35 35 0.41 4 C004 has 591 197 197 0.00 5 C005 has 1605 535 535 0.00 6 C006 has 510 170 170 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1769 588 588 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1662 554 554 0.00 12 C012 has 84 28 28 0.00 13 C013 has 468 156 156 0.00 14 C014 has 126 42 42 1.25 Total of13114 atoms and 4363 groups and 4358 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3833 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1266 Number of atoms = 3833 Number of groups = 1271 Number of bonds = 3826 Number of angles = 1370 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1268 Number of HB donors = 2514 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1266 Number of atoms = 3833 Number of groups = 1271 Number of bonds = 3826 Number of angles = 1370 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1268 Number of HB donors = 2514 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.74" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1266" Evaluating: 1266-7 Parameter: NUMWAT <- "1259" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1259" Comparing "1081" and "1259". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.74" Parameter: BOX -> "33.74" Parameter: BOX -> "33.74" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.74000 B = 33.74000 C = 33.74000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6845 2 1 -1 0 -1 3.1609 3 1 -1 1 -1 6.4742 4 1 0 -1 -1 4.3070 5 1 0 0 -1 1.2735 6 1 0 1 -1 5.0670 7 1 -1 -1 0 5.2571 8 1 -1 0 0 1.9608 9 1 -1 1 0 5.8901 10 1 0 -1 0 2.5739 11 1 0 1 0 2.5739 12 1 -1 -1 1 5.2620 13 1 -1 0 1 3.5779 14 1 -1 1 1 5.9176 15 1 0 -1 1 5.0670 16 1 0 0 1 1.2735 17 1 0 1 1 4.3070 18 1 1 1 1 6.6845 19 1 1 0 1 3.1609 20 1 1 -1 1 6.4742 21 1 1 1 0 5.2571 22 1 1 0 0 1.9608 23 1 1 -1 0 5.8901 24 1 1 1 -1 5.2620 25 1 1 0 -1 3.5779 26 1 1 -1 -1 5.9176 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3759 atoms have been selected out of 3833 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 723 241 241 0.00 3 C003 has 105 35 35 0.40 4 C004 has 591 197 197 0.00 5 C005 has 1605 535 535 0.00 6 C006 has 510 170 170 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1769 588 588 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1662 554 554 0.00 12 C012 has 84 28 28 0.00 13 C013 has 468 156 156 0.00 14 C014 has 126 42 42 1.25 Total of13120 atoms and 4365 groups and 4360 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3833 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1266 Number of atoms = 3833 Number of groups = 1271 Number of bonds = 3826 Number of angles = 1370 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1268 Number of HB donors = 2514 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1266 Number of atoms = 3833 Number of groups = 1271 Number of bonds = 3826 Number of angles = 1370 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1268 Number of HB donors = 2514 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.738" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1266" Evaluating: 1266-7 Parameter: NUMWAT <- "1259" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1259" Comparing "1081" and "1259". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.738" Parameter: BOX -> "33.738" Parameter: BOX -> "33.738" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.73800 B = 33.73800 C = 33.73800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6825 2 1 -1 0 -1 3.1581 3 1 -1 1 -1 6.4708 4 1 0 -1 -1 4.3083 5 1 0 0 -1 1.2716 6 1 0 1 -1 5.0647 7 1 -1 -1 0 5.2544 8 1 -1 0 0 1.9589 9 1 -1 1 0 5.8881 10 1 0 -1 0 2.5719 11 1 0 1 0 2.5719 12 1 -1 -1 1 5.2588 13 1 -1 0 1 3.5755 14 1 -1 1 1 5.9148 15 1 0 -1 1 5.0647 16 1 0 0 1 1.2716 17 1 0 1 1 4.3083 18 1 1 1 1 6.6825 19 1 1 0 1 3.1581 20 1 1 -1 1 6.4708 21 1 1 1 0 5.2544 22 1 1 0 0 1.9589 23 1 1 -1 0 5.8881 24 1 1 1 -1 5.2588 25 1 1 0 -1 3.5755 26 1 1 -1 -1 5.9148 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3759 atoms have been selected out of 3833 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 723 241 241 0.00 3 C003 has 105 35 35 0.40 4 C004 has 591 197 197 0.00 5 C005 has 1605 535 535 0.00 6 C006 has 510 170 170 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1769 588 588 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1662 554 554 0.00 12 C012 has 84 28 28 0.00 13 C013 has 468 156 156 0.00 14 C014 has 126 42 42 1.24 Total of13120 atoms and 4365 groups and 4360 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3833 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1266 Number of atoms = 3833 Number of groups = 1271 Number of bonds = 3826 Number of angles = 1370 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1268 Number of HB donors = 2514 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1266 Number of atoms = 3833 Number of groups = 1271 Number of bonds = 3826 Number of angles = 1370 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1268 Number of HB donors = 2514 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.736" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1266" Evaluating: 1266-7 Parameter: NUMWAT <- "1259" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1259" Comparing "1081" and "1259". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.736" Parameter: BOX -> "33.736" Parameter: BOX -> "33.736" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.73600 B = 33.73600 C = 33.73600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6805 2 1 -1 0 -1 3.1554 3 1 -1 1 -1 6.4673 4 1 0 -1 -1 4.3096 5 1 0 0 -1 1.2698 6 1 0 1 -1 5.0623 7 1 -1 -1 0 5.2517 8 1 -1 0 0 1.9571 9 1 -1 1 0 5.8860 10 1 0 -1 0 2.5699 11 1 0 1 0 2.5699 12 1 -1 -1 1 5.2556 13 1 -1 0 1 3.5732 14 1 -1 1 1 5.9120 15 1 0 -1 1 5.0623 16 1 0 0 1 1.2698 17 1 0 1 1 4.3096 18 1 1 1 1 6.6805 19 1 1 0 1 3.1554 20 1 1 -1 1 6.4673 21 1 1 1 0 5.2517 22 1 1 0 0 1.9571 23 1 1 -1 0 5.8860 24 1 1 1 -1 5.2556 25 1 1 0 -1 3.5732 26 1 1 -1 -1 5.9120 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3759 atoms have been selected out of 3833 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 726 242 242 0.00 3 C003 has 105 35 35 0.40 4 C004 has 591 197 197 0.00 5 C005 has 1605 535 535 0.00 6 C006 has 510 170 170 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1769 588 588 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1662 554 554 0.00 12 C012 has 84 28 28 0.00 13 C013 has 468 156 156 0.00 14 C014 has 126 42 42 1.24 Total of13123 atoms and 4366 groups and 4361 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3833 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1266 Number of atoms = 3833 Number of groups = 1271 Number of bonds = 3826 Number of angles = 1370 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1268 Number of HB donors = 2514 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1266 Number of atoms = 3833 Number of groups = 1271 Number of bonds = 3826 Number of angles = 1370 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1268 Number of HB donors = 2514 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.734" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1266" Evaluating: 1266-7 Parameter: NUMWAT <- "1259" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1259" Comparing "1081" and "1259". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.734" Parameter: BOX -> "33.734" Parameter: BOX -> "33.734" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.73400 B = 33.73400 C = 33.73400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6785 2 1 -1 0 -1 3.1526 3 1 -1 1 -1 6.4639 4 1 0 -1 -1 4.3108 5 1 0 0 -1 1.2680 6 1 0 1 -1 5.0599 7 1 -1 -1 0 5.2490 8 1 -1 0 0 1.9552 9 1 -1 1 0 5.8840 10 1 0 -1 0 2.5679 11 1 0 1 0 2.5679 12 1 -1 -1 1 5.2524 13 1 -1 0 1 3.5708 14 1 -1 1 1 5.9092 15 1 0 -1 1 5.0599 16 1 0 0 1 1.2680 17 1 0 1 1 4.3108 18 1 1 1 1 6.6785 19 1 1 0 1 3.1526 20 1 1 -1 1 6.4639 21 1 1 1 0 5.2490 22 1 1 0 0 1.9552 23 1 1 -1 0 5.8840 24 1 1 1 -1 5.2524 25 1 1 0 -1 3.5708 26 1 1 -1 -1 5.9092 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3759 atoms have been selected out of 3833 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 729 243 243 0.00 3 C003 has 105 35 35 0.40 4 C004 has 591 197 197 0.00 5 C005 has 1605 535 535 0.00 6 C006 has 510 170 170 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1769 588 588 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1662 554 554 0.00 12 C012 has 84 28 28 0.00 13 C013 has 468 156 156 0.00 14 C014 has 126 42 42 1.24 Total of13126 atoms and 4367 groups and 4362 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3833 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1266 Number of atoms = 3833 Number of groups = 1271 Number of bonds = 3826 Number of angles = 1370 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1268 Number of HB donors = 2514 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1266 Number of atoms = 3833 Number of groups = 1271 Number of bonds = 3826 Number of angles = 1370 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1268 Number of HB donors = 2514 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.732" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1266" Evaluating: 1266-7 Parameter: NUMWAT <- "1259" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1259" Comparing "1081" and "1259". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.732" Parameter: BOX -> "33.732" Parameter: BOX -> "33.732" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.73200 B = 33.73200 C = 33.73200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6765 2 1 -1 0 -1 3.1499 3 1 -1 1 -1 6.4604 4 1 0 -1 -1 4.3121 5 1 0 0 -1 1.2662 6 1 0 1 -1 5.0576 7 1 -1 -1 0 5.2463 8 1 -1 0 0 1.9533 9 1 -1 1 0 5.8819 10 1 0 -1 0 2.5659 11 1 0 1 0 2.5659 12 1 -1 -1 1 5.2492 13 1 -1 0 1 3.5685 14 1 -1 1 1 5.9063 15 1 0 -1 1 5.0576 16 1 0 0 1 1.2662 17 1 0 1 1 4.3121 18 1 1 1 1 6.6765 19 1 1 0 1 3.1499 20 1 1 -1 1 6.4604 21 1 1 1 0 5.2463 22 1 1 0 0 1.9533 23 1 1 -1 0 5.8819 24 1 1 1 -1 5.2492 25 1 1 0 -1 3.5685 26 1 1 -1 -1 5.9063 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3759 atoms have been selected out of 3833 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 729 243 243 0.00 3 C003 has 105 35 35 0.40 4 C004 has 591 197 197 0.00 5 C005 has 1605 535 535 0.00 6 C006 has 510 170 170 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1769 588 588 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1662 554 554 0.00 12 C012 has 84 28 28 0.00 13 C013 has 468 156 156 0.00 14 C014 has 126 42 42 1.24 Total of13126 atoms and 4367 groups and 4362 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3833 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1266 Number of atoms = 3833 Number of groups = 1271 Number of bonds = 3826 Number of angles = 1370 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1268 Number of HB donors = 2514 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1266 Number of atoms = 3833 Number of groups = 1271 Number of bonds = 3826 Number of angles = 1370 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1268 Number of HB donors = 2514 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.73" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1266" Evaluating: 1266-7 Parameter: NUMWAT <- "1259" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1259" Comparing "1081" and "1259". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.73" Parameter: BOX -> "33.73" Parameter: BOX -> "33.73" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.73000 B = 33.73000 C = 33.73000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6744 2 1 -1 0 -1 3.1471 3 1 -1 1 -1 6.4570 4 1 0 -1 -1 4.3134 5 1 0 0 -1 1.2644 6 1 0 1 -1 5.0552 7 1 -1 -1 0 5.2436 8 1 -1 0 0 1.9514 9 1 -1 1 0 5.8799 10 1 0 -1 0 2.5639 11 1 0 1 0 2.5639 12 1 -1 -1 1 5.2460 13 1 -1 0 1 3.5661 14 1 -1 1 1 5.9035 15 1 0 -1 1 5.0552 16 1 0 0 1 1.2644 17 1 0 1 1 4.3134 18 1 1 1 1 6.6744 19 1 1 0 1 3.1471 20 1 1 -1 1 6.4570 21 1 1 1 0 5.2436 22 1 1 0 0 1.9514 23 1 1 -1 0 5.8799 24 1 1 1 -1 5.2460 25 1 1 0 -1 3.5661 26 1 1 -1 -1 5.9035 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3759 atoms have been selected out of 3833 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 554 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1025 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1197 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1237 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 735 245 245 0.00 3 C003 has 108 36 36 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1602 534 534 0.00 6 C006 has 468 156 156 0.00 7 C007 has 726 242 242 0.00 8 C008 has 1763 586 586 0.00 9 C009 has 495 165 165 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 81 27 27 0.00 13 C013 has 468 156 156 0.00 14 C014 has 129 43 43 0.00 Total of13114 atoms and 4363 groups and 4358 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 12 atoms have been selected out of 3833 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 4 residues deleted. DELTIC: 12 bonds deleted DELTIC: 4 angles deleted DELTIC: 8 donors deleted DELTIC: 4 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1262 Number of atoms = 3821 Number of groups = 1267 Number of bonds = 3814 Number of angles = 1366 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1264 Number of HB donors = 2506 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1262 Number of atoms = 3821 Number of groups = 1267 Number of bonds = 3814 Number of angles = 1366 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1264 Number of HB donors = 2506 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.728" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1262" Evaluating: 1262-7 Parameter: NUMWAT <- "1255" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1255" Comparing "1081" and "1255". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.728" Parameter: BOX -> "33.728" Parameter: BOX -> "33.728" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.72800 B = 33.72800 C = 33.72800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6724 2 1 -1 0 -1 3.1444 3 1 -1 1 -1 6.4536 4 1 0 -1 -1 4.3147 5 1 0 0 -1 1.2626 6 1 0 1 -1 5.0528 7 1 -1 -1 0 5.2409 8 1 -1 0 0 1.9495 9 1 -1 1 0 5.8779 10 1 0 -1 0 2.5619 11 1 0 1 0 2.5619 12 1 -1 -1 1 5.2428 13 1 -1 0 1 3.5637 14 1 -1 1 1 5.9007 15 1 0 -1 1 5.0528 16 1 0 0 1 1.2626 17 1 0 1 1 4.3147 18 1 1 1 1 6.6724 19 1 1 0 1 3.1444 20 1 1 -1 1 6.4536 21 1 1 1 0 5.2409 22 1 1 0 0 1.9495 23 1 1 -1 0 5.8779 24 1 1 1 -1 5.2428 25 1 1 0 -1 3.5637 26 1 1 -1 -1 5.9007 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3747 atoms have been selected out of 3821 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 729 243 243 0.00 3 C003 has 105 35 35 0.39 4 C004 has 585 195 195 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 462 154 154 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1754 583 583 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 81 27 27 0.00 13 C013 has 465 155 155 0.00 14 C014 has 126 42 42 1.42 Total of13006 atoms and 4327 groups and 4322 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3821 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1262 Number of atoms = 3821 Number of groups = 1267 Number of bonds = 3814 Number of angles = 1366 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1264 Number of HB donors = 2506 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1262 Number of atoms = 3821 Number of groups = 1267 Number of bonds = 3814 Number of angles = 1366 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1264 Number of HB donors = 2506 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.726" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1262" Evaluating: 1262-7 Parameter: NUMWAT <- "1255" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1255" Comparing "1081" and "1255". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.726" Parameter: BOX -> "33.726" Parameter: BOX -> "33.726" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.72600 B = 33.72600 C = 33.72600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6704 2 1 -1 0 -1 3.1417 3 1 -1 1 -1 6.4501 4 1 0 -1 -1 4.3160 5 1 0 0 -1 1.2608 6 1 0 1 -1 5.0504 7 1 -1 -1 0 5.2382 8 1 -1 0 0 1.9476 9 1 -1 1 0 5.8758 10 1 0 -1 0 2.5599 11 1 0 1 0 2.5599 12 1 -1 -1 1 5.2396 13 1 -1 0 1 3.5614 14 1 -1 1 1 5.8979 15 1 0 -1 1 5.0504 16 1 0 0 1 1.2608 17 1 0 1 1 4.3160 18 1 1 1 1 6.6704 19 1 1 0 1 3.1417 20 1 1 -1 1 6.4501 21 1 1 1 0 5.2382 22 1 1 0 0 1.9476 23 1 1 -1 0 5.8758 24 1 1 1 -1 5.2396 25 1 1 0 -1 3.5614 26 1 1 -1 -1 5.8979 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3747 atoms have been selected out of 3821 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 729 243 243 0.00 3 C003 has 105 35 35 0.39 4 C004 has 585 195 195 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 462 154 154 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1754 583 583 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 81 27 27 0.00 13 C013 has 468 156 156 0.00 14 C014 has 126 42 42 1.42 Total of13009 atoms and 4328 groups and 4323 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3821 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1262 Number of atoms = 3821 Number of groups = 1267 Number of bonds = 3814 Number of angles = 1366 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1264 Number of HB donors = 2506 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1262 Number of atoms = 3821 Number of groups = 1267 Number of bonds = 3814 Number of angles = 1366 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1264 Number of HB donors = 2506 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.724" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1262" Evaluating: 1262-7 Parameter: NUMWAT <- "1255" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1255" Comparing "1081" and "1255". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.724" Parameter: BOX -> "33.724" Parameter: BOX -> "33.724" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.72400 B = 33.72400 C = 33.72400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6684 2 1 -1 0 -1 3.1389 3 1 -1 1 -1 6.4467 4 1 0 -1 -1 4.3173 5 1 0 0 -1 1.2589 6 1 0 1 -1 5.0481 7 1 -1 -1 0 5.2355 8 1 -1 0 0 1.9457 9 1 -1 1 0 5.8738 10 1 0 -1 0 2.5579 11 1 0 1 0 2.5579 12 1 -1 -1 1 5.2365 13 1 -1 0 1 3.5590 14 1 -1 1 1 5.8950 15 1 0 -1 1 5.0481 16 1 0 0 1 1.2589 17 1 0 1 1 4.3173 18 1 1 1 1 6.6684 19 1 1 0 1 3.1389 20 1 1 -1 1 6.4467 21 1 1 1 0 5.2355 22 1 1 0 0 1.9457 23 1 1 -1 0 5.8738 24 1 1 1 -1 5.2365 25 1 1 0 -1 3.5590 26 1 1 -1 -1 5.8950 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3747 atoms have been selected out of 3821 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 729 243 243 0.00 3 C003 has 105 35 35 0.39 4 C004 has 585 195 195 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 462 154 154 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1754 583 583 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 81 27 27 0.00 13 C013 has 468 156 156 0.00 14 C014 has 126 42 42 1.42 Total of13009 atoms and 4328 groups and 4323 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3821 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1262 Number of atoms = 3821 Number of groups = 1267 Number of bonds = 3814 Number of angles = 1366 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1264 Number of HB donors = 2506 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1262 Number of atoms = 3821 Number of groups = 1267 Number of bonds = 3814 Number of angles = 1366 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1264 Number of HB donors = 2506 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.722" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1262" Evaluating: 1262-7 Parameter: NUMWAT <- "1255" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1255" Comparing "1081" and "1255". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.722" Parameter: BOX -> "33.722" Parameter: BOX -> "33.722" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.72200 B = 33.72200 C = 33.72200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6664 2 1 -1 0 -1 3.1362 3 1 -1 1 -1 6.4432 4 1 0 -1 -1 4.3186 5 1 0 0 -1 1.2571 6 1 0 1 -1 5.0457 7 1 -1 -1 0 5.2328 8 1 -1 0 0 1.9438 9 1 -1 1 0 5.8718 10 1 0 -1 0 2.5559 11 1 0 1 0 2.5559 12 1 -1 -1 1 5.2333 13 1 -1 0 1 3.5567 14 1 -1 1 1 5.8922 15 1 0 -1 1 5.0457 16 1 0 0 1 1.2571 17 1 0 1 1 4.3186 18 1 1 1 1 6.6664 19 1 1 0 1 3.1362 20 1 1 -1 1 6.4432 21 1 1 1 0 5.2328 22 1 1 0 0 1.9438 23 1 1 -1 0 5.8718 24 1 1 1 -1 5.2333 25 1 1 0 -1 3.5567 26 1 1 -1 -1 5.8922 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3747 atoms have been selected out of 3821 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 952 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 729 243 243 0.00 3 C003 has 105 35 35 0.39 4 C004 has 582 194 194 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 465 155 155 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1754 583 583 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 81 27 27 0.00 13 C013 has 468 156 156 0.00 14 C014 has 126 42 42 1.42 Total of13015 atoms and 4330 groups and 4325 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3821 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1261 Number of atoms = 3818 Number of groups = 1266 Number of bonds = 3811 Number of angles = 1365 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1263 Number of HB donors = 2504 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1261 Number of atoms = 3818 Number of groups = 1266 Number of bonds = 3811 Number of angles = 1365 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1263 Number of HB donors = 2504 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.72" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1261" Evaluating: 1261-7 Parameter: NUMWAT <- "1254" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1254" Comparing "1081" and "1254". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.72" Parameter: BOX -> "33.72" Parameter: BOX -> "33.72" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.72000 B = 33.72000 C = 33.72000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6644 2 1 -1 0 -1 3.1334 3 1 -1 1 -1 6.4398 4 1 0 -1 -1 4.3199 5 1 0 0 -1 1.2553 6 1 0 1 -1 5.0433 7 1 -1 -1 0 5.2301 8 1 -1 0 0 1.9419 9 1 -1 1 0 5.8698 10 1 0 -1 0 2.5539 11 1 0 1 0 2.5539 12 1 -1 -1 1 5.2301 13 1 -1 0 1 3.5543 14 1 -1 1 1 5.8894 15 1 0 -1 1 5.0433 16 1 0 0 1 1.2553 17 1 0 1 1 4.3199 18 1 1 1 1 6.6644 19 1 1 0 1 3.1334 20 1 1 -1 1 6.4398 21 1 1 1 0 5.2301 22 1 1 0 0 1.9419 23 1 1 -1 0 5.8698 24 1 1 1 -1 5.2301 25 1 1 0 -1 3.5543 26 1 1 -1 -1 5.8894 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3744 atoms have been selected out of 3818 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 729 243 243 0.00 3 C003 has 105 35 35 0.38 4 C004 has 582 194 194 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1754 583 583 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 81 27 27 0.00 13 C013 has 468 156 156 0.00 14 C014 has 126 42 42 1.42 Total of13006 atoms and 4327 groups and 4322 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3818 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1261 Number of atoms = 3818 Number of groups = 1266 Number of bonds = 3811 Number of angles = 1365 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1263 Number of HB donors = 2504 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1261 Number of atoms = 3818 Number of groups = 1266 Number of bonds = 3811 Number of angles = 1365 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1263 Number of HB donors = 2504 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.718" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1261" Evaluating: 1261-7 Parameter: NUMWAT <- "1254" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1254" Comparing "1081" and "1254". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.718" Parameter: BOX -> "33.718" Parameter: BOX -> "33.718" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.71800 B = 33.71800 C = 33.71800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6624 2 1 -1 0 -1 3.1307 3 1 -1 1 -1 6.4364 4 1 0 -1 -1 4.3212 5 1 0 0 -1 1.2535 6 1 0 1 -1 5.0410 7 1 -1 -1 0 5.2274 8 1 -1 0 0 1.9400 9 1 -1 1 0 5.8677 10 1 0 -1 0 2.5519 11 1 0 1 0 2.5519 12 1 -1 -1 1 5.2269 13 1 -1 0 1 3.5520 14 1 -1 1 1 5.8866 15 1 0 -1 1 5.0410 16 1 0 0 1 1.2535 17 1 0 1 1 4.3212 18 1 1 1 1 6.6624 19 1 1 0 1 3.1307 20 1 1 -1 1 6.4364 21 1 1 1 0 5.2274 22 1 1 0 0 1.9400 23 1 1 -1 0 5.8677 24 1 1 1 -1 5.2269 25 1 1 0 -1 3.5520 26 1 1 -1 -1 5.8866 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3744 atoms have been selected out of 3818 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 729 243 243 0.00 3 C003 has 105 35 35 0.38 4 C004 has 582 194 194 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1754 583 583 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 81 27 27 0.00 13 C013 has 468 156 156 0.00 14 C014 has 126 42 42 1.41 Total of13006 atoms and 4327 groups and 4322 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3818 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1261 Number of atoms = 3818 Number of groups = 1266 Number of bonds = 3811 Number of angles = 1365 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1263 Number of HB donors = 2504 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1261 Number of atoms = 3818 Number of groups = 1266 Number of bonds = 3811 Number of angles = 1365 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1263 Number of HB donors = 2504 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.716" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1261" Evaluating: 1261-7 Parameter: NUMWAT <- "1254" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1254" Comparing "1081" and "1254". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.716" Parameter: BOX -> "33.716" Parameter: BOX -> "33.716" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.71600 B = 33.71600 C = 33.71600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6604 2 1 -1 0 -1 3.1279 3 1 -1 1 -1 6.4329 4 1 0 -1 -1 4.3225 5 1 0 0 -1 1.2517 6 1 0 1 -1 5.0386 7 1 -1 -1 0 5.2247 8 1 -1 0 0 1.9381 9 1 -1 1 0 5.8657 10 1 0 -1 0 2.5499 11 1 0 1 0 2.5499 12 1 -1 -1 1 5.2237 13 1 -1 0 1 3.5496 14 1 -1 1 1 5.8837 15 1 0 -1 1 5.0386 16 1 0 0 1 1.2517 17 1 0 1 1 4.3225 18 1 1 1 1 6.6604 19 1 1 0 1 3.1279 20 1 1 -1 1 6.4329 21 1 1 1 0 5.2247 22 1 1 0 0 1.9381 23 1 1 -1 0 5.8657 24 1 1 1 -1 5.2237 25 1 1 0 -1 3.5496 26 1 1 -1 -1 5.8837 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3744 atoms have been selected out of 3818 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 729 243 243 0.00 3 C003 has 105 35 35 0.38 4 C004 has 582 194 194 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1757 584 584 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 81 27 27 0.00 13 C013 has 468 156 156 0.00 14 C014 has 126 42 42 1.41 Total of13009 atoms and 4328 groups and 4323 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3818 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1261 Number of atoms = 3818 Number of groups = 1266 Number of bonds = 3811 Number of angles = 1365 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1263 Number of HB donors = 2504 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1261 Number of atoms = 3818 Number of groups = 1266 Number of bonds = 3811 Number of angles = 1365 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1263 Number of HB donors = 2504 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.714" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1261" Evaluating: 1261-7 Parameter: NUMWAT <- "1254" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1254" Comparing "1081" and "1254". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.714" Parameter: BOX -> "33.714" Parameter: BOX -> "33.714" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.71400 B = 33.71400 C = 33.71400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6583 2 1 -1 0 -1 3.1252 3 1 -1 1 -1 6.4295 4 1 0 -1 -1 4.3238 5 1 0 0 -1 1.2499 6 1 0 1 -1 5.0362 7 1 -1 -1 0 5.2220 8 1 -1 0 0 1.9362 9 1 -1 1 0 5.8637 10 1 0 -1 0 2.5479 11 1 0 1 0 2.5479 12 1 -1 -1 1 5.2205 13 1 -1 0 1 3.5473 14 1 -1 1 1 5.8809 15 1 0 -1 1 5.0362 16 1 0 0 1 1.2499 17 1 0 1 1 4.3238 18 1 1 1 1 6.6583 19 1 1 0 1 3.1252 20 1 1 -1 1 6.4295 21 1 1 1 0 5.2220 22 1 1 0 0 1.9362 23 1 1 -1 0 5.8637 24 1 1 1 -1 5.2205 25 1 1 0 -1 3.5473 26 1 1 -1 -1 5.8809 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3744 atoms have been selected out of 3818 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 729 243 243 0.00 3 C003 has 105 35 35 0.38 4 C004 has 582 194 194 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1757 584 584 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 81 27 27 0.00 13 C013 has 468 156 156 0.00 14 C014 has 126 42 42 1.41 Total of13009 atoms and 4328 groups and 4323 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3818 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1261 Number of atoms = 3818 Number of groups = 1266 Number of bonds = 3811 Number of angles = 1365 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1263 Number of HB donors = 2504 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1261 Number of atoms = 3818 Number of groups = 1266 Number of bonds = 3811 Number of angles = 1365 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1263 Number of HB donors = 2504 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.712" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1261" Evaluating: 1261-7 Parameter: NUMWAT <- "1254" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1254" Comparing "1081" and "1254". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.712" Parameter: BOX -> "33.712" Parameter: BOX -> "33.712" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.71200 B = 33.71200 C = 33.71200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6563 2 1 -1 0 -1 3.1225 3 1 -1 1 -1 6.4260 4 1 0 -1 -1 4.3251 5 1 0 0 -1 1.2481 6 1 0 1 -1 5.0339 7 1 -1 -1 0 5.2193 8 1 -1 0 0 1.9344 9 1 -1 1 0 5.8616 10 1 0 -1 0 2.5459 11 1 0 1 0 2.5459 12 1 -1 -1 1 5.2173 13 1 -1 0 1 3.5449 14 1 -1 1 1 5.8781 15 1 0 -1 1 5.0339 16 1 0 0 1 1.2481 17 1 0 1 1 4.3251 18 1 1 1 1 6.6563 19 1 1 0 1 3.1225 20 1 1 -1 1 6.4260 21 1 1 1 0 5.2193 22 1 1 0 0 1.9344 23 1 1 -1 0 5.8616 24 1 1 1 -1 5.2173 25 1 1 0 -1 3.5449 26 1 1 -1 -1 5.8781 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3744 atoms have been selected out of 3818 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.38 4 C004 has 582 194 194 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1760 585 585 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 81 27 27 0.00 13 C013 has 468 156 156 0.00 14 C014 has 126 42 42 1.41 Total of13018 atoms and 4331 groups and 4326 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3818 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1261 Number of atoms = 3818 Number of groups = 1266 Number of bonds = 3811 Number of angles = 1365 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1263 Number of HB donors = 2504 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1261 Number of atoms = 3818 Number of groups = 1266 Number of bonds = 3811 Number of angles = 1365 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1263 Number of HB donors = 2504 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.71" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1261" Evaluating: 1261-7 Parameter: NUMWAT <- "1254" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1254" Comparing "1081" and "1254". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.71" Parameter: BOX -> "33.71" Parameter: BOX -> "33.71" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.71000 B = 33.71000 C = 33.71000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6543 2 1 -1 0 -1 3.1197 3 1 -1 1 -1 6.4226 4 1 0 -1 -1 4.3264 5 1 0 0 -1 1.2463 6 1 0 1 -1 5.0315 7 1 -1 -1 0 5.2166 8 1 -1 0 0 1.9325 9 1 -1 1 0 5.8596 10 1 0 -1 0 2.5439 11 1 0 1 0 2.5439 12 1 -1 -1 1 5.2141 13 1 -1 0 1 3.5426 14 1 -1 1 1 5.8753 15 1 0 -1 1 5.0315 16 1 0 0 1 1.2463 17 1 0 1 1 4.3264 18 1 1 1 1 6.6543 19 1 1 0 1 3.1197 20 1 1 -1 1 6.4226 21 1 1 1 0 5.2166 22 1 1 0 0 1.9325 23 1 1 -1 0 5.8596 24 1 1 1 -1 5.2141 25 1 1 0 -1 3.5426 26 1 1 -1 -1 5.8753 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3744 atoms have been selected out of 3818 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.37 4 C004 has 582 194 194 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1760 585 585 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 81 27 27 0.00 13 C013 has 468 156 156 0.00 14 C014 has 126 42 42 1.41 Total of13018 atoms and 4331 groups and 4326 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3818 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1261 Number of atoms = 3818 Number of groups = 1266 Number of bonds = 3811 Number of angles = 1365 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1263 Number of HB donors = 2504 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1261 Number of atoms = 3818 Number of groups = 1266 Number of bonds = 3811 Number of angles = 1365 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1263 Number of HB donors = 2504 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.708" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1261" Evaluating: 1261-7 Parameter: NUMWAT <- "1254" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1254" Comparing "1081" and "1254". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.708" Parameter: BOX -> "33.708" Parameter: BOX -> "33.708" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.70800 B = 33.70800 C = 33.70800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6523 2 1 -1 0 -1 3.1170 3 1 -1 1 -1 6.4191 4 1 0 -1 -1 4.3277 5 1 0 0 -1 1.2445 6 1 0 1 -1 5.0292 7 1 -1 -1 0 5.2139 8 1 -1 0 0 1.9306 9 1 -1 1 0 5.8576 10 1 0 -1 0 2.5419 11 1 0 1 0 2.5419 12 1 -1 -1 1 5.2110 13 1 -1 0 1 3.5402 14 1 -1 1 1 5.8724 15 1 0 -1 1 5.0292 16 1 0 0 1 1.2445 17 1 0 1 1 4.3277 18 1 1 1 1 6.6523 19 1 1 0 1 3.1170 20 1 1 -1 1 6.4191 21 1 1 1 0 5.2139 22 1 1 0 0 1.9306 23 1 1 -1 0 5.8576 24 1 1 1 -1 5.2110 25 1 1 0 -1 3.5402 26 1 1 -1 -1 5.8724 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3744 atoms have been selected out of 3818 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.37 4 C004 has 582 194 194 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1763 586 586 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 81 27 27 0.00 13 C013 has 468 156 156 0.00 14 C014 has 126 42 42 1.40 Total of13021 atoms and 4332 groups and 4327 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3818 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1261 Number of atoms = 3818 Number of groups = 1266 Number of bonds = 3811 Number of angles = 1365 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1263 Number of HB donors = 2504 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1261 Number of atoms = 3818 Number of groups = 1266 Number of bonds = 3811 Number of angles = 1365 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1263 Number of HB donors = 2504 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.706" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1261" Evaluating: 1261-7 Parameter: NUMWAT <- "1254" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1254" Comparing "1081" and "1254". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.706" Parameter: BOX -> "33.706" Parameter: BOX -> "33.706" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.70600 B = 33.70600 C = 33.70600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6503 2 1 -1 0 -1 3.1142 3 1 -1 1 -1 6.4157 4 1 0 -1 -1 4.3291 5 1 0 0 -1 1.2427 6 1 0 1 -1 5.0268 7 1 -1 -1 0 5.2112 8 1 -1 0 0 1.9287 9 1 -1 1 0 5.8556 10 1 0 -1 0 2.5399 11 1 0 1 0 2.5399 12 1 -1 -1 1 5.2078 13 1 -1 0 1 3.5379 14 1 -1 1 1 5.8696 15 1 0 -1 1 5.0268 16 1 0 0 1 1.2427 17 1 0 1 1 4.3291 18 1 1 1 1 6.6503 19 1 1 0 1 3.1142 20 1 1 -1 1 6.4157 21 1 1 1 0 5.2112 22 1 1 0 0 1.9287 23 1 1 -1 0 5.8556 24 1 1 1 -1 5.2078 25 1 1 0 -1 3.5379 26 1 1 -1 -1 5.8696 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3744 atoms have been selected out of 3818 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.37 4 C004 has 582 194 194 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1763 586 586 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 81 27 27 0.00 13 C013 has 468 156 156 0.00 14 C014 has 126 42 42 1.40 Total of13021 atoms and 4332 groups and 4327 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3818 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1261 Number of atoms = 3818 Number of groups = 1266 Number of bonds = 3811 Number of angles = 1365 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1263 Number of HB donors = 2504 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1261 Number of atoms = 3818 Number of groups = 1266 Number of bonds = 3811 Number of angles = 1365 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1263 Number of HB donors = 2504 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.704" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1261" Evaluating: 1261-7 Parameter: NUMWAT <- "1254" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1254" Comparing "1081" and "1254". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.704" Parameter: BOX -> "33.704" Parameter: BOX -> "33.704" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.70400 B = 33.70400 C = 33.70400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6483 2 1 -1 0 -1 3.1115 3 1 -1 1 -1 6.4123 4 1 0 -1 -1 4.3304 5 1 0 0 -1 1.2408 6 1 0 1 -1 5.0244 7 1 -1 -1 0 5.2085 8 1 -1 0 0 1.9268 9 1 -1 1 0 5.8535 10 1 0 -1 0 2.5379 11 1 0 1 0 2.5379 12 1 -1 -1 1 5.2046 13 1 -1 0 1 3.5355 14 1 -1 1 1 5.8668 15 1 0 -1 1 5.0244 16 1 0 0 1 1.2408 17 1 0 1 1 4.3304 18 1 1 1 1 6.6483 19 1 1 0 1 3.1115 20 1 1 -1 1 6.4123 21 1 1 1 0 5.2085 22 1 1 0 0 1.9268 23 1 1 -1 0 5.8535 24 1 1 1 -1 5.2046 25 1 1 0 -1 3.5355 26 1 1 -1 -1 5.8668 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3744 atoms have been selected out of 3818 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.37 4 C004 has 582 194 194 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1763 586 586 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.40 Total of13024 atoms and 4333 groups and 4328 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3818 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1261 Number of atoms = 3818 Number of groups = 1266 Number of bonds = 3811 Number of angles = 1365 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1263 Number of HB donors = 2504 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1261 Number of atoms = 3818 Number of groups = 1266 Number of bonds = 3811 Number of angles = 1365 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1263 Number of HB donors = 2504 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.702" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1261" Evaluating: 1261-7 Parameter: NUMWAT <- "1254" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1254" Comparing "1081" and "1254". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.702" Parameter: BOX -> "33.702" Parameter: BOX -> "33.702" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.70200 B = 33.70200 C = 33.70200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6463 2 1 -1 0 -1 3.1088 3 1 -1 1 -1 6.4088 4 1 0 -1 -1 4.3317 5 1 0 0 -1 1.2390 6 1 0 1 -1 5.0221 7 1 -1 -1 0 5.2058 8 1 -1 0 0 1.9249 9 1 -1 1 0 5.8515 10 1 0 -1 0 2.5359 11 1 0 1 0 2.5359 12 1 -1 -1 1 5.2014 13 1 -1 0 1 3.5332 14 1 -1 1 1 5.8640 15 1 0 -1 1 5.0221 16 1 0 0 1 1.2390 17 1 0 1 1 4.3317 18 1 1 1 1 6.6463 19 1 1 0 1 3.1088 20 1 1 -1 1 6.4088 21 1 1 1 0 5.2058 22 1 1 0 0 1.9249 23 1 1 -1 0 5.8515 24 1 1 1 -1 5.2014 25 1 1 0 -1 3.5332 26 1 1 -1 -1 5.8640 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3744 atoms have been selected out of 3818 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.37 4 C004 has 582 194 194 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1763 586 586 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.40 Total of13024 atoms and 4333 groups and 4328 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3818 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1261 Number of atoms = 3818 Number of groups = 1266 Number of bonds = 3811 Number of angles = 1365 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1263 Number of HB donors = 2504 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1261 Number of atoms = 3818 Number of groups = 1266 Number of bonds = 3811 Number of angles = 1365 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1263 Number of HB donors = 2504 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.7" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1261" Evaluating: 1261-7 Parameter: NUMWAT <- "1254" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1254" Comparing "1081" and "1254". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.7" Parameter: BOX -> "33.7" Parameter: BOX -> "33.7" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.70000 B = 33.70000 C = 33.70000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6443 2 1 -1 0 -1 3.1060 3 1 -1 1 -1 6.4054 4 1 0 -1 -1 4.3330 5 1 0 0 -1 1.2372 6 1 0 1 -1 5.0197 7 1 -1 -1 0 5.2031 8 1 -1 0 0 1.9230 9 1 -1 1 0 5.8495 10 1 0 -1 0 2.5339 11 1 0 1 0 2.5339 12 1 -1 -1 1 5.1982 13 1 -1 0 1 3.5309 14 1 -1 1 1 5.8612 15 1 0 -1 1 5.0197 16 1 0 0 1 1.2372 17 1 0 1 1 4.3330 18 1 1 1 1 6.6443 19 1 1 0 1 3.1060 20 1 1 -1 1 6.4054 21 1 1 1 0 5.2031 22 1 1 0 0 1.9230 23 1 1 -1 0 5.8495 24 1 1 1 -1 5.1982 25 1 1 0 -1 3.5309 26 1 1 -1 -1 5.8612 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3744 atoms have been selected out of 3818 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.36 4 C004 has 582 194 194 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1763 586 586 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.40 Total of13024 atoms and 4333 groups and 4328 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3818 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1261 Number of atoms = 3818 Number of groups = 1266 Number of bonds = 3811 Number of angles = 1365 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1263 Number of HB donors = 2504 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1261 Number of atoms = 3818 Number of groups = 1266 Number of bonds = 3811 Number of angles = 1365 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1263 Number of HB donors = 2504 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.698" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1261" Evaluating: 1261-7 Parameter: NUMWAT <- "1254" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1254" Comparing "1081" and "1254". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.698" Parameter: BOX -> "33.698" Parameter: BOX -> "33.698" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.69800 B = 33.69800 C = 33.69800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6423 2 1 -1 0 -1 3.1033 3 1 -1 1 -1 6.4019 4 1 0 -1 -1 4.3343 5 1 0 0 -1 1.2354 6 1 0 1 -1 5.0173 7 1 -1 -1 0 5.2004 8 1 -1 0 0 1.9211 9 1 -1 1 0 5.8475 10 1 0 -1 0 2.5319 11 1 0 1 0 2.5319 12 1 -1 -1 1 5.1950 13 1 -1 0 1 3.5285 14 1 -1 1 1 5.8584 15 1 0 -1 1 5.0173 16 1 0 0 1 1.2354 17 1 0 1 1 4.3343 18 1 1 1 1 6.6423 19 1 1 0 1 3.1033 20 1 1 -1 1 6.4019 21 1 1 1 0 5.2004 22 1 1 0 0 1.9211 23 1 1 -1 0 5.8475 24 1 1 1 -1 5.1950 25 1 1 0 -1 3.5285 26 1 1 -1 -1 5.8584 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3744 atoms have been selected out of 3818 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 669 OPERATED ON BY TRANSFORMATION C005 RESIDUE 987 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.36 4 C004 has 579 193 193 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 465 155 155 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1763 586 586 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.39 Total of13015 atoms and 4330 groups and 4325 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3818 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1259 Number of atoms = 3812 Number of groups = 1264 Number of bonds = 3805 Number of angles = 1363 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1261 Number of HB donors = 2500 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1259 Number of atoms = 3812 Number of groups = 1264 Number of bonds = 3805 Number of angles = 1363 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1261 Number of HB donors = 2500 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.696" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1259" Evaluating: 1259-7 Parameter: NUMWAT <- "1252" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1252" Comparing "1081" and "1252". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.696" Parameter: BOX -> "33.696" Parameter: BOX -> "33.696" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.69600 B = 33.69600 C = 33.69600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6403 2 1 -1 0 -1 3.1005 3 1 -1 1 -1 6.3985 4 1 0 -1 -1 4.3356 5 1 0 0 -1 1.2336 6 1 0 1 -1 3.0779 7 1 -1 -1 0 5.1977 8 1 -1 0 0 1.9192 9 1 -1 1 0 5.8454 10 1 0 -1 0 2.5299 11 1 0 1 0 2.5299 12 1 -1 -1 1 5.1918 13 1 -1 0 1 3.5262 14 1 -1 1 1 5.8555 15 1 0 -1 1 3.0779 16 1 0 0 1 1.2336 17 1 0 1 1 4.3356 18 1 1 1 1 6.6403 19 1 1 0 1 3.1005 20 1 1 -1 1 6.3985 21 1 1 1 0 5.1977 22 1 1 0 0 1.9192 23 1 1 -1 0 5.8454 24 1 1 1 -1 5.1918 25 1 1 0 -1 3.5262 26 1 1 -1 -1 5.8555 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3738 atoms have been selected out of 3812 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.36 4 C004 has 579 193 193 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 465 155 155 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1763 586 586 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1644 548 548 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.39 Total of13006 atoms and 4327 groups and 4322 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3812 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1259 Number of atoms = 3812 Number of groups = 1264 Number of bonds = 3805 Number of angles = 1363 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1261 Number of HB donors = 2500 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1259 Number of atoms = 3812 Number of groups = 1264 Number of bonds = 3805 Number of angles = 1363 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1261 Number of HB donors = 2500 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.694" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1259" Evaluating: 1259-7 Parameter: NUMWAT <- "1252" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1252" Comparing "1081" and "1252". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.694" Parameter: BOX -> "33.694" Parameter: BOX -> "33.694" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.69400 B = 33.69400 C = 33.69400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6383 2 1 -1 0 -1 3.0978 3 1 -1 1 -1 6.3951 4 1 0 -1 -1 4.3369 5 1 0 0 -1 1.2318 6 1 0 1 -1 3.0765 7 1 -1 -1 0 5.1950 8 1 -1 0 0 1.9174 9 1 -1 1 0 5.8434 10 1 0 -1 0 2.5279 11 1 0 1 0 2.5279 12 1 -1 -1 1 5.1887 13 1 -1 0 1 3.5238 14 1 -1 1 1 5.8527 15 1 0 -1 1 3.0765 16 1 0 0 1 1.2318 17 1 0 1 1 4.3369 18 1 1 1 1 6.6383 19 1 1 0 1 3.0978 20 1 1 -1 1 6.3951 21 1 1 1 0 5.1950 22 1 1 0 0 1.9174 23 1 1 -1 0 5.8434 24 1 1 1 -1 5.1887 25 1 1 0 -1 3.5238 26 1 1 -1 -1 5.8527 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3738 atoms have been selected out of 3812 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.36 4 C004 has 579 193 193 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 465 155 155 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1766 587 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1644 548 548 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.39 Total of13009 atoms and 4328 groups and 4323 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3812 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1259 Number of atoms = 3812 Number of groups = 1264 Number of bonds = 3805 Number of angles = 1363 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1261 Number of HB donors = 2500 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1259 Number of atoms = 3812 Number of groups = 1264 Number of bonds = 3805 Number of angles = 1363 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1261 Number of HB donors = 2500 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.692" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1259" Evaluating: 1259-7 Parameter: NUMWAT <- "1252" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1252" Comparing "1081" and "1252". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.692" Parameter: BOX -> "33.692" Parameter: BOX -> "33.692" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.69200 B = 33.69200 C = 33.69200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6363 2 1 -1 0 -1 3.0951 3 1 -1 1 -1 6.3916 4 1 0 -1 -1 4.3383 5 1 0 0 -1 1.2300 6 1 0 1 -1 3.0752 7 1 -1 -1 0 5.1923 8 1 -1 0 0 1.9155 9 1 -1 1 0 5.8414 10 1 0 -1 0 2.5259 11 1 0 1 0 2.5259 12 1 -1 -1 1 5.1855 13 1 -1 0 1 3.5215 14 1 -1 1 1 5.8499 15 1 0 -1 1 3.0752 16 1 0 0 1 1.2300 17 1 0 1 1 4.3383 18 1 1 1 1 6.6363 19 1 1 0 1 3.0951 20 1 1 -1 1 6.3916 21 1 1 1 0 5.1923 22 1 1 0 0 1.9155 23 1 1 -1 0 5.8414 24 1 1 1 -1 5.1855 25 1 1 0 -1 3.5215 26 1 1 -1 -1 5.8499 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3738 atoms have been selected out of 3812 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.36 4 C004 has 579 193 193 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 465 155 155 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1766 587 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1644 548 548 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.39 Total of13009 atoms and 4328 groups and 4323 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3812 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1259 Number of atoms = 3812 Number of groups = 1264 Number of bonds = 3805 Number of angles = 1363 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1261 Number of HB donors = 2500 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1259 Number of atoms = 3812 Number of groups = 1264 Number of bonds = 3805 Number of angles = 1363 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1261 Number of HB donors = 2500 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.69" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1259" Evaluating: 1259-7 Parameter: NUMWAT <- "1252" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1252" Comparing "1081" and "1252". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.69" Parameter: BOX -> "33.69" Parameter: BOX -> "33.69" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.69000 B = 33.69000 C = 33.69000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6343 2 1 -1 0 -1 3.0923 3 1 -1 1 -1 6.3882 4 1 0 -1 -1 4.3396 5 1 0 0 -1 1.2282 6 1 0 1 -1 3.0738 7 1 -1 -1 0 5.1896 8 1 -1 0 0 1.9136 9 1 -1 1 0 5.8394 10 1 0 -1 0 2.5239 11 1 0 1 0 2.5239 12 1 -1 -1 1 5.1823 13 1 -1 0 1 3.5191 14 1 -1 1 1 5.8471 15 1 0 -1 1 3.0738 16 1 0 0 1 1.2282 17 1 0 1 1 4.3396 18 1 1 1 1 6.6343 19 1 1 0 1 3.0923 20 1 1 -1 1 6.3882 21 1 1 1 0 5.1896 22 1 1 0 0 1.9136 23 1 1 -1 0 5.8394 24 1 1 1 -1 5.1823 25 1 1 0 -1 3.5191 26 1 1 -1 -1 5.8471 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3738 atoms have been selected out of 3812 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.35 4 C004 has 579 193 193 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 465 155 155 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1766 587 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1644 548 548 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.39 Total of13012 atoms and 4329 groups and 4324 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3812 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1259 Number of atoms = 3812 Number of groups = 1264 Number of bonds = 3805 Number of angles = 1363 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1261 Number of HB donors = 2500 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1259 Number of atoms = 3812 Number of groups = 1264 Number of bonds = 3805 Number of angles = 1363 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1261 Number of HB donors = 2500 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.688" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1259" Evaluating: 1259-7 Parameter: NUMWAT <- "1252" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1252" Comparing "1081" and "1252". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.688" Parameter: BOX -> "33.688" Parameter: BOX -> "33.688" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.68800 B = 33.68800 C = 33.68800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6323 2 1 -1 0 -1 3.0896 3 1 -1 1 -1 6.3847 4 1 0 -1 -1 4.3409 5 1 0 0 -1 1.2264 6 1 0 1 -1 3.0725 7 1 -1 -1 0 5.1869 8 1 -1 0 0 1.9117 9 1 -1 1 0 5.8373 10 1 0 -1 0 2.5219 11 1 0 1 0 2.5219 12 1 -1 -1 1 5.1791 13 1 -1 0 1 3.5168 14 1 -1 1 1 5.8443 15 1 0 -1 1 3.0725 16 1 0 0 1 1.2264 17 1 0 1 1 4.3409 18 1 1 1 1 6.6323 19 1 1 0 1 3.0896 20 1 1 -1 1 6.3847 21 1 1 1 0 5.1869 22 1 1 0 0 1.9117 23 1 1 -1 0 5.8373 24 1 1 1 -1 5.1791 25 1 1 0 -1 3.5168 26 1 1 -1 -1 5.8443 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3738 atoms have been selected out of 3812 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 166 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.35 4 C004 has 579 193 193 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1644 548 548 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.38 Total of13014 atoms and 4329 groups and 4323 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3812 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.686" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1258" Evaluating: 1258-7 Parameter: NUMWAT <- "1251" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1251" Comparing "1081" and "1251". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.686" Parameter: BOX -> "33.686" Parameter: BOX -> "33.686" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.68600 B = 33.68600 C = 33.68600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6304 2 1 -1 0 -1 3.0868 3 1 -1 1 -1 6.3813 4 1 0 -1 -1 4.3422 5 1 0 0 -1 1.2246 6 1 0 1 -1 3.0711 7 1 -1 -1 0 5.1842 8 1 -1 0 0 1.9098 9 1 -1 1 0 5.8353 10 1 0 -1 0 2.5199 11 1 0 1 0 2.5199 12 1 -1 -1 1 5.1759 13 1 -1 0 1 3.5145 14 1 -1 1 1 5.8415 15 1 0 -1 1 3.0711 16 1 0 0 1 1.2246 17 1 0 1 1 4.3422 18 1 1 1 1 6.6304 19 1 1 0 1 3.0868 20 1 1 -1 1 6.3813 21 1 1 1 0 5.1842 22 1 1 0 0 1.9098 23 1 1 -1 0 5.8353 24 1 1 1 -1 5.1759 25 1 1 0 -1 3.5145 26 1 1 -1 -1 5.8415 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3735 atoms have been selected out of 3809 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.35 4 C004 has 579 193 193 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 465 155 155 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1644 548 548 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.38 Total of13002 atoms and 4325 groups and 4319 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3809 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.684" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1258" Evaluating: 1258-7 Parameter: NUMWAT <- "1251" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1251" Comparing "1081" and "1251". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.684" Parameter: BOX -> "33.684" Parameter: BOX -> "33.684" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.68400 B = 33.68400 C = 33.68400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6284 2 1 -1 0 -1 3.0841 3 1 -1 1 -1 6.3779 4 1 0 -1 -1 4.3436 5 1 0 0 -1 1.2228 6 1 0 1 -1 3.0698 7 1 -1 -1 0 5.1815 8 1 -1 0 0 1.9079 9 1 -1 1 0 5.8333 10 1 0 -1 0 2.5179 11 1 0 1 0 2.5179 12 1 -1 -1 1 5.1727 13 1 -1 0 1 3.5121 14 1 -1 1 1 5.8387 15 1 0 -1 1 3.0698 16 1 0 0 1 1.2228 17 1 0 1 1 4.3436 18 1 1 1 1 6.6284 19 1 1 0 1 3.0841 20 1 1 -1 1 6.3779 21 1 1 1 0 5.1815 22 1 1 0 0 1.9079 23 1 1 -1 0 5.8333 24 1 1 1 -1 5.1727 25 1 1 0 -1 3.5121 26 1 1 -1 -1 5.8387 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3735 atoms have been selected out of 3809 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.35 4 C004 has 579 193 193 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 465 155 155 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1644 548 548 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.38 Total of13005 atoms and 4326 groups and 4320 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3809 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.682" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1258" Evaluating: 1258-7 Parameter: NUMWAT <- "1251" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1251" Comparing "1081" and "1251". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.682" Parameter: BOX -> "33.682" Parameter: BOX -> "33.682" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.68200 B = 33.68200 C = 33.68200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6264 2 1 -1 0 -1 3.0814 3 1 -1 1 -1 6.3744 4 1 0 -1 -1 4.3449 5 1 0 0 -1 1.2210 6 1 0 1 -1 3.0684 7 1 -1 -1 0 5.1788 8 1 -1 0 0 1.9060 9 1 -1 1 0 5.8313 10 1 0 -1 0 2.5159 11 1 0 1 0 2.5159 12 1 -1 -1 1 5.1696 13 1 -1 0 1 3.5098 14 1 -1 1 1 5.8359 15 1 0 -1 1 3.0684 16 1 0 0 1 1.2210 17 1 0 1 1 4.3449 18 1 1 1 1 6.6264 19 1 1 0 1 3.0814 20 1 1 -1 1 6.3744 21 1 1 1 0 5.1788 22 1 1 0 0 1.9060 23 1 1 -1 0 5.8313 24 1 1 1 -1 5.1696 25 1 1 0 -1 3.5098 26 1 1 -1 -1 5.8359 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3735 atoms have been selected out of 3809 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.35 4 C004 has 579 193 193 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 465 155 155 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1644 548 548 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.38 Total of13005 atoms and 4326 groups and 4320 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3809 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.68" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1258" Evaluating: 1258-7 Parameter: NUMWAT <- "1251" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1251" Comparing "1081" and "1251". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.68" Parameter: BOX -> "33.68" Parameter: BOX -> "33.68" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.68000 B = 33.68000 C = 33.68000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6244 2 1 -1 0 -1 3.0786 3 1 -1 1 -1 6.3710 4 1 0 -1 -1 4.3462 5 1 0 0 -1 1.2192 6 1 0 1 -1 3.0671 7 1 -1 -1 0 5.1761 8 1 -1 0 0 1.9041 9 1 -1 1 0 5.8293 10 1 0 -1 0 2.5139 11 1 0 1 0 2.5139 12 1 -1 -1 1 5.1664 13 1 -1 0 1 3.5074 14 1 -1 1 1 5.8330 15 1 0 -1 1 3.0671 16 1 0 0 1 1.2192 17 1 0 1 1 4.3462 18 1 1 1 1 6.6244 19 1 1 0 1 3.0786 20 1 1 -1 1 6.3710 21 1 1 1 0 5.1761 22 1 1 0 0 1.9041 23 1 1 -1 0 5.8293 24 1 1 1 -1 5.1664 25 1 1 0 -1 3.5074 26 1 1 -1 -1 5.8330 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3735 atoms have been selected out of 3809 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.34 4 C004 has 579 193 193 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 465 155 155 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1644 548 548 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.38 Total of13005 atoms and 4326 groups and 4320 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3809 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.678" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1258" Evaluating: 1258-7 Parameter: NUMWAT <- "1251" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1251" Comparing "1081" and "1251". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.678" Parameter: BOX -> "33.678" Parameter: BOX -> "33.678" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.67800 B = 33.67800 C = 33.67800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6224 2 1 -1 0 -1 3.0759 3 1 -1 1 -1 6.3675 4 1 0 -1 -1 4.3475 5 1 0 0 -1 1.2174 6 1 0 1 -1 3.0658 7 1 -1 -1 0 5.1734 8 1 -1 0 0 1.9023 9 1 -1 1 0 5.8272 10 1 0 -1 0 2.5119 11 1 0 1 0 2.5119 12 1 -1 -1 1 5.1632 13 1 -1 0 1 3.5051 14 1 -1 1 1 5.8302 15 1 0 -1 1 3.0658 16 1 0 0 1 1.2174 17 1 0 1 1 4.3475 18 1 1 1 1 6.6224 19 1 1 0 1 3.0759 20 1 1 -1 1 6.3675 21 1 1 1 0 5.1734 22 1 1 0 0 1.9023 23 1 1 -1 0 5.8272 24 1 1 1 -1 5.1632 25 1 1 0 -1 3.5051 26 1 1 -1 -1 5.8302 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3735 atoms have been selected out of 3809 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.34 4 C004 has 579 193 193 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 465 155 155 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1644 548 548 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.37 Total of13005 atoms and 4326 groups and 4320 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3809 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.676" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1258" Evaluating: 1258-7 Parameter: NUMWAT <- "1251" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1251" Comparing "1081" and "1251". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.676" Parameter: BOX -> "33.676" Parameter: BOX -> "33.676" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.67600 B = 33.67600 C = 33.67600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6204 2 1 -1 0 -1 3.0731 3 1 -1 1 -1 6.3641 4 1 0 -1 -1 4.3489 5 1 0 0 -1 1.2156 6 1 0 1 -1 3.0644 7 1 -1 -1 0 5.1707 8 1 -1 0 0 1.9004 9 1 -1 1 0 5.8252 10 1 0 -1 0 2.5099 11 1 0 1 0 2.5099 12 1 -1 -1 1 5.1600 13 1 -1 0 1 3.5028 14 1 -1 1 1 5.8274 15 1 0 -1 1 3.0644 16 1 0 0 1 1.2156 17 1 0 1 1 4.3489 18 1 1 1 1 6.6204 19 1 1 0 1 3.0731 20 1 1 -1 1 6.3641 21 1 1 1 0 5.1707 22 1 1 0 0 1.9004 23 1 1 -1 0 5.8252 24 1 1 1 -1 5.1600 25 1 1 0 -1 3.5028 26 1 1 -1 -1 5.8274 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3735 atoms have been selected out of 3809 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.34 4 C004 has 579 193 193 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1644 548 548 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.37 Total of13011 atoms and 4328 groups and 4322 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3809 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.674" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1258" Evaluating: 1258-7 Parameter: NUMWAT <- "1251" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1251" Comparing "1081" and "1251". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.674" Parameter: BOX -> "33.674" Parameter: BOX -> "33.674" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.67400 B = 33.67400 C = 33.67400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6184 2 1 -1 0 -1 3.0704 3 1 -1 1 -1 6.3607 4 1 0 -1 -1 4.3502 5 1 0 0 -1 1.2138 6 1 0 1 -1 3.0631 7 1 -1 -1 0 5.1680 8 1 -1 0 0 1.8985 9 1 -1 1 0 5.8232 10 1 0 -1 0 2.5079 11 1 0 1 0 2.5079 12 1 -1 -1 1 5.1568 13 1 -1 0 1 3.5004 14 1 -1 1 1 5.8246 15 1 0 -1 1 3.0631 16 1 0 0 1 1.2138 17 1 0 1 1 4.3502 18 1 1 1 1 6.6184 19 1 1 0 1 3.0704 20 1 1 -1 1 6.3607 21 1 1 1 0 5.1680 22 1 1 0 0 1.8985 23 1 1 -1 0 5.8232 24 1 1 1 -1 5.1568 25 1 1 0 -1 3.5004 26 1 1 -1 -1 5.8246 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3735 atoms have been selected out of 3809 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.34 4 C004 has 579 193 193 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1644 548 548 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.37 Total of13011 atoms and 4328 groups and 4322 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3809 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.672" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1258" Evaluating: 1258-7 Parameter: NUMWAT <- "1251" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1251" Comparing "1081" and "1251". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.672" Parameter: BOX -> "33.672" Parameter: BOX -> "33.672" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.67200 B = 33.67200 C = 33.67200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6164 2 1 -1 0 -1 3.0677 3 1 -1 1 -1 6.3572 4 1 0 -1 -1 4.3515 5 1 0 0 -1 1.2120 6 1 0 1 -1 3.0618 7 1 -1 -1 0 5.1653 8 1 -1 0 0 1.8966 9 1 -1 1 0 5.8212 10 1 0 -1 0 2.5059 11 1 0 1 0 2.5059 12 1 -1 -1 1 5.1536 13 1 -1 0 1 3.4981 14 1 -1 1 1 5.8218 15 1 0 -1 1 3.0618 16 1 0 0 1 1.2120 17 1 0 1 1 4.3515 18 1 1 1 1 6.6164 19 1 1 0 1 3.0677 20 1 1 -1 1 6.3572 21 1 1 1 0 5.1653 22 1 1 0 0 1.8966 23 1 1 -1 0 5.8212 24 1 1 1 -1 5.1536 25 1 1 0 -1 3.4981 26 1 1 -1 -1 5.8218 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3735 atoms have been selected out of 3809 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.34 4 C004 has 579 193 193 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.37 Total of13014 atoms and 4329 groups and 4323 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3809 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.67" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1258" Evaluating: 1258-7 Parameter: NUMWAT <- "1251" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1251" Comparing "1081" and "1251". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.67" Parameter: BOX -> "33.67" Parameter: BOX -> "33.67" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.67000 B = 33.67000 C = 33.67000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6145 2 1 -1 0 -1 3.0649 3 1 -1 1 -1 6.3538 4 1 0 -1 -1 4.3529 5 1 0 0 -1 1.2102 6 1 0 1 -1 3.0604 7 1 -1 -1 0 5.1626 8 1 -1 0 0 1.8947 9 1 -1 1 0 5.8192 10 1 0 -1 0 2.5039 11 1 0 1 0 2.5039 12 1 -1 -1 1 5.1505 13 1 -1 0 1 3.4958 14 1 -1 1 1 5.8190 15 1 0 -1 1 3.0604 16 1 0 0 1 1.2102 17 1 0 1 1 4.3529 18 1 1 1 1 6.6145 19 1 1 0 1 3.0649 20 1 1 -1 1 6.3538 21 1 1 1 0 5.1626 22 1 1 0 0 1.8947 23 1 1 -1 0 5.8192 24 1 1 1 -1 5.1505 25 1 1 0 -1 3.4958 26 1 1 -1 -1 5.8190 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3735 atoms have been selected out of 3809 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.33 4 C004 has 579 193 193 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.37 Total of13014 atoms and 4329 groups and 4323 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3809 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.668" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1258" Evaluating: 1258-7 Parameter: NUMWAT <- "1251" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1251" Comparing "1081" and "1251". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.668" Parameter: BOX -> "33.668" Parameter: BOX -> "33.668" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.66800 B = 33.66800 C = 33.66800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6125 2 1 -1 0 -1 3.0622 3 1 -1 1 -1 6.3503 4 1 0 -1 -1 4.3542 5 1 0 0 -1 1.2084 6 1 0 1 -1 3.0591 7 1 -1 -1 0 5.1599 8 1 -1 0 0 1.8928 9 1 -1 1 0 5.8172 10 1 0 -1 0 2.5019 11 1 0 1 0 2.5019 12 1 -1 -1 1 5.1473 13 1 -1 0 1 3.4934 14 1 -1 1 1 5.8162 15 1 0 -1 1 3.0591 16 1 0 0 1 1.2084 17 1 0 1 1 4.3542 18 1 1 1 1 6.6125 19 1 1 0 1 3.0622 20 1 1 -1 1 6.3503 21 1 1 1 0 5.1599 22 1 1 0 0 1.8928 23 1 1 -1 0 5.8172 24 1 1 1 -1 5.1473 25 1 1 0 -1 3.4934 26 1 1 -1 -1 5.8162 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3735 atoms have been selected out of 3809 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.33 4 C004 has 579 193 193 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.36 Total of13014 atoms and 4329 groups and 4323 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3809 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.666" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1258" Evaluating: 1258-7 Parameter: NUMWAT <- "1251" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1251" Comparing "1081" and "1251". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.666" Parameter: BOX -> "33.666" Parameter: BOX -> "33.666" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.66600 B = 33.66600 C = 33.66600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6105 2 1 -1 0 -1 3.0594 3 1 -1 1 -1 6.3469 4 1 0 -1 -1 4.3556 5 1 0 0 -1 1.2066 6 1 0 1 -1 3.0578 7 1 -1 -1 0 5.1572 8 1 -1 0 0 1.8909 9 1 -1 1 0 5.8152 10 1 0 -1 0 2.4999 11 1 0 1 0 2.4999 12 1 -1 -1 1 5.1441 13 1 -1 0 1 3.4911 14 1 -1 1 1 5.8134 15 1 0 -1 1 3.0578 16 1 0 0 1 1.2066 17 1 0 1 1 4.3556 18 1 1 1 1 6.6105 19 1 1 0 1 3.0594 20 1 1 -1 1 6.3469 21 1 1 1 0 5.1572 22 1 1 0 0 1.8909 23 1 1 -1 0 5.8152 24 1 1 1 -1 5.1441 25 1 1 0 -1 3.4911 26 1 1 -1 -1 5.8134 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3735 atoms have been selected out of 3809 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.33 4 C004 has 579 193 193 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.36 Total of13014 atoms and 4329 groups and 4323 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3809 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.664" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1258" Evaluating: 1258-7 Parameter: NUMWAT <- "1251" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1251" Comparing "1081" and "1251". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.664" Parameter: BOX -> "33.664" Parameter: BOX -> "33.664" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.66400 B = 33.66400 C = 33.66400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6085 2 1 -1 0 -1 3.0567 3 1 -1 1 -1 6.3435 4 1 0 -1 -1 4.3569 5 1 0 0 -1 1.2048 6 1 0 1 -1 3.0565 7 1 -1 -1 0 5.1545 8 1 -1 0 0 1.8891 9 1 -1 1 0 5.8131 10 1 0 -1 0 2.4979 11 1 0 1 0 2.4979 12 1 -1 -1 1 5.1409 13 1 -1 0 1 3.4888 14 1 -1 1 1 5.8106 15 1 0 -1 1 3.0565 16 1 0 0 1 1.2048 17 1 0 1 1 4.3569 18 1 1 1 1 6.6085 19 1 1 0 1 3.0567 20 1 1 -1 1 6.3435 21 1 1 1 0 5.1545 22 1 1 0 0 1.8891 23 1 1 -1 0 5.8131 24 1 1 1 -1 5.1409 25 1 1 0 -1 3.4888 26 1 1 -1 -1 5.8106 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3735 atoms have been selected out of 3809 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.33 4 C004 has 579 193 193 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.36 Total of13014 atoms and 4329 groups and 4323 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3809 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.662" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1258" Evaluating: 1258-7 Parameter: NUMWAT <- "1251" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1251" Comparing "1081" and "1251". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.662" Parameter: BOX -> "33.662" Parameter: BOX -> "33.662" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.66200 B = 33.66200 C = 33.66200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6065 2 1 -1 0 -1 3.0540 3 1 -1 1 -1 6.3400 4 1 0 -1 -1 4.3582 5 1 0 0 -1 1.2030 6 1 0 1 -1 3.0551 7 1 -1 -1 0 5.1518 8 1 -1 0 0 1.8872 9 1 -1 1 0 5.8111 10 1 0 -1 0 2.4959 11 1 0 1 0 2.4959 12 1 -1 -1 1 5.1378 13 1 -1 0 1 3.4864 14 1 -1 1 1 5.8078 15 1 0 -1 1 3.0551 16 1 0 0 1 1.2030 17 1 0 1 1 4.3582 18 1 1 1 1 6.6065 19 1 1 0 1 3.0540 20 1 1 -1 1 6.3400 21 1 1 1 0 5.1518 22 1 1 0 0 1.8872 23 1 1 -1 0 5.8111 24 1 1 1 -1 5.1378 25 1 1 0 -1 3.4864 26 1 1 -1 -1 5.8078 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3735 atoms have been selected out of 3809 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.33 4 C004 has 579 193 193 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.36 Total of13017 atoms and 4330 groups and 4324 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3809 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.66" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1258" Evaluating: 1258-7 Parameter: NUMWAT <- "1251" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1251" Comparing "1081" and "1251". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.66" Parameter: BOX -> "33.66" Parameter: BOX -> "33.66" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.66000 B = 33.66000 C = 33.66000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6046 2 1 -1 0 -1 3.0512 3 1 -1 1 -1 6.3366 4 1 0 -1 -1 4.3596 5 1 0 0 -1 1.2012 6 1 0 1 -1 3.0538 7 1 -1 -1 0 5.1492 8 1 -1 0 0 1.8853 9 1 -1 1 0 5.8091 10 1 0 -1 0 2.4939 11 1 0 1 0 2.4939 12 1 -1 -1 1 5.1346 13 1 -1 0 1 3.4841 14 1 -1 1 1 5.8050 15 1 0 -1 1 3.0538 16 1 0 0 1 1.2012 17 1 0 1 1 4.3596 18 1 1 1 1 6.6046 19 1 1 0 1 3.0512 20 1 1 -1 1 6.3366 21 1 1 1 0 5.1492 22 1 1 0 0 1.8853 23 1 1 -1 0 5.8091 24 1 1 1 -1 5.1346 25 1 1 0 -1 3.4841 26 1 1 -1 -1 5.8050 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3735 atoms have been selected out of 3809 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.32 4 C004 has 579 193 193 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.36 Total of13017 atoms and 4330 groups and 4324 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3809 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.658" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1258" Evaluating: 1258-7 Parameter: NUMWAT <- "1251" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1251" Comparing "1081" and "1251". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.658" Parameter: BOX -> "33.658" Parameter: BOX -> "33.658" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.65800 B = 33.65800 C = 33.65800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6026 2 1 -1 0 -1 3.0485 3 1 -1 1 -1 6.3331 4 1 0 -1 -1 4.3609 5 1 0 0 -1 1.1995 6 1 0 1 -1 3.0525 7 1 -1 -1 0 5.1465 8 1 -1 0 0 1.8834 9 1 -1 1 0 5.8071 10 1 0 -1 0 2.4919 11 1 0 1 0 2.4919 12 1 -1 -1 1 5.1314 13 1 -1 0 1 3.4818 14 1 -1 1 1 5.8022 15 1 0 -1 1 3.0525 16 1 0 0 1 1.1995 17 1 0 1 1 4.3609 18 1 1 1 1 6.6026 19 1 1 0 1 3.0485 20 1 1 -1 1 6.3331 21 1 1 1 0 5.1465 22 1 1 0 0 1.8834 23 1 1 -1 0 5.8071 24 1 1 1 -1 5.1314 25 1 1 0 -1 3.4818 26 1 1 -1 -1 5.8022 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3735 atoms have been selected out of 3809 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 423 141 141 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.32 4 C004 has 579 193 193 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.35 Total of13020 atoms and 4331 groups and 4325 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3809 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.656" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1258" Evaluating: 1258-7 Parameter: NUMWAT <- "1251" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1251" Comparing "1081" and "1251". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.656" Parameter: BOX -> "33.656" Parameter: BOX -> "33.656" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.65600 B = 33.65600 C = 33.65600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6006 2 1 -1 0 -1 3.0458 3 1 -1 1 -1 6.3297 4 1 0 -1 -1 4.3623 5 1 0 0 -1 1.1977 6 1 0 1 -1 3.0512 7 1 -1 -1 0 5.1438 8 1 -1 0 0 1.8815 9 1 -1 1 0 5.8051 10 1 0 -1 0 2.4899 11 1 0 1 0 2.4899 12 1 -1 -1 1 5.1282 13 1 -1 0 1 3.4794 14 1 -1 1 1 5.7994 15 1 0 -1 1 3.0512 16 1 0 0 1 1.1977 17 1 0 1 1 4.3623 18 1 1 1 1 6.6006 19 1 1 0 1 3.0458 20 1 1 -1 1 6.3297 21 1 1 1 0 5.1438 22 1 1 0 0 1.8815 23 1 1 -1 0 5.8051 24 1 1 1 -1 5.1282 25 1 1 0 -1 3.4794 26 1 1 -1 -1 5.7994 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3735 atoms have been selected out of 3809 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 423 141 141 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.32 4 C004 has 579 193 193 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.35 Total of13020 atoms and 4331 groups and 4325 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3809 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.654" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1258" Evaluating: 1258-7 Parameter: NUMWAT <- "1251" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1251" Comparing "1081" and "1251". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.654" Parameter: BOX -> "33.654" Parameter: BOX -> "33.654" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.65400 B = 33.65400 C = 33.65400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5987 2 1 -1 0 -1 3.0430 3 1 -1 1 -1 6.3263 4 1 0 -1 -1 4.3636 5 1 0 0 -1 1.1959 6 1 0 1 -1 3.0499 7 1 -1 -1 0 5.1411 8 1 -1 0 0 1.8796 9 1 -1 1 0 5.8031 10 1 0 -1 0 2.4879 11 1 0 1 0 2.4879 12 1 -1 -1 1 5.1250 13 1 -1 0 1 3.4771 14 1 -1 1 1 5.7966 15 1 0 -1 1 3.0499 16 1 0 0 1 1.1959 17 1 0 1 1 4.3636 18 1 1 1 1 6.5987 19 1 1 0 1 3.0430 20 1 1 -1 1 6.3263 21 1 1 1 0 5.1411 22 1 1 0 0 1.8796 23 1 1 -1 0 5.8031 24 1 1 1 -1 5.1250 25 1 1 0 -1 3.4771 26 1 1 -1 -1 5.7966 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3735 atoms have been selected out of 3809 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 423 141 141 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.32 4 C004 has 579 193 193 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.35 Total of13020 atoms and 4331 groups and 4325 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3809 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1258 Number of atoms = 3809 Number of groups = 1263 Number of bonds = 3802 Number of angles = 1362 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1260 Number of HB donors = 2498 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.652" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1258" Evaluating: 1258-7 Parameter: NUMWAT <- "1251" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1251" Comparing "1081" and "1251". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.652" Parameter: BOX -> "33.652" Parameter: BOX -> "33.652" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.65200 B = 33.65200 C = 33.65200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5967 2 1 -1 0 -1 3.0403 3 1 -1 1 -1 6.3228 4 1 0 -1 -1 4.3650 5 1 0 0 -1 1.1941 6 1 0 1 -1 3.0486 7 1 -1 -1 0 5.1384 8 1 -1 0 0 1.8778 9 1 -1 1 0 5.8011 10 1 0 -1 0 2.4859 11 1 0 1 0 2.4859 12 1 -1 -1 1 5.1219 13 1 -1 0 1 3.4748 14 1 -1 1 1 5.7938 15 1 0 -1 1 3.0486 16 1 0 0 1 1.1941 17 1 0 1 1 4.3650 18 1 1 1 1 6.5967 19 1 1 0 1 3.0403 20 1 1 -1 1 6.3228 21 1 1 1 0 5.1384 22 1 1 0 0 1.8778 23 1 1 -1 0 5.8011 24 1 1 1 -1 5.1219 25 1 1 0 -1 3.4748 26 1 1 -1 -1 5.7938 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3735 atoms have been selected out of 3809 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 857 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 423 141 141 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.32 4 C004 has 582 194 194 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.35 Total of13017 atoms and 4330 groups and 4324 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3809 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1257 Number of atoms = 3806 Number of groups = 1262 Number of bonds = 3799 Number of angles = 1361 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1259 Number of HB donors = 2496 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1257 Number of atoms = 3806 Number of groups = 1262 Number of bonds = 3799 Number of angles = 1361 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1259 Number of HB donors = 2496 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.65" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1257" Evaluating: 1257-7 Parameter: NUMWAT <- "1250" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1250" Comparing "1081" and "1250". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.65" Parameter: BOX -> "33.65" Parameter: BOX -> "33.65" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.65000 B = 33.65000 C = 33.65000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5947 2 1 -1 0 -1 3.0375 3 1 -1 1 -1 6.3194 4 1 0 -1 -1 4.3663 5 1 0 0 -1 1.1923 6 1 0 1 -1 3.0473 7 1 -1 -1 0 5.1357 8 1 -1 0 0 1.8759 9 1 -1 1 0 5.7991 10 1 0 -1 0 2.4839 11 1 0 1 0 2.4839 12 1 -1 -1 1 5.1187 13 1 -1 0 1 3.4725 14 1 -1 1 1 5.7910 15 1 0 -1 1 3.0473 16 1 0 0 1 1.1923 17 1 0 1 1 4.3663 18 1 1 1 1 6.5947 19 1 1 0 1 3.0375 20 1 1 -1 1 6.3194 21 1 1 1 0 5.1357 22 1 1 0 0 1.8759 23 1 1 -1 0 5.7991 24 1 1 1 -1 5.1187 25 1 1 0 -1 3.4725 26 1 1 -1 -1 5.7910 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3732 atoms have been selected out of 3806 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 423 141 141 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.31 4 C004 has 585 195 195 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.35 Total of13020 atoms and 4331 groups and 4325 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3806 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1257 Number of atoms = 3806 Number of groups = 1262 Number of bonds = 3799 Number of angles = 1361 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1259 Number of HB donors = 2496 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1257 Number of atoms = 3806 Number of groups = 1262 Number of bonds = 3799 Number of angles = 1361 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1259 Number of HB donors = 2496 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.648" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1257" Evaluating: 1257-7 Parameter: NUMWAT <- "1250" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1250" Comparing "1081" and "1250". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.648" Parameter: BOX -> "33.648" Parameter: BOX -> "33.648" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.64800 B = 33.64800 C = 33.64800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5927 2 1 -1 0 -1 3.0348 3 1 -1 1 -1 6.3159 4 1 0 -1 -1 4.3677 5 1 0 0 -1 1.1905 6 1 0 1 -1 3.0460 7 1 -1 -1 0 5.1330 8 1 -1 0 0 1.8740 9 1 -1 1 0 5.7971 10 1 0 -1 0 2.4819 11 1 0 1 0 2.4819 12 1 -1 -1 1 5.1155 13 1 -1 0 1 3.4701 14 1 -1 1 1 5.7882 15 1 0 -1 1 3.0460 16 1 0 0 1 1.1905 17 1 0 1 1 4.3677 18 1 1 1 1 6.5927 19 1 1 0 1 3.0348 20 1 1 -1 1 6.3159 21 1 1 1 0 5.1330 22 1 1 0 0 1.8740 23 1 1 -1 0 5.7971 24 1 1 1 -1 5.1155 25 1 1 0 -1 3.4701 26 1 1 -1 -1 5.7882 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3732 atoms have been selected out of 3806 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 423 141 141 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.31 4 C004 has 585 195 195 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 81 27 27 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.34 Total of13026 atoms and 4333 groups and 4327 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3806 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1257 Number of atoms = 3806 Number of groups = 1262 Number of bonds = 3799 Number of angles = 1361 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1259 Number of HB donors = 2496 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1257 Number of atoms = 3806 Number of groups = 1262 Number of bonds = 3799 Number of angles = 1361 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1259 Number of HB donors = 2496 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.646" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1257" Evaluating: 1257-7 Parameter: NUMWAT <- "1250" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1250" Comparing "1081" and "1250". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.646" Parameter: BOX -> "33.646" Parameter: BOX -> "33.646" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.64600 B = 33.64600 C = 33.64600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5908 2 1 -1 0 -1 3.0321 3 1 -1 1 -1 6.3125 4 1 0 -1 -1 4.3690 5 1 0 0 -1 1.1887 6 1 0 1 -1 3.0447 7 1 -1 -1 0 5.1303 8 1 -1 0 0 1.8721 9 1 -1 1 0 5.7951 10 1 0 -1 0 2.4799 11 1 0 1 0 2.4799 12 1 -1 -1 1 5.1123 13 1 -1 0 1 3.4678 14 1 -1 1 1 5.7854 15 1 0 -1 1 3.0447 16 1 0 0 1 1.1887 17 1 0 1 1 4.3690 18 1 1 1 1 6.5908 19 1 1 0 1 3.0321 20 1 1 -1 1 6.3125 21 1 1 1 0 5.1303 22 1 1 0 0 1.8721 23 1 1 -1 0 5.7951 24 1 1 1 -1 5.1123 25 1 1 0 -1 3.4678 26 1 1 -1 -1 5.7854 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3732 atoms have been selected out of 3806 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 423 141 141 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.31 4 C004 has 585 195 195 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 468 156 156 0.00 7 C007 has 723 241 241 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 84 28 28 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.34 Total of13029 atoms and 4334 groups and 4328 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3806 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1257 Number of atoms = 3806 Number of groups = 1262 Number of bonds = 3799 Number of angles = 1361 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1259 Number of HB donors = 2496 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1257 Number of atoms = 3806 Number of groups = 1262 Number of bonds = 3799 Number of angles = 1361 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1259 Number of HB donors = 2496 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.644" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1257" Evaluating: 1257-7 Parameter: NUMWAT <- "1250" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1250" Comparing "1081" and "1250". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.644" Parameter: BOX -> "33.644" Parameter: BOX -> "33.644" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.64400 B = 33.64400 C = 33.64400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5888 2 1 -1 0 -1 3.0293 3 1 -1 1 -1 6.3091 4 1 0 -1 -1 4.3704 5 1 0 0 -1 1.1869 6 1 0 1 -1 3.0434 7 1 -1 -1 0 5.1276 8 1 -1 0 0 1.8702 9 1 -1 1 0 5.7931 10 1 0 -1 0 2.4779 11 1 0 1 0 2.4779 12 1 -1 -1 1 5.1092 13 1 -1 0 1 3.4655 14 1 -1 1 1 5.7826 15 1 0 -1 1 3.0434 16 1 0 0 1 1.1869 17 1 0 1 1 4.3704 18 1 1 1 1 6.5888 19 1 1 0 1 3.0293 20 1 1 -1 1 6.3091 21 1 1 1 0 5.1276 22 1 1 0 0 1.8702 23 1 1 -1 0 5.7931 24 1 1 1 -1 5.1092 25 1 1 0 -1 3.4655 26 1 1 -1 -1 5.7826 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3732 atoms have been selected out of 3806 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 900 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 423 141 141 0.00 2 C002 has 738 246 246 0.00 3 C003 has 102 34 34 0.31 4 C004 has 585 195 195 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 465 155 155 0.00 7 C007 has 726 242 242 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 84 28 28 0.00 13 C013 has 474 158 158 0.00 14 C014 has 129 43 43 1.34 Total of13032 atoms and 4335 groups and 4329 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3806 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1256 Number of atoms = 3803 Number of groups = 1261 Number of bonds = 3796 Number of angles = 1360 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1258 Number of HB donors = 2494 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1256 Number of atoms = 3803 Number of groups = 1261 Number of bonds = 3796 Number of angles = 1360 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1258 Number of HB donors = 2494 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.642" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1256" Evaluating: 1256-7 Parameter: NUMWAT <- "1249" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1249" Comparing "1081" and "1249". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.642" Parameter: BOX -> "33.642" Parameter: BOX -> "33.642" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.64200 B = 33.64200 C = 33.64200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5868 2 1 -1 0 -1 3.0266 3 1 -1 1 -1 6.3056 4 1 0 -1 -1 4.3717 5 1 0 0 -1 1.1851 6 1 0 1 -1 3.0421 7 1 -1 -1 0 5.1249 8 1 -1 0 0 1.8683 9 1 -1 1 0 5.7911 10 1 0 -1 0 2.4759 11 1 0 1 0 2.4759 12 1 -1 -1 1 5.1060 13 1 -1 0 1 3.4632 14 1 -1 1 1 5.7798 15 1 0 -1 1 3.0421 16 1 0 0 1 1.1851 17 1 0 1 1 4.3717 18 1 1 1 1 6.5868 19 1 1 0 1 3.0266 20 1 1 -1 1 6.3056 21 1 1 1 0 5.1249 22 1 1 0 0 1.8683 23 1 1 -1 0 5.7911 24 1 1 1 -1 5.1060 25 1 1 0 -1 3.4632 26 1 1 -1 -1 5.7798 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3729 atoms have been selected out of 3803 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 423 141 141 0.00 2 C002 has 738 246 246 0.00 3 C003 has 102 34 34 0.31 4 C004 has 585 195 195 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 465 155 155 0.00 7 C007 has 726 242 242 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 84 28 28 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.34 Total of13017 atoms and 4330 groups and 4324 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3803 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1256 Number of atoms = 3803 Number of groups = 1261 Number of bonds = 3796 Number of angles = 1360 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1258 Number of HB donors = 2494 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1256 Number of atoms = 3803 Number of groups = 1261 Number of bonds = 3796 Number of angles = 1360 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1258 Number of HB donors = 2494 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.64" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1256" Evaluating: 1256-7 Parameter: NUMWAT <- "1249" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1249" Comparing "1081" and "1249". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.64" Parameter: BOX -> "33.64" Parameter: BOX -> "33.64" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.64000 B = 33.64000 C = 33.64000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5849 2 1 -1 0 -1 3.0239 3 1 -1 1 -1 6.3022 4 1 0 -1 -1 4.3731 5 1 0 0 -1 1.1833 6 1 0 1 -1 3.0408 7 1 -1 -1 0 5.1222 8 1 -1 0 0 1.8665 9 1 -1 1 0 5.7890 10 1 0 -1 0 2.4739 11 1 0 1 0 2.4739 12 1 -1 -1 1 5.1028 13 1 -1 0 1 3.4608 14 1 -1 1 1 5.7770 15 1 0 -1 1 3.0408 16 1 0 0 1 1.1833 17 1 0 1 1 4.3731 18 1 1 1 1 6.5849 19 1 1 0 1 3.0239 20 1 1 -1 1 6.3022 21 1 1 1 0 5.1222 22 1 1 0 0 1.8665 23 1 1 -1 0 5.7890 24 1 1 1 -1 5.1028 25 1 1 0 -1 3.4608 26 1 1 -1 -1 5.7770 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3729 atoms have been selected out of 3803 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 423 141 141 0.00 2 C002 has 738 246 246 0.00 3 C003 has 102 34 34 0.30 4 C004 has 585 195 195 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 465 155 155 0.00 7 C007 has 726 242 242 0.00 8 C008 has 1774 589 588 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 84 28 28 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.34 Total of13020 atoms and 4331 groups and 4325 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3803 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1256 Number of atoms = 3803 Number of groups = 1261 Number of bonds = 3796 Number of angles = 1360 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1258 Number of HB donors = 2494 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1256 Number of atoms = 3803 Number of groups = 1261 Number of bonds = 3796 Number of angles = 1360 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1258 Number of HB donors = 2494 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.638" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1256" Evaluating: 1256-7 Parameter: NUMWAT <- "1249" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1249" Comparing "1081" and "1249". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.638" Parameter: BOX -> "33.638" Parameter: BOX -> "33.638" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.63800 B = 33.63800 C = 33.63800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5829 2 1 -1 0 -1 3.0211 3 1 -1 1 -1 6.2987 4 1 0 -1 -1 4.3744 5 1 0 0 -1 1.1816 6 1 0 1 -1 3.0395 7 1 -1 -1 0 5.1195 8 1 -1 0 0 1.8646 9 1 -1 1 0 5.7870 10 1 0 -1 0 2.4719 11 1 0 1 0 2.4719 12 1 -1 -1 1 5.0996 13 1 -1 0 1 3.4585 14 1 -1 1 1 5.7742 15 1 0 -1 1 3.0395 16 1 0 0 1 1.1816 17 1 0 1 1 4.3744 18 1 1 1 1 6.5829 19 1 1 0 1 3.0211 20 1 1 -1 1 6.2987 21 1 1 1 0 5.1195 22 1 1 0 0 1.8646 23 1 1 -1 0 5.7870 24 1 1 1 -1 5.0996 25 1 1 0 -1 3.4585 26 1 1 -1 -1 5.7742 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3729 atoms have been selected out of 3803 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 423 141 141 0.00 2 C002 has 738 246 246 0.00 3 C003 has 102 34 34 0.30 4 C004 has 585 195 195 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 465 155 155 0.00 7 C007 has 726 242 242 0.00 8 C008 has 1777 590 589 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 84 28 28 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.33 Total of13023 atoms and 4332 groups and 4326 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3803 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1256 Number of atoms = 3803 Number of groups = 1261 Number of bonds = 3796 Number of angles = 1360 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1258 Number of HB donors = 2494 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1256 Number of atoms = 3803 Number of groups = 1261 Number of bonds = 3796 Number of angles = 1360 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1258 Number of HB donors = 2494 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.636" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1256" Evaluating: 1256-7 Parameter: NUMWAT <- "1249" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1249" Comparing "1081" and "1249". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.636" Parameter: BOX -> "33.636" Parameter: BOX -> "33.636" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.63600 B = 33.63600 C = 33.63600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5810 2 1 -1 0 -1 3.0184 3 1 -1 1 -1 6.2953 4 1 0 -1 -1 4.3758 5 1 0 0 -1 1.1798 6 1 0 1 -1 3.0382 7 1 -1 -1 0 5.1168 8 1 -1 0 0 1.8627 9 1 -1 1 0 5.7850 10 1 0 -1 0 2.4699 11 1 0 1 0 2.4699 12 1 -1 -1 1 5.0965 13 1 -1 0 1 3.4562 14 1 -1 1 1 5.7714 15 1 0 -1 1 3.0382 16 1 0 0 1 1.1798 17 1 0 1 1 4.3758 18 1 1 1 1 6.5810 19 1 1 0 1 3.0184 20 1 1 -1 1 6.2953 21 1 1 1 0 5.1168 22 1 1 0 0 1.8627 23 1 1 -1 0 5.7850 24 1 1 1 -1 5.0965 25 1 1 0 -1 3.4562 26 1 1 -1 -1 5.7714 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3729 atoms have been selected out of 3803 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 423 141 141 0.00 2 C002 has 738 246 246 0.00 3 C003 has 102 34 34 0.30 4 C004 has 585 195 195 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 465 155 155 0.00 7 C007 has 726 242 242 0.00 8 C008 has 1777 590 589 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 84 28 28 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 1.33 Total of13023 atoms and 4332 groups and 4326 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3803 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1256 Number of atoms = 3803 Number of groups = 1261 Number of bonds = 3796 Number of angles = 1360 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1258 Number of HB donors = 2494 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1256 Number of atoms = 3803 Number of groups = 1261 Number of bonds = 3796 Number of angles = 1360 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1258 Number of HB donors = 2494 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.634" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1256" Evaluating: 1256-7 Parameter: NUMWAT <- "1249" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1249" Comparing "1081" and "1249". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.634" Parameter: BOX -> "33.634" Parameter: BOX -> "33.634" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.63400 B = 33.63400 C = 33.63400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5790 2 1 -1 0 -1 3.0157 3 1 -1 1 -1 6.2919 4 1 0 -1 -1 4.3772 5 1 0 0 -1 1.1780 6 1 0 1 -1 3.0369 7 1 -1 -1 0 5.1141 8 1 -1 0 0 1.8608 9 1 -1 1 0 5.7830 10 1 0 -1 0 2.4679 11 1 0 1 0 2.4679 12 1 -1 -1 1 5.0933 13 1 -1 0 1 3.4539 14 1 -1 1 1 5.7686 15 1 0 -1 1 3.0369 16 1 0 0 1 1.1780 17 1 0 1 1 4.3772 18 1 1 1 1 6.5790 19 1 1 0 1 3.0157 20 1 1 -1 1 6.2919 21 1 1 1 0 5.1141 22 1 1 0 0 1.8608 23 1 1 -1 0 5.7830 24 1 1 1 -1 5.0933 25 1 1 0 -1 3.4539 26 1 1 -1 -1 5.7686 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3729 atoms have been selected out of 3803 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1251 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 735 245 245 0.00 3 C003 has 102 34 34 0.30 4 C004 has 585 195 195 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1777 590 589 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 84 28 28 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 1.33 Total of13026 atoms and 4333 groups and 4327 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3803 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1255 Number of atoms = 3800 Number of groups = 1260 Number of bonds = 3793 Number of angles = 1359 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1257 Number of HB donors = 2492 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1255 Number of atoms = 3800 Number of groups = 1260 Number of bonds = 3793 Number of angles = 1359 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1257 Number of HB donors = 2492 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.632" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1255" Evaluating: 1255-7 Parameter: NUMWAT <- "1248" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1248" Comparing "1081" and "1248". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.632" Parameter: BOX -> "33.632" Parameter: BOX -> "33.632" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.63200 B = 33.63200 C = 33.63200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5770 2 1 -1 0 -1 3.0129 3 1 -1 1 -1 6.2884 4 1 0 -1 -1 4.3785 5 1 0 0 -1 1.1762 6 1 0 1 -1 3.0356 7 1 -1 -1 0 5.1114 8 1 -1 0 0 1.8589 9 1 -1 1 0 5.7810 10 1 0 -1 0 2.4659 11 1 0 1 0 2.4659 12 1 -1 -1 1 5.0901 13 1 -1 0 1 3.4515 14 1 -1 1 1 5.7658 15 1 0 -1 1 3.0356 16 1 0 0 1 1.1762 17 1 0 1 1 4.3785 18 1 1 1 1 6.5770 19 1 1 0 1 3.0129 20 1 1 -1 1 6.2884 21 1 1 1 0 5.1114 22 1 1 0 0 1.8589 23 1 1 -1 0 5.7810 24 1 1 1 -1 5.0901 25 1 1 0 -1 3.4515 26 1 1 -1 -1 5.7658 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3726 atoms have been selected out of 3800 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 176 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 735 245 245 0.00 3 C003 has 102 34 34 0.30 4 C004 has 585 195 195 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 465 155 155 0.00 7 C007 has 726 242 242 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 84 28 28 0.00 13 C013 has 471 157 157 0.00 14 C014 has 123 41 41 1.33 Total of12999 atoms and 4324 groups and 4318 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3800 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1254 Number of atoms = 3797 Number of groups = 1259 Number of bonds = 3790 Number of angles = 1358 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1256 Number of HB donors = 2490 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1254 Number of atoms = 3797 Number of groups = 1259 Number of bonds = 3790 Number of angles = 1358 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1256 Number of HB donors = 2490 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.63" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1254" Evaluating: 1254-7 Parameter: NUMWAT <- "1247" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1247" Comparing "1081" and "1247". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.63" Parameter: BOX -> "33.63" Parameter: BOX -> "33.63" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.63000 B = 33.63000 C = 33.63000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5751 2 1 -1 0 -1 3.0102 3 1 -1 1 -1 6.2850 4 1 0 -1 -1 4.3799 5 1 0 0 -1 1.1744 6 1 0 1 -1 3.0343 7 1 -1 -1 0 5.1087 8 1 -1 0 0 1.8571 9 1 -1 1 0 5.7790 10 1 0 -1 0 2.4639 11 1 0 1 0 2.4639 12 1 -1 -1 1 5.0869 13 1 -1 0 1 3.4492 14 1 -1 1 1 5.7630 15 1 0 -1 1 3.0343 16 1 0 0 1 1.1744 17 1 0 1 1 4.3799 18 1 1 1 1 6.5751 19 1 1 0 1 3.0102 20 1 1 -1 1 6.2850 21 1 1 1 0 5.1087 22 1 1 0 0 1.8571 23 1 1 -1 0 5.7790 24 1 1 1 -1 5.0869 25 1 1 0 -1 3.4492 26 1 1 -1 -1 5.7630 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3723 atoms have been selected out of 3797 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 735 245 245 0.00 3 C003 has 102 34 34 0.29 4 C004 has 588 196 196 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 465 155 155 0.00 7 C007 has 726 242 242 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 84 28 28 0.00 13 C013 has 471 157 157 0.00 14 C014 has 123 41 41 1.33 Total of12999 atoms and 4324 groups and 4318 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3797 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1254 Number of atoms = 3797 Number of groups = 1259 Number of bonds = 3790 Number of angles = 1358 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1256 Number of HB donors = 2490 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1254 Number of atoms = 3797 Number of groups = 1259 Number of bonds = 3790 Number of angles = 1358 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1256 Number of HB donors = 2490 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.628" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1254" Evaluating: 1254-7 Parameter: NUMWAT <- "1247" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1247" Comparing "1081" and "1247". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.628" Parameter: BOX -> "33.628" Parameter: BOX -> "33.628" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.62800 B = 33.62800 C = 33.62800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5731 2 1 -1 0 -1 3.0074 3 1 -1 1 -1 6.2815 4 1 0 -1 -1 4.3813 5 1 0 0 -1 1.1726 6 1 0 1 -1 3.0330 7 1 -1 -1 0 5.1060 8 1 -1 0 0 1.8552 9 1 -1 1 0 5.7770 10 1 0 -1 0 2.4619 11 1 0 1 0 2.4619 12 1 -1 -1 1 5.0838 13 1 -1 0 1 3.4469 14 1 -1 1 1 5.7602 15 1 0 -1 1 3.0330 16 1 0 0 1 1.1726 17 1 0 1 1 4.3813 18 1 1 1 1 6.5731 19 1 1 0 1 3.0074 20 1 1 -1 1 6.2815 21 1 1 1 0 5.1060 22 1 1 0 0 1.8552 23 1 1 -1 0 5.7770 24 1 1 1 -1 5.0838 25 1 1 0 -1 3.4469 26 1 1 -1 -1 5.7602 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3723 atoms have been selected out of 3797 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 735 245 245 0.00 3 C003 has 102 34 34 0.29 4 C004 has 588 196 196 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 465 155 155 0.00 7 C007 has 726 242 242 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 84 28 28 0.00 13 C013 has 471 157 157 0.00 14 C014 has 123 41 41 1.32 Total of12999 atoms and 4324 groups and 4318 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3797 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1254 Number of atoms = 3797 Number of groups = 1259 Number of bonds = 3790 Number of angles = 1358 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1256 Number of HB donors = 2490 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1254 Number of atoms = 3797 Number of groups = 1259 Number of bonds = 3790 Number of angles = 1358 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1256 Number of HB donors = 2490 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.626" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1254" Evaluating: 1254-7 Parameter: NUMWAT <- "1247" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1247" Comparing "1081" and "1247". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.626" Parameter: BOX -> "33.626" Parameter: BOX -> "33.626" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.62600 B = 33.62600 C = 33.62600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5712 2 1 -1 0 -1 3.0047 3 1 -1 1 -1 6.2781 4 1 0 -1 -1 4.3826 5 1 0 0 -1 1.1709 6 1 0 1 -1 3.0317 7 1 -1 -1 0 5.1033 8 1 -1 0 0 1.8533 9 1 -1 1 0 5.7750 10 1 0 -1 0 2.4599 11 1 0 1 0 2.4599 12 1 -1 -1 1 5.0806 13 1 -1 0 1 3.4446 14 1 -1 1 1 5.7574 15 1 0 -1 1 3.0317 16 1 0 0 1 1.1709 17 1 0 1 1 4.3826 18 1 1 1 1 6.5712 19 1 1 0 1 3.0047 20 1 1 -1 1 6.2781 21 1 1 1 0 5.1033 22 1 1 0 0 1.8533 23 1 1 -1 0 5.7750 24 1 1 1 -1 5.0806 25 1 1 0 -1 3.4446 26 1 1 -1 -1 5.7574 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3723 atoms have been selected out of 3797 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 420 140 140 0.00 2 C002 has 735 245 245 0.00 3 C003 has 102 34 34 0.29 4 C004 has 588 196 196 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 465 155 155 0.00 7 C007 has 726 242 242 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 84 28 28 0.00 13 C013 has 471 157 157 0.00 14 C014 has 123 41 41 1.32 Total of12999 atoms and 4324 groups and 4318 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3797 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1254 Number of atoms = 3797 Number of groups = 1259 Number of bonds = 3790 Number of angles = 1358 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1256 Number of HB donors = 2490 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1254 Number of atoms = 3797 Number of groups = 1259 Number of bonds = 3790 Number of angles = 1358 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1256 Number of HB donors = 2490 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.624" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1254" Evaluating: 1254-7 Parameter: NUMWAT <- "1247" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1247" Comparing "1081" and "1247". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.624" Parameter: BOX -> "33.624" Parameter: BOX -> "33.624" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.62400 B = 33.62400 C = 33.62400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5692 2 1 -1 0 -1 3.0020 3 1 -1 1 -1 6.2747 4 1 0 -1 -1 4.3840 5 1 0 0 -1 1.1691 6 1 0 1 -1 3.0305 7 1 -1 -1 0 5.1006 8 1 -1 0 0 1.8514 9 1 -1 1 0 5.7730 10 1 0 -1 0 2.4579 11 1 0 1 0 2.4579 12 1 -1 -1 1 5.0774 13 1 -1 0 1 3.4423 14 1 -1 1 1 5.7547 15 1 0 -1 1 3.0305 16 1 0 0 1 1.1691 17 1 0 1 1 4.3840 18 1 1 1 1 6.5692 19 1 1 0 1 3.0020 20 1 1 -1 1 6.2747 21 1 1 1 0 5.1006 22 1 1 0 0 1.8514 23 1 1 -1 0 5.7730 24 1 1 1 -1 5.0774 25 1 1 0 -1 3.4423 26 1 1 -1 -1 5.7547 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3723 atoms have been selected out of 3797 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 423 141 141 0.00 2 C002 has 735 245 245 0.00 3 C003 has 102 34 34 0.29 4 C004 has 588 196 196 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 465 155 155 0.00 7 C007 has 726 242 242 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 84 28 28 0.00 13 C013 has 471 157 157 0.00 14 C014 has 123 41 41 1.32 Total of13002 atoms and 4325 groups and 4319 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3797 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1254 Number of atoms = 3797 Number of groups = 1259 Number of bonds = 3790 Number of angles = 1358 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1256 Number of HB donors = 2490 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1254 Number of atoms = 3797 Number of groups = 1259 Number of bonds = 3790 Number of angles = 1358 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1256 Number of HB donors = 2490 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.622" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1254" Evaluating: 1254-7 Parameter: NUMWAT <- "1247" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1247" Comparing "1081" and "1247". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.622" Parameter: BOX -> "33.622" Parameter: BOX -> "33.622" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.62200 B = 33.62200 C = 33.62200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5673 2 1 -1 0 -1 2.9992 3 1 -1 1 -1 6.2712 4 1 0 -1 -1 4.3854 5 1 0 0 -1 1.1673 6 1 0 1 -1 3.0292 7 1 -1 -1 0 5.0979 8 1 -1 0 0 1.8495 9 1 -1 1 0 5.7710 10 1 0 -1 0 2.4559 11 1 0 1 0 2.4559 12 1 -1 -1 1 5.0743 13 1 -1 0 1 3.4400 14 1 -1 1 1 5.7519 15 1 0 -1 1 3.0292 16 1 0 0 1 1.1673 17 1 0 1 1 4.3854 18 1 1 1 1 6.5673 19 1 1 0 1 2.9992 20 1 1 -1 1 6.2712 21 1 1 1 0 5.0979 22 1 1 0 0 1.8495 23 1 1 -1 0 5.7710 24 1 1 1 -1 5.0743 25 1 1 0 -1 3.4400 26 1 1 -1 -1 5.7519 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3723 atoms have been selected out of 3797 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 423 141 141 0.00 2 C002 has 735 245 245 0.00 3 C003 has 102 34 34 0.29 4 C004 has 588 196 196 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 465 155 155 0.00 7 C007 has 726 242 242 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1653 551 551 0.00 12 C012 has 84 28 28 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 1.32 Total of13008 atoms and 4327 groups and 4321 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3797 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1254 Number of atoms = 3797 Number of groups = 1259 Number of bonds = 3790 Number of angles = 1358 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1256 Number of HB donors = 2490 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1254 Number of atoms = 3797 Number of groups = 1259 Number of bonds = 3790 Number of angles = 1358 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1256 Number of HB donors = 2490 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.62" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1254" Evaluating: 1254-7 Parameter: NUMWAT <- "1247" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1247" Comparing "1081" and "1247". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.62" Parameter: BOX -> "33.62" Parameter: BOX -> "33.62" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.62000 B = 33.62000 C = 33.62000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5653 2 1 -1 0 -1 2.9965 3 1 -1 1 -1 6.2678 4 1 0 -1 -1 4.3867 5 1 0 0 -1 1.1655 6 1 0 1 -1 3.0279 7 1 -1 -1 0 5.0953 8 1 -1 0 0 1.8477 9 1 -1 1 0 5.7690 10 1 0 -1 0 2.4539 11 1 0 1 0 2.4539 12 1 -1 -1 1 5.0711 13 1 -1 0 1 3.4376 14 1 -1 1 1 5.7491 15 1 0 -1 1 3.0279 16 1 0 0 1 1.1655 17 1 0 1 1 4.3867 18 1 1 1 1 6.5653 19 1 1 0 1 2.9965 20 1 1 -1 1 6.2678 21 1 1 1 0 5.0953 22 1 1 0 0 1.8477 23 1 1 -1 0 5.7690 24 1 1 1 -1 5.0711 25 1 1 0 -1 3.4376 26 1 1 -1 -1 5.7491 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3723 atoms have been selected out of 3797 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 423 141 141 0.00 2 C002 has 735 245 245 0.00 3 C003 has 102 34 34 0.28 4 C004 has 588 196 196 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 465 155 155 0.00 7 C007 has 726 242 242 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1653 551 551 0.00 12 C012 has 84 28 28 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 1.32 Total of13008 atoms and 4327 groups and 4321 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3797 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1254 Number of atoms = 3797 Number of groups = 1259 Number of bonds = 3790 Number of angles = 1358 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1256 Number of HB donors = 2490 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1254 Number of atoms = 3797 Number of groups = 1259 Number of bonds = 3790 Number of angles = 1358 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1256 Number of HB donors = 2490 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.618" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1254" Evaluating: 1254-7 Parameter: NUMWAT <- "1247" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1247" Comparing "1081" and "1247". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.618" Parameter: BOX -> "33.618" Parameter: BOX -> "33.618" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.61800 B = 33.61800 C = 33.61800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5634 2 1 -1 0 -1 2.9938 3 1 -1 1 -1 6.2643 4 1 0 -1 -1 4.3881 5 1 0 0 -1 1.1637 6 1 0 1 -1 3.0266 7 1 -1 -1 0 5.0926 8 1 -1 0 0 1.8458 9 1 -1 1 0 5.7670 10 1 0 -1 0 2.4519 11 1 0 1 0 2.4519 12 1 -1 -1 1 5.0679 13 1 -1 0 1 3.4353 14 1 -1 1 1 5.7463 15 1 0 -1 1 3.0266 16 1 0 0 1 1.1637 17 1 0 1 1 4.3881 18 1 1 1 1 6.5634 19 1 1 0 1 2.9938 20 1 1 -1 1 6.2643 21 1 1 1 0 5.0926 22 1 1 0 0 1.8458 23 1 1 -1 0 5.7670 24 1 1 1 -1 5.0679 25 1 1 0 -1 3.4353 26 1 1 -1 -1 5.7463 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3723 atoms have been selected out of 3797 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 423 141 141 0.00 2 C002 has 735 245 245 0.00 3 C003 has 102 34 34 0.28 4 C004 has 588 196 196 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1653 551 551 0.00 12 C012 has 84 28 28 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 1.31 Total of13011 atoms and 4328 groups and 4322 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3797 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1254 Number of atoms = 3797 Number of groups = 1259 Number of bonds = 3790 Number of angles = 1358 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1256 Number of HB donors = 2490 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1254 Number of atoms = 3797 Number of groups = 1259 Number of bonds = 3790 Number of angles = 1358 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1256 Number of HB donors = 2490 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.616" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1254" Evaluating: 1254-7 Parameter: NUMWAT <- "1247" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1247" Comparing "1081" and "1247". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.616" Parameter: BOX -> "33.616" Parameter: BOX -> "33.616" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.61600 B = 33.61600 C = 33.61600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5614 2 1 -1 0 -1 2.9910 3 1 -1 1 -1 6.2609 4 1 0 -1 -1 4.3895 5 1 0 0 -1 1.1620 6 1 0 1 -1 3.0253 7 1 -1 -1 0 5.0899 8 1 -1 0 0 1.8439 9 1 -1 1 0 5.7650 10 1 0 -1 0 2.4499 11 1 0 1 0 2.4499 12 1 -1 -1 1 5.0648 13 1 -1 0 1 3.4330 14 1 -1 1 1 5.7435 15 1 0 -1 1 3.0253 16 1 0 0 1 1.1620 17 1 0 1 1 4.3895 18 1 1 1 1 6.5614 19 1 1 0 1 2.9910 20 1 1 -1 1 6.2609 21 1 1 1 0 5.0899 22 1 1 0 0 1.8439 23 1 1 -1 0 5.7650 24 1 1 1 -1 5.0648 25 1 1 0 -1 3.4330 26 1 1 -1 -1 5.7435 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3723 atoms have been selected out of 3797 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 423 141 141 0.00 2 C002 has 735 245 245 0.00 3 C003 has 102 34 34 0.28 4 C004 has 588 196 196 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1653 551 551 0.00 12 C012 has 84 28 28 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 1.31 Total of13011 atoms and 4328 groups and 4322 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3797 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1254 Number of atoms = 3797 Number of groups = 1259 Number of bonds = 3790 Number of angles = 1358 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1256 Number of HB donors = 2490 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1254 Number of atoms = 3797 Number of groups = 1259 Number of bonds = 3790 Number of angles = 1358 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1256 Number of HB donors = 2490 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.614" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1254" Evaluating: 1254-7 Parameter: NUMWAT <- "1247" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1247" Comparing "1081" and "1247". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.614" Parameter: BOX -> "33.614" Parameter: BOX -> "33.614" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.61400 B = 33.61400 C = 33.61400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5595 2 1 -1 0 -1 2.9883 3 1 -1 1 -1 6.2575 4 1 0 -1 -1 4.3909 5 1 0 0 -1 1.1602 6 1 0 1 -1 3.0241 7 1 -1 -1 0 5.0872 8 1 -1 0 0 1.8420 9 1 -1 1 0 5.7631 10 1 0 -1 0 2.4479 11 1 0 1 0 2.4479 12 1 -1 -1 1 5.0616 13 1 -1 0 1 3.4307 14 1 -1 1 1 5.7407 15 1 0 -1 1 3.0241 16 1 0 0 1 1.1602 17 1 0 1 1 4.3909 18 1 1 1 1 6.5595 19 1 1 0 1 2.9883 20 1 1 -1 1 6.2575 21 1 1 1 0 5.0872 22 1 1 0 0 1.8420 23 1 1 -1 0 5.7631 24 1 1 1 -1 5.0616 25 1 1 0 -1 3.4307 26 1 1 -1 -1 5.7407 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3723 atoms have been selected out of 3797 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 423 141 141 0.00 2 C002 has 735 245 245 0.00 3 C003 has 102 34 34 0.28 4 C004 has 588 196 196 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1653 551 551 0.00 12 C012 has 84 28 28 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 1.31 Total of13011 atoms and 4328 groups and 4322 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3797 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1254 Number of atoms = 3797 Number of groups = 1259 Number of bonds = 3790 Number of angles = 1358 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1256 Number of HB donors = 2490 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1254 Number of atoms = 3797 Number of groups = 1259 Number of bonds = 3790 Number of angles = 1358 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1256 Number of HB donors = 2490 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.612" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1254" Evaluating: 1254-7 Parameter: NUMWAT <- "1247" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1247" Comparing "1081" and "1247". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.612" Parameter: BOX -> "33.612" Parameter: BOX -> "33.612" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.61200 B = 33.61200 C = 33.61200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5575 2 1 -1 0 -1 2.9856 3 1 -1 1 -1 6.2540 4 1 0 -1 -1 4.3922 5 1 0 0 -1 1.1584 6 1 0 1 -1 3.0228 7 1 -1 -1 0 5.0845 8 1 -1 0 0 1.8402 9 1 -1 1 0 5.7611 10 1 0 -1 0 2.4459 11 1 0 1 0 2.4459 12 1 -1 -1 1 5.0584 13 1 -1 0 1 3.4284 14 1 -1 1 1 5.7379 15 1 0 -1 1 3.0228 16 1 0 0 1 1.1584 17 1 0 1 1 4.3922 18 1 1 1 1 6.5575 19 1 1 0 1 2.9856 20 1 1 -1 1 6.2540 21 1 1 1 0 5.0845 22 1 1 0 0 1.8402 23 1 1 -1 0 5.7611 24 1 1 1 -1 5.0584 25 1 1 0 -1 3.4284 26 1 1 -1 -1 5.7379 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3723 atoms have been selected out of 3797 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 423 141 141 0.00 2 C002 has 735 245 245 0.00 3 C003 has 102 34 34 0.28 4 C004 has 588 196 196 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1653 551 551 0.00 12 C012 has 84 28 28 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 1.31 Total of13011 atoms and 4328 groups and 4322 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3797 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1254 Number of atoms = 3797 Number of groups = 1259 Number of bonds = 3790 Number of angles = 1358 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1256 Number of HB donors = 2490 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1254 Number of atoms = 3797 Number of groups = 1259 Number of bonds = 3790 Number of angles = 1358 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1256 Number of HB donors = 2490 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.61" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1254" Evaluating: 1254-7 Parameter: NUMWAT <- "1247" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1247" Comparing "1081" and "1247". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.61" Parameter: BOX -> "33.61" Parameter: BOX -> "33.61" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.61000 B = 33.61000 C = 33.61000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5556 2 1 -1 0 -1 2.9828 3 1 -1 1 -1 6.2506 4 1 0 -1 -1 4.3936 5 1 0 0 -1 1.1566 6 1 0 1 -1 3.0215 7 1 -1 -1 0 5.0818 8 1 -1 0 0 1.8383 9 1 -1 1 0 5.7591 10 1 0 -1 0 2.4439 11 1 0 1 0 2.4439 12 1 -1 -1 1 5.0552 13 1 -1 0 1 3.4261 14 1 -1 1 1 5.7351 15 1 0 -1 1 3.0215 16 1 0 0 1 1.1566 17 1 0 1 1 4.3936 18 1 1 1 1 6.5556 19 1 1 0 1 2.9828 20 1 1 -1 1 6.2506 21 1 1 1 0 5.0818 22 1 1 0 0 1.8383 23 1 1 -1 0 5.7591 24 1 1 1 -1 5.0552 25 1 1 0 -1 3.4261 26 1 1 -1 -1 5.7351 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3723 atoms have been selected out of 3797 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 423 141 141 0.00 2 C002 has 735 245 245 0.00 3 C003 has 102 34 34 0.27 4 C004 has 588 196 196 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1653 551 551 0.00 12 C012 has 84 28 28 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 1.31 Total of13011 atoms and 4328 groups and 4322 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3797 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1254 Number of atoms = 3797 Number of groups = 1259 Number of bonds = 3790 Number of angles = 1358 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1256 Number of HB donors = 2490 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1254 Number of atoms = 3797 Number of groups = 1259 Number of bonds = 3790 Number of angles = 1358 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1256 Number of HB donors = 2490 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.608" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1254" Evaluating: 1254-7 Parameter: NUMWAT <- "1247" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1247" Comparing "1081" and "1247". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.608" Parameter: BOX -> "33.608" Parameter: BOX -> "33.608" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.60800 B = 33.60800 C = 33.60800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5536 2 1 -1 0 -1 2.9801 3 1 -1 1 -1 6.2471 4 1 0 -1 -1 4.3950 5 1 0 0 -1 1.1549 6 1 0 1 -1 3.0203 7 1 -1 -1 0 5.0791 8 1 -1 0 0 1.8364 9 1 -1 1 0 5.7571 10 1 0 -1 0 2.4419 11 1 0 1 0 2.4419 12 1 -1 -1 1 5.0521 13 1 -1 0 1 3.4238 14 1 -1 1 1 5.7324 15 1 0 -1 1 3.0203 16 1 0 0 1 1.1549 17 1 0 1 1 4.3950 18 1 1 1 1 6.5536 19 1 1 0 1 2.9801 20 1 1 -1 1 6.2471 21 1 1 1 0 5.0791 22 1 1 0 0 1.8364 23 1 1 -1 0 5.7571 24 1 1 1 -1 5.0521 25 1 1 0 -1 3.4238 26 1 1 -1 -1 5.7324 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3723 atoms have been selected out of 3797 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 423 141 141 0.00 2 C002 has 735 245 245 0.00 3 C003 has 102 34 34 0.27 4 C004 has 588 196 196 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 468 156 156 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1653 551 551 0.00 12 C012 has 84 28 28 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 1.30 Total of13014 atoms and 4329 groups and 4323 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3797 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1254 Number of atoms = 3797 Number of groups = 1259 Number of bonds = 3790 Number of angles = 1358 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1256 Number of HB donors = 2490 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1254 Number of atoms = 3797 Number of groups = 1259 Number of bonds = 3790 Number of angles = 1358 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1256 Number of HB donors = 2490 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.606" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1254" Evaluating: 1254-7 Parameter: NUMWAT <- "1247" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1247" Comparing "1081" and "1247". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.606" Parameter: BOX -> "33.606" Parameter: BOX -> "33.606" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.60600 B = 33.60600 C = 33.60600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5517 2 1 -1 0 -1 2.9774 3 1 -1 1 -1 6.2437 4 1 0 -1 -1 4.3964 5 1 0 0 -1 1.1531 6 1 0 1 -1 3.0190 7 1 -1 -1 0 5.0764 8 1 -1 0 0 1.8345 9 1 -1 1 0 5.7551 10 1 0 -1 0 2.4399 11 1 0 1 0 2.4399 12 1 -1 -1 1 5.0489 13 1 -1 0 1 3.4214 14 1 -1 1 1 5.7296 15 1 0 -1 1 3.0190 16 1 0 0 1 1.1531 17 1 0 1 1 4.3964 18 1 1 1 1 6.5517 19 1 1 0 1 2.9774 20 1 1 -1 1 6.2437 21 1 1 1 0 5.0764 22 1 1 0 0 1.8345 23 1 1 -1 0 5.7551 24 1 1 1 -1 5.0489 25 1 1 0 -1 3.4214 26 1 1 -1 -1 5.7296 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3723 atoms have been selected out of 3797 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 732 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 738 246 246 0.00 3 C003 has 102 34 34 0.27 4 C004 has 588 196 196 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 468 156 156 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1653 551 551 0.00 12 C012 has 84 28 28 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 1.30 Total of13014 atoms and 4329 groups and 4323 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3797 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1253 Number of atoms = 3794 Number of groups = 1258 Number of bonds = 3787 Number of angles = 1357 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1255 Number of HB donors = 2488 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1253 Number of atoms = 3794 Number of groups = 1258 Number of bonds = 3787 Number of angles = 1357 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1255 Number of HB donors = 2488 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.604" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1253" Evaluating: 1253-7 Parameter: NUMWAT <- "1246" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1246" Comparing "1081" and "1246". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.604" Parameter: BOX -> "33.604" Parameter: BOX -> "33.604" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.60400 B = 33.60400 C = 33.60400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5498 2 1 -1 0 -1 2.9746 3 1 -1 1 -1 6.2403 4 1 0 -1 -1 4.3978 5 1 0 0 -1 1.1513 6 1 0 1 -1 3.0178 7 1 -1 -1 0 5.0737 8 1 -1 0 0 1.8326 9 1 -1 1 0 5.7531 10 1 0 -1 0 2.4379 11 1 0 1 0 2.4379 12 1 -1 -1 1 5.0457 13 1 -1 0 1 3.4191 14 1 -1 1 1 5.7268 15 1 0 -1 1 3.0178 16 1 0 0 1 1.1513 17 1 0 1 1 4.3978 18 1 1 1 1 6.5498 19 1 1 0 1 2.9746 20 1 1 -1 1 6.2403 21 1 1 1 0 5.0737 22 1 1 0 0 1.8326 23 1 1 -1 0 5.7531 24 1 1 1 -1 5.0457 25 1 1 0 -1 3.4191 26 1 1 -1 -1 5.7268 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3720 atoms have been selected out of 3794 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 102 34 34 0.27 4 C004 has 588 196 196 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 468 156 156 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1653 551 551 0.00 12 C012 has 84 28 28 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 1.30 Total of12999 atoms and 4324 groups and 4318 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3794 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1253 Number of atoms = 3794 Number of groups = 1258 Number of bonds = 3787 Number of angles = 1357 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1255 Number of HB donors = 2488 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1253 Number of atoms = 3794 Number of groups = 1258 Number of bonds = 3787 Number of angles = 1357 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1255 Number of HB donors = 2488 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.602" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1253" Evaluating: 1253-7 Parameter: NUMWAT <- "1246" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1246" Comparing "1081" and "1246". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.602" Parameter: BOX -> "33.602" Parameter: BOX -> "33.602" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.60200 B = 33.60200 C = 33.60200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5478 2 1 -1 0 -1 2.9719 3 1 -1 1 -1 6.2368 4 1 0 -1 -1 4.3991 5 1 0 0 -1 1.1495 6 1 0 1 -1 3.0165 7 1 -1 -1 0 5.0710 8 1 -1 0 0 1.8308 9 1 -1 1 0 5.7511 10 1 0 -1 0 2.4359 11 1 0 1 0 2.4359 12 1 -1 -1 1 5.0426 13 1 -1 0 1 3.4168 14 1 -1 1 1 5.7240 15 1 0 -1 1 3.0165 16 1 0 0 1 1.1495 17 1 0 1 1 4.3991 18 1 1 1 1 6.5478 19 1 1 0 1 2.9719 20 1 1 -1 1 6.2368 21 1 1 1 0 5.0710 22 1 1 0 0 1.8308 23 1 1 -1 0 5.7511 24 1 1 1 -1 5.0426 25 1 1 0 -1 3.4168 26 1 1 -1 -1 5.7240 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3720 atoms have been selected out of 3794 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 102 34 34 0.27 4 C004 has 588 196 196 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 468 156 156 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1653 551 551 0.00 12 C012 has 84 28 28 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 1.30 Total of13002 atoms and 4325 groups and 4319 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3794 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1253 Number of atoms = 3794 Number of groups = 1258 Number of bonds = 3787 Number of angles = 1357 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1255 Number of HB donors = 2488 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1253 Number of atoms = 3794 Number of groups = 1258 Number of bonds = 3787 Number of angles = 1357 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1255 Number of HB donors = 2488 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.6" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1253" Evaluating: 1253-7 Parameter: NUMWAT <- "1246" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1246" Comparing "1081" and "1246". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.6" Parameter: BOX -> "33.6" Parameter: BOX -> "33.6" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.60000 B = 33.60000 C = 33.60000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5459 2 1 -1 0 -1 2.9692 3 1 -1 1 -1 6.2334 4 1 0 -1 -1 4.4005 5 1 0 0 -1 1.1478 6 1 0 1 -1 3.0152 7 1 -1 -1 0 5.0683 8 1 -1 0 0 1.8289 9 1 -1 1 0 5.7491 10 1 0 -1 0 2.4339 11 1 0 1 0 2.4339 12 1 -1 -1 1 5.0394 13 1 -1 0 1 3.4145 14 1 -1 1 1 5.7212 15 1 0 -1 1 3.0152 16 1 0 0 1 1.1478 17 1 0 1 1 4.4005 18 1 1 1 1 6.5459 19 1 1 0 1 2.9692 20 1 1 -1 1 6.2334 21 1 1 1 0 5.0683 22 1 1 0 0 1.8289 23 1 1 -1 0 5.7491 24 1 1 1 -1 5.0394 25 1 1 0 -1 3.4145 26 1 1 -1 -1 5.7212 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3720 atoms have been selected out of 3794 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 672 OPERATED ON BY TRANSFORMATION C022 RESIDUE 783 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.26 4 C004 has 591 197 197 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 84 28 28 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 1.30 Total of13005 atoms and 4326 groups and 4320 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3794 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1251 Number of atoms = 3788 Number of groups = 1256 Number of bonds = 3781 Number of angles = 1355 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1253 Number of HB donors = 2484 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1251 Number of atoms = 3788 Number of groups = 1256 Number of bonds = 3781 Number of angles = 1355 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1253 Number of HB donors = 2484 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.598" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1251" Evaluating: 1251-7 Parameter: NUMWAT <- "1244" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1244" Comparing "1081" and "1244". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.598" Parameter: BOX -> "33.598" Parameter: BOX -> "33.598" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.59800 B = 33.59800 C = 33.59800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5439 2 1 -1 0 -1 2.9664 3 1 -1 1 -1 6.2299 4 1 0 -1 -1 4.4019 5 1 0 0 -1 1.1460 6 1 0 1 -1 3.0140 7 1 -1 -1 0 5.0656 8 1 -1 0 0 1.8270 9 1 -1 1 0 5.7471 10 1 0 -1 0 2.4319 11 1 0 1 0 2.4319 12 1 -1 -1 1 5.0362 13 1 -1 0 1 3.4122 14 1 -1 1 1 5.7184 15 1 0 -1 1 3.0140 16 1 0 0 1 1.1460 17 1 0 1 1 4.4019 18 1 1 1 1 6.5439 19 1 1 0 1 2.9664 20 1 1 -1 1 6.2299 21 1 1 1 0 5.0656 22 1 1 0 0 1.8270 23 1 1 -1 0 5.7471 24 1 1 1 -1 5.0362 25 1 1 0 -1 3.4122 26 1 1 -1 -1 5.7184 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3714 atoms have been selected out of 3788 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 738 246 246 0.00 3 C003 has 102 34 34 0.26 4 C004 has 588 196 196 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1756 583 582 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 84 28 28 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 1.29 Total of12981 atoms and 4318 groups and 4312 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3788 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1251 Number of atoms = 3788 Number of groups = 1256 Number of bonds = 3781 Number of angles = 1355 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1253 Number of HB donors = 2484 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1251 Number of atoms = 3788 Number of groups = 1256 Number of bonds = 3781 Number of angles = 1355 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1253 Number of HB donors = 2484 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.596" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1251" Evaluating: 1251-7 Parameter: NUMWAT <- "1244" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1244" Comparing "1081" and "1244". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.596" Parameter: BOX -> "33.596" Parameter: BOX -> "33.596" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.59600 B = 33.59600 C = 33.59600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5420 2 1 -1 0 -1 2.9637 3 1 -1 1 -1 6.2265 4 1 0 -1 -1 4.4033 5 1 0 0 -1 1.1442 6 1 0 1 -1 3.0127 7 1 -1 -1 0 5.0629 8 1 -1 0 0 1.8251 9 1 -1 1 0 5.7451 10 1 0 -1 0 2.4299 11 1 0 1 0 2.4299 12 1 -1 -1 1 5.0331 13 1 -1 0 1 3.4099 14 1 -1 1 1 5.7157 15 1 0 -1 1 3.0127 16 1 0 0 1 1.1442 17 1 0 1 1 4.4033 18 1 1 1 1 6.5420 19 1 1 0 1 2.9637 20 1 1 -1 1 6.2265 21 1 1 1 0 5.0629 22 1 1 0 0 1.8251 23 1 1 -1 0 5.7451 24 1 1 1 -1 5.0331 25 1 1 0 -1 3.4099 26 1 1 -1 -1 5.7157 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3714 atoms have been selected out of 3788 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 738 246 246 0.00 3 C003 has 102 34 34 0.26 4 C004 has 588 196 196 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1756 583 582 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 84 28 28 0.00 13 C013 has 477 159 159 0.00 14 C014 has 123 41 41 1.29 Total of12984 atoms and 4319 groups and 4313 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3788 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1251 Number of atoms = 3788 Number of groups = 1256 Number of bonds = 3781 Number of angles = 1355 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1253 Number of HB donors = 2484 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1251 Number of atoms = 3788 Number of groups = 1256 Number of bonds = 3781 Number of angles = 1355 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1253 Number of HB donors = 2484 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.594" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1251" Evaluating: 1251-7 Parameter: NUMWAT <- "1244" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1244" Comparing "1081" and "1244". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.594" Parameter: BOX -> "33.594" Parameter: BOX -> "33.594" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.59400 B = 33.59400 C = 33.59400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5401 2 1 -1 0 -1 2.9610 3 1 -1 1 -1 6.2231 4 1 0 -1 -1 4.4047 5 1 0 0 -1 1.1425 6 1 0 1 -1 3.0115 7 1 -1 -1 0 5.0603 8 1 -1 0 0 1.8233 9 1 -1 1 0 5.7431 10 1 0 -1 0 2.4279 11 1 0 1 0 2.4279 12 1 -1 -1 1 5.0299 13 1 -1 0 1 3.4076 14 1 -1 1 1 5.7129 15 1 0 -1 1 3.0115 16 1 0 0 1 1.1425 17 1 0 1 1 4.4047 18 1 1 1 1 6.5401 19 1 1 0 1 2.9610 20 1 1 -1 1 6.2231 21 1 1 1 0 5.0603 22 1 1 0 0 1.8233 23 1 1 -1 0 5.7431 24 1 1 1 -1 5.0299 25 1 1 0 -1 3.4076 26 1 1 -1 -1 5.7129 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3714 atoms have been selected out of 3788 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 429 143 143 0.00 2 C002 has 738 246 246 0.00 3 C003 has 102 34 34 0.26 4 C004 has 588 196 196 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1756 583 582 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 84 28 28 0.00 13 C013 has 477 159 159 0.00 14 C014 has 123 41 41 1.29 Total of12987 atoms and 4320 groups and 4314 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3788 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1251 Number of atoms = 3788 Number of groups = 1256 Number of bonds = 3781 Number of angles = 1355 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1253 Number of HB donors = 2484 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1251 Number of atoms = 3788 Number of groups = 1256 Number of bonds = 3781 Number of angles = 1355 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1253 Number of HB donors = 2484 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.592" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1251" Evaluating: 1251-7 Parameter: NUMWAT <- "1244" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1244" Comparing "1081" and "1244". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.592" Parameter: BOX -> "33.592" Parameter: BOX -> "33.592" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.59200 B = 33.59200 C = 33.59200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5381 2 1 -1 0 -1 2.9582 3 1 -1 1 -1 6.2196 4 1 0 -1 -1 4.4061 5 1 0 0 -1 1.1407 6 1 0 1 -1 3.0102 7 1 -1 -1 0 5.0576 8 1 -1 0 0 1.8214 9 1 -1 1 0 5.7411 10 1 0 -1 0 2.4259 11 1 0 1 0 2.4259 12 1 -1 -1 1 5.0267 13 1 -1 0 1 3.4053 14 1 -1 1 1 5.7101 15 1 0 -1 1 3.0102 16 1 0 0 1 1.1407 17 1 0 1 1 4.4061 18 1 1 1 1 6.5381 19 1 1 0 1 2.9582 20 1 1 -1 1 6.2196 21 1 1 1 0 5.0576 22 1 1 0 0 1.8214 23 1 1 -1 0 5.7411 24 1 1 1 -1 5.0267 25 1 1 0 -1 3.4053 26 1 1 -1 -1 5.7101 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3714 atoms have been selected out of 3788 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 429 143 143 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.26 4 C004 has 588 196 196 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1756 583 582 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 84 28 28 0.00 13 C013 has 477 159 159 0.00 14 C014 has 123 41 41 1.29 Total of12990 atoms and 4321 groups and 4315 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3788 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1251 Number of atoms = 3788 Number of groups = 1256 Number of bonds = 3781 Number of angles = 1355 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1253 Number of HB donors = 2484 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1251 Number of atoms = 3788 Number of groups = 1256 Number of bonds = 3781 Number of angles = 1355 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1253 Number of HB donors = 2484 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.59" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1251" Evaluating: 1251-7 Parameter: NUMWAT <- "1244" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1244" Comparing "1081" and "1244". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.59" Parameter: BOX -> "33.59" Parameter: BOX -> "33.59" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.59000 B = 33.59000 C = 33.59000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5362 2 1 -1 0 -1 2.9555 3 1 -1 1 -1 6.2162 4 1 0 -1 -1 4.4075 5 1 0 0 -1 1.1389 6 1 0 1 -1 3.0090 7 1 -1 -1 0 5.0549 8 1 -1 0 0 1.8195 9 1 -1 1 0 5.7392 10 1 0 -1 0 2.4239 11 1 0 1 0 2.4239 12 1 -1 -1 1 5.0236 13 1 -1 0 1 3.4030 14 1 -1 1 1 5.7073 15 1 0 -1 1 3.0090 16 1 0 0 1 1.1389 17 1 0 1 1 4.4075 18 1 1 1 1 6.5362 19 1 1 0 1 2.9555 20 1 1 -1 1 6.2162 21 1 1 1 0 5.0549 22 1 1 0 0 1.8195 23 1 1 -1 0 5.7392 24 1 1 1 -1 5.0236 25 1 1 0 -1 3.4030 26 1 1 -1 -1 5.7073 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3714 atoms have been selected out of 3788 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 429 143 143 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.25 4 C004 has 588 196 196 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1756 583 582 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 84 28 28 0.00 13 C013 has 477 159 159 0.00 14 C014 has 123 41 41 1.29 Total of12993 atoms and 4322 groups and 4316 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3788 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1251 Number of atoms = 3788 Number of groups = 1256 Number of bonds = 3781 Number of angles = 1355 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1253 Number of HB donors = 2484 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1251 Number of atoms = 3788 Number of groups = 1256 Number of bonds = 3781 Number of angles = 1355 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1253 Number of HB donors = 2484 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.588" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1251" Evaluating: 1251-7 Parameter: NUMWAT <- "1244" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1244" Comparing "1081" and "1244". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.588" Parameter: BOX -> "33.588" Parameter: BOX -> "33.588" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.58800 B = 33.58800 C = 33.58800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5343 2 1 -1 0 -1 2.9528 3 1 -1 1 -1 6.2127 4 1 0 -1 -1 4.4089 5 1 0 0 -1 1.1371 6 1 0 1 -1 3.0078 7 1 -1 -1 0 5.0522 8 1 -1 0 0 1.8176 9 1 -1 1 0 5.7372 10 1 0 -1 0 2.4219 11 1 0 1 0 2.4219 12 1 -1 -1 1 5.0204 13 1 -1 0 1 3.4007 14 1 -1 1 1 5.7046 15 1 0 -1 1 3.0078 16 1 0 0 1 1.1371 17 1 0 1 1 4.4089 18 1 1 1 1 6.5343 19 1 1 0 1 2.9528 20 1 1 -1 1 6.2127 21 1 1 1 0 5.0522 22 1 1 0 0 1.8176 23 1 1 -1 0 5.7372 24 1 1 1 -1 5.0204 25 1 1 0 -1 3.4007 26 1 1 -1 -1 5.7046 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3714 atoms have been selected out of 3788 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 829 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 432 144 144 0.00 2 C002 has 738 246 246 0.00 3 C003 has 102 34 34 0.25 4 C004 has 588 196 196 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 465 155 155 0.00 7 C007 has 732 244 244 0.00 8 C008 has 1756 583 582 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 84 28 28 0.00 13 C013 has 477 159 159 0.00 14 C014 has 123 41 41 1.21 Total of12993 atoms and 4322 groups and 4316 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3788 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1250 Number of atoms = 3785 Number of groups = 1255 Number of bonds = 3778 Number of angles = 1354 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1252 Number of HB donors = 2482 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1250 Number of atoms = 3785 Number of groups = 1255 Number of bonds = 3778 Number of angles = 1354 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1252 Number of HB donors = 2482 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.586" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1250" Evaluating: 1250-7 Parameter: NUMWAT <- "1243" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1243" Comparing "1081" and "1243". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.586" Parameter: BOX -> "33.586" Parameter: BOX -> "33.586" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.58600 B = 33.58600 C = 33.58600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5323 2 1 -1 0 -1 2.9500 3 1 -1 1 -1 6.2093 4 1 0 -1 -1 4.4103 5 1 0 0 -1 1.1354 6 1 0 1 -1 3.0065 7 1 -1 -1 0 5.0495 8 1 -1 0 0 1.8158 9 1 -1 1 0 5.7352 10 1 0 -1 0 2.4199 11 1 0 1 0 2.4199 12 1 -1 -1 1 5.0173 13 1 -1 0 1 3.3984 14 1 -1 1 1 5.7018 15 1 0 -1 1 3.0065 16 1 0 0 1 1.1354 17 1 0 1 1 4.4103 18 1 1 1 1 6.5323 19 1 1 0 1 2.9500 20 1 1 -1 1 6.2093 21 1 1 1 0 5.0495 22 1 1 0 0 1.8158 23 1 1 -1 0 5.7352 24 1 1 1 -1 5.0173 25 1 1 0 -1 3.3984 26 1 1 -1 -1 5.7018 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3711 atoms have been selected out of 3785 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 429 143 143 0.00 2 C002 has 738 246 246 0.00 3 C003 has 102 34 34 0.25 4 C004 has 588 196 196 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 465 155 155 0.00 7 C007 has 732 244 244 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1644 548 548 0.00 12 C012 has 84 28 28 0.00 13 C013 has 477 159 159 0.00 14 C014 has 123 41 41 1.28 Total of12981 atoms and 4318 groups and 4312 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3785 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1250 Number of atoms = 3785 Number of groups = 1255 Number of bonds = 3778 Number of angles = 1354 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1252 Number of HB donors = 2482 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1250 Number of atoms = 3785 Number of groups = 1255 Number of bonds = 3778 Number of angles = 1354 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1252 Number of HB donors = 2482 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.584" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1250" Evaluating: 1250-7 Parameter: NUMWAT <- "1243" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1243" Comparing "1081" and "1243". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.584" Parameter: BOX -> "33.584" Parameter: BOX -> "33.584" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.58400 B = 33.58400 C = 33.58400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5304 2 1 -1 0 -1 2.9473 3 1 -1 1 -1 6.2059 4 1 0 -1 -1 4.4117 5 1 0 0 -1 1.1336 6 1 0 1 -1 3.0053 7 1 -1 -1 0 5.0468 8 1 -1 0 0 1.8139 9 1 -1 1 0 5.7332 10 1 0 -1 0 2.4179 11 1 0 1 0 2.4179 12 1 -1 -1 1 5.0141 13 1 -1 0 1 3.3961 14 1 -1 1 1 5.6990 15 1 0 -1 1 3.0053 16 1 0 0 1 1.1336 17 1 0 1 1 4.4117 18 1 1 1 1 6.5304 19 1 1 0 1 2.9473 20 1 1 -1 1 6.2059 21 1 1 1 0 5.0468 22 1 1 0 0 1.8139 23 1 1 -1 0 5.7332 24 1 1 1 -1 5.0141 25 1 1 0 -1 3.3961 26 1 1 -1 -1 5.6990 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3711 atoms have been selected out of 3785 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 429 143 143 0.00 2 C002 has 738 246 246 0.00 3 C003 has 102 34 34 0.25 4 C004 has 588 196 196 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 465 155 155 0.00 7 C007 has 732 244 244 0.00 8 C008 has 1756 583 582 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1644 548 548 0.00 12 C012 has 84 28 28 0.00 13 C013 has 477 159 159 0.00 14 C014 has 123 41 41 1.28 Total of12984 atoms and 4319 groups and 4313 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3785 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1250 Number of atoms = 3785 Number of groups = 1255 Number of bonds = 3778 Number of angles = 1354 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1252 Number of HB donors = 2482 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1250 Number of atoms = 3785 Number of groups = 1255 Number of bonds = 3778 Number of angles = 1354 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1252 Number of HB donors = 2482 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.582" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1250" Evaluating: 1250-7 Parameter: NUMWAT <- "1243" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1243" Comparing "1081" and "1243". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.582" Parameter: BOX -> "33.582" Parameter: BOX -> "33.582" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.58200 B = 33.58200 C = 33.58200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5285 2 1 -1 0 -1 2.9446 3 1 -1 1 -1 6.2024 4 1 0 -1 -1 4.4131 5 1 0 0 -1 1.1318 6 1 0 1 -1 3.0040 7 1 -1 -1 0 5.0441 8 1 -1 0 0 1.8120 9 1 -1 1 0 5.7312 10 1 0 -1 0 2.4159 11 1 0 1 0 2.4159 12 1 -1 -1 1 5.0109 13 1 -1 0 1 3.3938 14 1 -1 1 1 5.6962 15 1 0 -1 1 3.0040 16 1 0 0 1 1.1318 17 1 0 1 1 4.4131 18 1 1 1 1 6.5285 19 1 1 0 1 2.9446 20 1 1 -1 1 6.2024 21 1 1 1 0 5.0441 22 1 1 0 0 1.8120 23 1 1 -1 0 5.7312 24 1 1 1 -1 5.0109 25 1 1 0 -1 3.3938 26 1 1 -1 -1 5.6962 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3711 atoms have been selected out of 3785 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1199 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 102 34 34 0.25 4 C004 has 585 195 195 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 465 155 155 0.00 7 C007 has 732 244 244 0.00 8 C008 has 1756 583 582 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1644 548 548 0.00 12 C012 has 87 29 29 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.28 Total of12987 atoms and 4320 groups and 4314 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3785 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1249 Number of atoms = 3782 Number of groups = 1254 Number of bonds = 3775 Number of angles = 1353 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1251 Number of HB donors = 2480 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1249 Number of atoms = 3782 Number of groups = 1254 Number of bonds = 3775 Number of angles = 1353 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1251 Number of HB donors = 2480 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.58" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1249" Evaluating: 1249-7 Parameter: NUMWAT <- "1242" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1242" Comparing "1081" and "1242". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.58" Parameter: BOX -> "33.58" Parameter: BOX -> "33.58" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.58000 B = 33.58000 C = 33.58000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5266 2 1 -1 0 -1 2.9419 3 1 -1 1 -1 6.1990 4 1 0 -1 -1 4.4145 5 1 0 0 -1 1.1301 6 1 0 1 -1 3.0028 7 1 -1 -1 0 5.0414 8 1 -1 0 0 1.8101 9 1 -1 1 0 5.7292 10 1 0 -1 0 2.4139 11 1 0 1 0 2.4139 12 1 -1 -1 1 5.0078 13 1 -1 0 1 3.3915 14 1 -1 1 1 5.6935 15 1 0 -1 1 3.0028 16 1 0 0 1 1.1301 17 1 0 1 1 4.4145 18 1 1 1 1 6.5266 19 1 1 0 1 2.9419 20 1 1 -1 1 6.1990 21 1 1 1 0 5.0414 22 1 1 0 0 1.8101 23 1 1 -1 0 5.7292 24 1 1 1 -1 5.0078 25 1 1 0 -1 3.3915 26 1 1 -1 -1 5.6935 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3708 atoms have been selected out of 3782 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 981 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 102 34 34 0.24 4 C004 has 582 194 194 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1641 547 547 0.00 12 C012 has 84 28 28 0.00 13 C013 has 477 159 159 0.00 14 C014 has 123 41 41 1.28 Total of12957 atoms and 4310 groups and 4304 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3782 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.578" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1248" Evaluating: 1248-7 Parameter: NUMWAT <- "1241" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1241" Comparing "1081" and "1241". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.578" Parameter: BOX -> "33.578" Parameter: BOX -> "33.578" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.57800 B = 33.57800 C = 33.57800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5246 2 1 -1 0 -1 2.9391 3 1 -1 1 -1 6.1955 4 1 0 -1 -1 4.4159 5 1 0 0 -1 1.1283 6 1 0 1 -1 3.0016 7 1 -1 -1 0 5.0387 8 1 -1 0 0 1.8083 9 1 -1 1 0 5.7273 10 1 0 -1 0 2.4119 11 1 0 1 0 2.4119 12 1 -1 -1 1 5.0046 13 1 -1 0 1 3.3892 14 1 -1 1 1 5.6907 15 1 0 -1 1 3.0016 16 1 0 0 1 1.1283 17 1 0 1 1 4.4159 18 1 1 1 1 6.5246 19 1 1 0 1 2.9391 20 1 1 -1 1 6.1955 21 1 1 1 0 5.0387 22 1 1 0 0 1.8083 23 1 1 -1 0 5.7273 24 1 1 1 -1 5.0046 25 1 1 0 -1 3.3892 26 1 1 -1 -1 5.6907 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3705 atoms have been selected out of 3779 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 102 34 34 0.24 4 C004 has 582 194 194 0.00 5 C005 has 1578 526 526 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1638 546 546 0.00 12 C012 has 84 28 28 0.00 13 C013 has 477 159 159 0.00 14 C014 has 123 41 41 1.27 Total of12948 atoms and 4307 groups and 4301 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3779 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.576" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1248" Evaluating: 1248-7 Parameter: NUMWAT <- "1241" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1241" Comparing "1081" and "1241". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.576" Parameter: BOX -> "33.576" Parameter: BOX -> "33.576" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.57600 B = 33.57600 C = 33.57600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5227 2 1 -1 0 -1 2.9364 3 1 -1 1 -1 6.1921 4 1 0 -1 -1 4.4173 5 1 0 0 -1 1.1266 6 1 0 1 -1 3.0004 7 1 -1 -1 0 5.0360 8 1 -1 0 0 1.8064 9 1 -1 1 0 5.7253 10 1 0 -1 0 2.4099 11 1 0 1 0 2.4099 12 1 -1 -1 1 5.0014 13 1 -1 0 1 3.3869 14 1 -1 1 1 5.6879 15 1 0 -1 1 3.0004 16 1 0 0 1 1.1266 17 1 0 1 1 4.4173 18 1 1 1 1 6.5227 19 1 1 0 1 2.9364 20 1 1 -1 1 6.1921 21 1 1 1 0 5.0360 22 1 1 0 0 1.8064 23 1 1 -1 0 5.7253 24 1 1 1 -1 5.0014 25 1 1 0 -1 3.3869 26 1 1 -1 -1 5.6879 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3705 atoms have been selected out of 3779 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 102 34 34 0.24 4 C004 has 582 194 194 0.00 5 C005 has 1578 526 526 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1638 546 546 0.00 12 C012 has 84 28 28 0.00 13 C013 has 477 159 159 0.00 14 C014 has 123 41 41 1.27 Total of12948 atoms and 4307 groups and 4301 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3779 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.574" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1248" Evaluating: 1248-7 Parameter: NUMWAT <- "1241" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1241" Comparing "1081" and "1241". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.574" Parameter: BOX -> "33.574" Parameter: BOX -> "33.574" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.57400 B = 33.57400 C = 33.57400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5208 2 1 -1 0 -1 2.9337 3 1 -1 1 -1 6.1887 4 1 0 -1 -1 4.4187 5 1 0 0 -1 1.1248 6 1 0 1 -1 2.9991 7 1 -1 -1 0 5.0333 8 1 -1 0 0 1.8045 9 1 -1 1 0 5.7233 10 1 0 -1 0 2.4079 11 1 0 1 0 2.4079 12 1 -1 -1 1 4.9983 13 1 -1 0 1 3.3846 14 1 -1 1 1 5.6851 15 1 0 -1 1 2.9991 16 1 0 0 1 1.1248 17 1 0 1 1 4.4187 18 1 1 1 1 6.5208 19 1 1 0 1 2.9337 20 1 1 -1 1 6.1887 21 1 1 1 0 5.0333 22 1 1 0 0 1.8045 23 1 1 -1 0 5.7233 24 1 1 1 -1 4.9983 25 1 1 0 -1 3.3846 26 1 1 -1 -1 5.6851 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3705 atoms have been selected out of 3779 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.24 4 C004 has 582 194 194 0.00 5 C005 has 1578 526 526 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1638 546 546 0.00 12 C012 has 84 28 28 0.00 13 C013 has 477 159 159 0.00 14 C014 has 123 41 41 1.27 Total of12951 atoms and 4308 groups and 4302 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3779 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.572" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1248" Evaluating: 1248-7 Parameter: NUMWAT <- "1241" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1241" Comparing "1081" and "1241". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.572" Parameter: BOX -> "33.572" Parameter: BOX -> "33.572" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.57200 B = 33.57200 C = 33.57200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5189 2 1 -1 0 -1 2.9309 3 1 -1 1 -1 6.1852 4 1 0 -1 -1 4.4201 5 1 0 0 -1 1.1230 6 1 0 1 -1 2.9979 7 1 -1 -1 0 5.0307 8 1 -1 0 0 1.8026 9 1 -1 1 0 5.7213 10 1 0 -1 0 2.4059 11 1 0 1 0 2.4059 12 1 -1 -1 1 4.9951 13 1 -1 0 1 3.3823 14 1 -1 1 1 5.6824 15 1 0 -1 1 2.9979 16 1 0 0 1 1.1230 17 1 0 1 1 4.4201 18 1 1 1 1 6.5189 19 1 1 0 1 2.9309 20 1 1 -1 1 6.1852 21 1 1 1 0 5.0307 22 1 1 0 0 1.8026 23 1 1 -1 0 5.7213 24 1 1 1 -1 4.9951 25 1 1 0 -1 3.3823 26 1 1 -1 -1 5.6824 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3705 atoms have been selected out of 3779 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.24 4 C004 has 582 194 194 0.00 5 C005 has 1578 526 526 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1638 546 546 0.00 12 C012 has 84 28 28 0.00 13 C013 has 477 159 159 0.00 14 C014 has 123 41 41 1.27 Total of12951 atoms and 4308 groups and 4302 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3779 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.57" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1248" Evaluating: 1248-7 Parameter: NUMWAT <- "1241" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1241" Comparing "1081" and "1241". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.57" Parameter: BOX -> "33.57" Parameter: BOX -> "33.57" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.57000 B = 33.57000 C = 33.57000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5169 2 1 -1 0 -1 2.9282 3 1 -1 1 -1 6.1818 4 1 0 -1 -1 4.4215 5 1 0 0 -1 1.1213 6 1 0 1 -1 2.9967 7 1 -1 -1 0 5.0280 8 1 -1 0 0 1.8008 9 1 -1 1 0 5.7193 10 1 0 -1 0 2.4039 11 1 0 1 0 2.4039 12 1 -1 -1 1 4.9920 13 1 -1 0 1 3.3800 14 1 -1 1 1 5.6796 15 1 0 -1 1 2.9967 16 1 0 0 1 1.1213 17 1 0 1 1 4.4215 18 1 1 1 1 6.5169 19 1 1 0 1 2.9282 20 1 1 -1 1 6.1818 21 1 1 1 0 5.0280 22 1 1 0 0 1.8008 23 1 1 -1 0 5.7193 24 1 1 1 -1 4.9920 25 1 1 0 -1 3.3800 26 1 1 -1 -1 5.6796 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3705 atoms have been selected out of 3779 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.23 4 C004 has 582 194 194 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1638 546 546 0.00 12 C012 has 84 28 28 0.00 13 C013 has 477 159 159 0.00 14 C014 has 123 41 41 1.27 Total of12954 atoms and 4309 groups and 4303 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3779 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.568" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1248" Evaluating: 1248-7 Parameter: NUMWAT <- "1241" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1241" Comparing "1081" and "1241". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.568" Parameter: BOX -> "33.568" Parameter: BOX -> "33.568" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.56800 B = 33.56800 C = 33.56800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5150 2 1 -1 0 -1 2.9255 3 1 -1 1 -1 6.1784 4 1 0 -1 -1 4.4229 5 1 0 0 -1 1.1195 6 1 0 1 -1 2.9955 7 1 -1 -1 0 5.0253 8 1 -1 0 0 1.7989 9 1 -1 1 0 5.7174 10 1 0 -1 0 2.4019 11 1 0 1 0 2.4019 12 1 -1 -1 1 4.9888 13 1 -1 0 1 3.3777 14 1 -1 1 1 5.6768 15 1 0 -1 1 2.9955 16 1 0 0 1 1.1195 17 1 0 1 1 4.4229 18 1 1 1 1 6.5150 19 1 1 0 1 2.9255 20 1 1 -1 1 6.1784 21 1 1 1 0 5.0253 22 1 1 0 0 1.7989 23 1 1 -1 0 5.7174 24 1 1 1 -1 4.9888 25 1 1 0 -1 3.3777 26 1 1 -1 -1 5.6768 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3705 atoms have been selected out of 3779 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.23 4 C004 has 582 194 194 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1641 547 547 0.00 12 C012 has 84 28 28 0.00 13 C013 has 477 159 159 0.00 14 C014 has 123 41 41 1.26 Total of12960 atoms and 4311 groups and 4305 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3779 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.566" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1248" Evaluating: 1248-7 Parameter: NUMWAT <- "1241" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1241" Comparing "1081" and "1241". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.566" Parameter: BOX -> "33.566" Parameter: BOX -> "33.566" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.56600 B = 33.56600 C = 33.56600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5131 2 1 -1 0 -1 2.9227 3 1 -1 1 -1 6.1749 4 1 0 -1 -1 4.4243 5 1 0 0 -1 1.1178 6 1 0 1 -1 2.9942 7 1 -1 -1 0 5.0226 8 1 -1 0 0 1.7970 9 1 -1 1 0 5.7154 10 1 0 -1 0 2.3999 11 1 0 1 0 2.3999 12 1 -1 -1 1 4.9856 13 1 -1 0 1 3.3754 14 1 -1 1 1 5.6741 15 1 0 -1 1 2.9942 16 1 0 0 1 1.1178 17 1 0 1 1 4.4243 18 1 1 1 1 6.5131 19 1 1 0 1 2.9227 20 1 1 -1 1 6.1749 21 1 1 1 0 5.0226 22 1 1 0 0 1.7970 23 1 1 -1 0 5.7154 24 1 1 1 -1 4.9856 25 1 1 0 -1 3.3754 26 1 1 -1 -1 5.6741 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3705 atoms have been selected out of 3779 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.23 4 C004 has 582 194 194 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1641 547 547 0.00 12 C012 has 84 28 28 0.00 13 C013 has 477 159 159 0.00 14 C014 has 123 41 41 1.26 Total of12960 atoms and 4311 groups and 4305 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3779 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.564" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1248" Evaluating: 1248-7 Parameter: NUMWAT <- "1241" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1241" Comparing "1081" and "1241". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.564" Parameter: BOX -> "33.564" Parameter: BOX -> "33.564" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.56400 B = 33.56400 C = 33.56400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5112 2 1 -1 0 -1 2.9200 3 1 -1 1 -1 6.1715 4 1 0 -1 -1 4.4257 5 1 0 0 -1 1.1160 6 1 0 1 -1 2.9930 7 1 -1 -1 0 5.0199 8 1 -1 0 0 1.7952 9 1 -1 1 0 5.7134 10 1 0 -1 0 2.3979 11 1 0 1 0 2.3979 12 1 -1 -1 1 4.9825 13 1 -1 0 1 3.3731 14 1 -1 1 1 5.6713 15 1 0 -1 1 2.9930 16 1 0 0 1 1.1160 17 1 0 1 1 4.4257 18 1 1 1 1 6.5112 19 1 1 0 1 2.9200 20 1 1 -1 1 6.1715 21 1 1 1 0 5.0199 22 1 1 0 0 1.7952 23 1 1 -1 0 5.7134 24 1 1 1 -1 4.9825 25 1 1 0 -1 3.3731 26 1 1 -1 -1 5.6713 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3705 atoms have been selected out of 3779 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.23 4 C004 has 585 195 195 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1641 547 547 0.00 12 C012 has 84 28 28 0.00 13 C013 has 477 159 159 0.00 14 C014 has 123 41 41 1.26 Total of12963 atoms and 4312 groups and 4306 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3779 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.562" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1248" Evaluating: 1248-7 Parameter: NUMWAT <- "1241" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1241" Comparing "1081" and "1241". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.562" Parameter: BOX -> "33.562" Parameter: BOX -> "33.562" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.56200 B = 33.56200 C = 33.56200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5093 2 1 -1 0 -1 2.9173 3 1 -1 1 -1 6.1680 4 1 0 -1 -1 4.4271 5 1 0 0 -1 1.1142 6 1 0 1 -1 2.9918 7 1 -1 -1 0 5.0172 8 1 -1 0 0 1.7933 9 1 -1 1 0 5.7114 10 1 0 -1 0 2.3959 11 1 0 1 0 2.3959 12 1 -1 -1 1 4.9793 13 1 -1 0 1 3.3708 14 1 -1 1 1 5.6685 15 1 0 -1 1 2.9918 16 1 0 0 1 1.1142 17 1 0 1 1 4.4271 18 1 1 1 1 6.5093 19 1 1 0 1 2.9173 20 1 1 -1 1 6.1680 21 1 1 1 0 5.0172 22 1 1 0 0 1.7933 23 1 1 -1 0 5.7114 24 1 1 1 -1 4.9793 25 1 1 0 -1 3.3708 26 1 1 -1 -1 5.6685 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3705 atoms have been selected out of 3779 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.23 4 C004 has 585 195 195 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1641 547 547 0.00 12 C012 has 84 28 28 0.00 13 C013 has 477 159 159 0.00 14 C014 has 123 41 41 1.26 Total of12963 atoms and 4312 groups and 4306 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3779 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.56" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1248" Evaluating: 1248-7 Parameter: NUMWAT <- "1241" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1241" Comparing "1081" and "1241". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.56" Parameter: BOX -> "33.56" Parameter: BOX -> "33.56" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.56000 B = 33.56000 C = 33.56000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5074 2 1 -1 0 -1 2.9146 3 1 -1 1 -1 6.1646 4 1 0 -1 -1 4.4285 5 1 0 0 -1 1.1125 6 1 0 1 -1 2.9906 7 1 -1 -1 0 5.0145 8 1 -1 0 0 1.7914 9 1 -1 1 0 5.7094 10 1 0 -1 0 2.3939 11 1 0 1 0 2.3939 12 1 -1 -1 1 4.9762 13 1 -1 0 1 3.3685 14 1 -1 1 1 5.6658 15 1 0 -1 1 2.9906 16 1 0 0 1 1.1125 17 1 0 1 1 4.4285 18 1 1 1 1 6.5074 19 1 1 0 1 2.9146 20 1 1 -1 1 6.1646 21 1 1 1 0 5.0145 22 1 1 0 0 1.7914 23 1 1 -1 0 5.7094 24 1 1 1 -1 4.9762 25 1 1 0 -1 3.3685 26 1 1 -1 -1 5.6658 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3705 atoms have been selected out of 3779 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.22 4 C004 has 585 195 195 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1641 547 547 0.00 12 C012 has 84 28 28 0.00 13 C013 has 477 159 159 0.00 14 C014 has 123 41 41 1.26 Total of12963 atoms and 4312 groups and 4306 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3779 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.558" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1248" Evaluating: 1248-7 Parameter: NUMWAT <- "1241" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1241" Comparing "1081" and "1241". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.558" Parameter: BOX -> "33.558" Parameter: BOX -> "33.558" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.55800 B = 33.55800 C = 33.55800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5055 2 1 -1 0 -1 2.9118 3 1 -1 1 -1 6.1612 4 1 0 -1 -1 4.4299 5 1 0 0 -1 1.1107 6 1 0 1 -1 2.9894 7 1 -1 -1 0 5.0118 8 1 -1 0 0 1.7895 9 1 -1 1 0 5.7075 10 1 0 -1 0 2.3919 11 1 0 1 0 2.3919 12 1 -1 -1 1 4.9730 13 1 -1 0 1 3.3662 14 1 -1 1 1 5.6630 15 1 0 -1 1 2.9894 16 1 0 0 1 1.1107 17 1 0 1 1 4.4299 18 1 1 1 1 6.5055 19 1 1 0 1 2.9118 20 1 1 -1 1 6.1612 21 1 1 1 0 5.0118 22 1 1 0 0 1.7895 23 1 1 -1 0 5.7075 24 1 1 1 -1 4.9730 25 1 1 0 -1 3.3662 26 1 1 -1 -1 5.6630 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3705 atoms have been selected out of 3779 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.22 4 C004 has 585 195 195 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1641 547 547 0.00 12 C012 has 84 28 28 0.00 13 C013 has 477 159 159 0.00 14 C014 has 123 41 41 1.25 Total of12963 atoms and 4312 groups and 4306 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3779 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.556" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1248" Evaluating: 1248-7 Parameter: NUMWAT <- "1241" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1241" Comparing "1081" and "1241". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.556" Parameter: BOX -> "33.556" Parameter: BOX -> "33.556" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.55600 B = 33.55600 C = 33.55600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5035 2 1 -1 0 -1 2.9091 3 1 -1 1 -1 6.1577 4 1 0 -1 -1 4.4313 5 1 0 0 -1 1.1090 6 1 0 1 -1 2.9882 7 1 -1 -1 0 5.0091 8 1 -1 0 0 1.7877 9 1 -1 1 0 5.7055 10 1 0 -1 0 2.3899 11 1 0 1 0 2.3899 12 1 -1 -1 1 4.9698 13 1 -1 0 1 3.3639 14 1 -1 1 1 5.6602 15 1 0 -1 1 2.9882 16 1 0 0 1 1.1090 17 1 0 1 1 4.4313 18 1 1 1 1 6.5035 19 1 1 0 1 2.9091 20 1 1 -1 1 6.1577 21 1 1 1 0 5.0091 22 1 1 0 0 1.7877 23 1 1 -1 0 5.7055 24 1 1 1 -1 4.9698 25 1 1 0 -1 3.3639 26 1 1 -1 -1 5.6602 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3705 atoms have been selected out of 3779 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.22 4 C004 has 585 195 195 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1644 548 548 0.00 12 C012 has 84 28 28 0.00 13 C013 has 477 159 159 0.00 14 C014 has 123 41 41 1.25 Total of12969 atoms and 4314 groups and 4308 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3779 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.554" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1248" Evaluating: 1248-7 Parameter: NUMWAT <- "1241" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1241" Comparing "1081" and "1241". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.554" Parameter: BOX -> "33.554" Parameter: BOX -> "33.554" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.55400 B = 33.55400 C = 33.55400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.5016 2 1 -1 0 -1 2.9064 3 1 -1 1 -1 6.1543 4 1 0 -1 -1 4.4328 5 1 0 0 -1 1.1072 6 1 0 1 -1 2.9870 7 1 -1 -1 0 5.0065 8 1 -1 0 0 1.7858 9 1 -1 1 0 5.7035 10 1 0 -1 0 2.3879 11 1 0 1 0 2.3879 12 1 -1 -1 1 4.9667 13 1 -1 0 1 3.3617 14 1 -1 1 1 5.6575 15 1 0 -1 1 2.9870 16 1 0 0 1 1.1072 17 1 0 1 1 4.4328 18 1 1 1 1 6.5016 19 1 1 0 1 2.9064 20 1 1 -1 1 6.1543 21 1 1 1 0 5.0065 22 1 1 0 0 1.7858 23 1 1 -1 0 5.7035 24 1 1 1 -1 4.9667 25 1 1 0 -1 3.3617 26 1 1 -1 -1 5.6575 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3705 atoms have been selected out of 3779 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.22 4 C004 has 585 195 195 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1644 548 548 0.00 12 C012 has 84 28 28 0.00 13 C013 has 477 159 159 0.00 14 C014 has 123 41 41 1.25 Total of12969 atoms and 4314 groups and 4308 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3779 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.552" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1248" Evaluating: 1248-7 Parameter: NUMWAT <- "1241" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1241" Comparing "1081" and "1241". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.552" Parameter: BOX -> "33.552" Parameter: BOX -> "33.552" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.55200 B = 33.55200 C = 33.55200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4997 2 1 -1 0 -1 2.9036 3 1 -1 1 -1 6.1508 4 1 0 -1 -1 4.4342 5 1 0 0 -1 1.1055 6 1 0 1 -1 2.9858 7 1 -1 -1 0 5.0038 8 1 -1 0 0 1.7839 9 1 -1 1 0 5.7015 10 1 0 -1 0 2.3859 11 1 0 1 0 2.3859 12 1 -1 -1 1 4.9635 13 1 -1 0 1 3.3594 14 1 -1 1 1 5.6547 15 1 0 -1 1 2.9858 16 1 0 0 1 1.1055 17 1 0 1 1 4.4342 18 1 1 1 1 6.4997 19 1 1 0 1 2.9036 20 1 1 -1 1 6.1508 21 1 1 1 0 5.0038 22 1 1 0 0 1.7839 23 1 1 -1 0 5.7015 24 1 1 1 -1 4.9635 25 1 1 0 -1 3.3594 26 1 1 -1 -1 5.6547 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3705 atoms have been selected out of 3779 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.22 4 C004 has 585 195 195 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1644 548 548 0.00 12 C012 has 84 28 28 0.00 13 C013 has 477 159 159 0.00 14 C014 has 123 41 41 1.25 Total of12969 atoms and 4314 groups and 4308 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3779 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.55" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1248" Evaluating: 1248-7 Parameter: NUMWAT <- "1241" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1241" Comparing "1081" and "1241". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.55" Parameter: BOX -> "33.55" Parameter: BOX -> "33.55" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.55000 B = 33.55000 C = 33.55000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4978 2 1 -1 0 -1 2.9009 3 1 -1 1 -1 6.1474 4 1 0 -1 -1 4.4356 5 1 0 0 -1 1.1037 6 1 0 1 -1 2.9846 7 1 -1 -1 0 5.0011 8 1 -1 0 0 1.7821 9 1 -1 1 0 5.6996 10 1 0 -1 0 2.3839 11 1 0 1 0 2.3839 12 1 -1 -1 1 4.9604 13 1 -1 0 1 3.3571 14 1 -1 1 1 5.6519 15 1 0 -1 1 2.9846 16 1 0 0 1 1.1037 17 1 0 1 1 4.4356 18 1 1 1 1 6.4978 19 1 1 0 1 2.9009 20 1 1 -1 1 6.1474 21 1 1 1 0 5.0011 22 1 1 0 0 1.7821 23 1 1 -1 0 5.6996 24 1 1 1 -1 4.9604 25 1 1 0 -1 3.3571 26 1 1 -1 -1 5.6519 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3705 atoms have been selected out of 3779 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.21 4 C004 has 585 195 195 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1644 548 548 0.00 12 C012 has 84 28 28 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.25 Total of12972 atoms and 4315 groups and 4309 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3779 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.548" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1248" Evaluating: 1248-7 Parameter: NUMWAT <- "1241" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1241" Comparing "1081" and "1241". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.548" Parameter: BOX -> "33.548" Parameter: BOX -> "33.548" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.54800 B = 33.54800 C = 33.54800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4959 2 1 -1 0 -1 2.8982 3 1 -1 1 -1 6.1440 4 1 0 -1 -1 4.4370 5 1 0 0 -1 1.1020 6 1 0 1 -1 2.9834 7 1 -1 -1 0 4.9984 8 1 -1 0 0 1.7802 9 1 -1 1 0 5.6976 10 1 0 -1 0 2.3819 11 1 0 1 0 2.3819 12 1 -1 -1 1 4.9572 13 1 -1 0 1 3.3548 14 1 -1 1 1 5.6492 15 1 0 -1 1 2.9834 16 1 0 0 1 1.1020 17 1 0 1 1 4.4370 18 1 1 1 1 6.4959 19 1 1 0 1 2.8982 20 1 1 -1 1 6.1440 21 1 1 1 0 4.9984 22 1 1 0 0 1.7802 23 1 1 -1 0 5.6976 24 1 1 1 -1 4.9572 25 1 1 0 -1 3.3548 26 1 1 -1 -1 5.6492 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3705 atoms have been selected out of 3779 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.21 4 C004 has 585 195 195 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1644 548 548 0.00 12 C012 has 84 28 28 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.24 Total of12972 atoms and 4315 groups and 4309 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3779 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.546" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1248" Evaluating: 1248-7 Parameter: NUMWAT <- "1241" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1241" Comparing "1081" and "1241". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.546" Parameter: BOX -> "33.546" Parameter: BOX -> "33.546" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.54600 B = 33.54600 C = 33.54600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4940 2 1 -1 0 -1 2.8955 3 1 -1 1 -1 6.1405 4 1 0 -1 -1 4.4384 5 1 0 0 -1 1.1002 6 1 0 1 -1 2.9822 7 1 -1 -1 0 4.9957 8 1 -1 0 0 1.7783 9 1 -1 1 0 5.6956 10 1 0 -1 0 2.3799 11 1 0 1 0 2.3799 12 1 -1 -1 1 4.9541 13 1 -1 0 1 3.3525 14 1 -1 1 1 5.6464 15 1 0 -1 1 2.9822 16 1 0 0 1 1.1002 17 1 0 1 1 4.4384 18 1 1 1 1 6.4940 19 1 1 0 1 2.8955 20 1 1 -1 1 6.1405 21 1 1 1 0 4.9957 22 1 1 0 0 1.7783 23 1 1 -1 0 5.6956 24 1 1 1 -1 4.9541 25 1 1 0 -1 3.3525 26 1 1 -1 -1 5.6464 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3705 atoms have been selected out of 3779 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.21 4 C004 has 585 195 195 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1644 548 548 0.00 12 C012 has 87 29 29 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.24 Total of12975 atoms and 4316 groups and 4310 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3779 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.544" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1248" Evaluating: 1248-7 Parameter: NUMWAT <- "1241" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1241" Comparing "1081" and "1241". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.544" Parameter: BOX -> "33.544" Parameter: BOX -> "33.544" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.54400 B = 33.54400 C = 33.54400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4921 2 1 -1 0 -1 2.8927 3 1 -1 1 -1 6.1371 4 1 0 -1 -1 4.4399 5 1 0 0 -1 1.0985 6 1 0 1 -1 2.9810 7 1 -1 -1 0 4.9930 8 1 -1 0 0 1.7765 9 1 -1 1 0 5.6937 10 1 0 -1 0 2.3779 11 1 0 1 0 2.3779 12 1 -1 -1 1 4.9509 13 1 -1 0 1 3.3502 14 1 -1 1 1 5.6437 15 1 0 -1 1 2.9810 16 1 0 0 1 1.0985 17 1 0 1 1 4.4399 18 1 1 1 1 6.4921 19 1 1 0 1 2.8927 20 1 1 -1 1 6.1371 21 1 1 1 0 4.9930 22 1 1 0 0 1.7765 23 1 1 -1 0 5.6937 24 1 1 1 -1 4.9509 25 1 1 0 -1 3.3502 26 1 1 -1 -1 5.6437 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3705 atoms have been selected out of 3779 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.21 4 C004 has 585 195 195 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 87 29 29 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.24 Total of12978 atoms and 4317 groups and 4311 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3779 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.542" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1248" Evaluating: 1248-7 Parameter: NUMWAT <- "1241" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1241" Comparing "1081" and "1241". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.542" Parameter: BOX -> "33.542" Parameter: BOX -> "33.542" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.54200 B = 33.54200 C = 33.54200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4902 2 1 -1 0 -1 2.8900 3 1 -1 1 -1 6.1336 4 1 0 -1 -1 4.4413 5 1 0 0 -1 1.0967 6 1 0 1 -1 2.9798 7 1 -1 -1 0 4.9903 8 1 -1 0 0 1.7746 9 1 -1 1 0 5.6917 10 1 0 -1 0 2.3759 11 1 0 1 0 2.3759 12 1 -1 -1 1 4.9477 13 1 -1 0 1 3.3479 14 1 -1 1 1 5.6409 15 1 0 -1 1 2.9798 16 1 0 0 1 1.0967 17 1 0 1 1 4.4413 18 1 1 1 1 6.4902 19 1 1 0 1 2.8900 20 1 1 -1 1 6.1336 21 1 1 1 0 4.9903 22 1 1 0 0 1.7746 23 1 1 -1 0 5.6917 24 1 1 1 -1 4.9477 25 1 1 0 -1 3.3479 26 1 1 -1 -1 5.6409 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3705 atoms have been selected out of 3779 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.21 4 C004 has 585 195 195 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 465 155 155 0.00 7 C007 has 729 243 243 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 90 30 30 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.24 Total of12981 atoms and 4318 groups and 4312 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3779 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.54" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1248" Evaluating: 1248-7 Parameter: NUMWAT <- "1241" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1241" Comparing "1081" and "1241". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.54" Parameter: BOX -> "33.54" Parameter: BOX -> "33.54" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.54000 B = 33.54000 C = 33.54000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4883 2 1 -1 0 -1 2.8873 3 1 -1 1 -1 6.1302 4 1 0 -1 -1 4.4427 5 1 0 0 -1 1.0950 6 1 0 1 -1 2.9786 7 1 -1 -1 0 4.9876 8 1 -1 0 0 1.7727 9 1 -1 1 0 5.6897 10 1 0 -1 0 2.3739 11 1 0 1 0 2.3739 12 1 -1 -1 1 4.9446 13 1 -1 0 1 3.3457 14 1 -1 1 1 5.6381 15 1 0 -1 1 2.9786 16 1 0 0 1 1.0950 17 1 0 1 1 4.4427 18 1 1 1 1 6.4883 19 1 1 0 1 2.8873 20 1 1 -1 1 6.1302 21 1 1 1 0 4.9876 22 1 1 0 0 1.7727 23 1 1 -1 0 5.6897 24 1 1 1 -1 4.9446 25 1 1 0 -1 3.3457 26 1 1 -1 -1 5.6381 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3705 atoms have been selected out of 3779 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.20 4 C004 has 585 195 195 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 465 155 155 0.00 7 C007 has 732 244 244 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 90 30 30 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.24 Total of12984 atoms and 4319 groups and 4313 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3779 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1248 Number of atoms = 3779 Number of groups = 1253 Number of bonds = 3772 Number of angles = 1352 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1250 Number of HB donors = 2478 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.538" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1248" Evaluating: 1248-7 Parameter: NUMWAT <- "1241" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1241" Comparing "1081" and "1241". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.538" Parameter: BOX -> "33.538" Parameter: BOX -> "33.538" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.53800 B = 33.53800 C = 33.53800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4864 2 1 -1 0 -1 2.8845 3 1 -1 1 -1 6.1268 4 1 0 -1 -1 4.4441 5 1 0 0 -1 1.0932 6 1 0 1 -1 2.9774 7 1 -1 -1 0 4.9849 8 1 -1 0 0 1.7708 9 1 -1 1 0 5.6878 10 1 0 -1 0 2.3719 11 1 0 1 0 2.3719 12 1 -1 -1 1 4.9414 13 1 -1 0 1 3.3434 14 1 -1 1 1 5.6354 15 1 0 -1 1 2.9774 16 1 0 0 1 1.0932 17 1 0 1 1 4.4441 18 1 1 1 1 6.4864 19 1 1 0 1 2.8845 20 1 1 -1 1 6.1268 21 1 1 1 0 4.9849 22 1 1 0 0 1.7708 23 1 1 -1 0 5.6878 24 1 1 1 -1 4.9414 25 1 1 0 -1 3.3434 26 1 1 -1 -1 5.6354 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3705 atoms have been selected out of 3779 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 691 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.20 4 C004 has 585 195 195 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 462 154 154 0.00 7 C007 has 732 244 244 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 90 30 30 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.23 Total of12978 atoms and 4317 groups and 4311 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3779 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.536" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.536" Parameter: BOX -> "33.536" Parameter: BOX -> "33.536" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.53600 B = 33.53600 C = 33.53600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4845 2 1 -1 0 -1 2.8818 3 1 -1 1 -1 6.1233 4 1 0 -1 -1 4.4456 5 1 0 0 -1 1.0915 6 1 0 1 -1 2.9762 7 1 -1 -1 0 4.9823 8 1 -1 0 0 1.7690 9 1 -1 1 0 5.6858 10 1 0 -1 0 2.3699 11 1 0 1 0 2.3699 12 1 -1 -1 1 4.9383 13 1 -1 0 1 3.3411 14 1 -1 1 1 5.6326 15 1 0 -1 1 2.9762 16 1 0 0 1 1.0915 17 1 0 1 1 4.4456 18 1 1 1 1 6.4845 19 1 1 0 1 2.8818 20 1 1 -1 1 6.1233 21 1 1 1 0 4.9823 22 1 1 0 0 1.7690 23 1 1 -1 0 5.6858 24 1 1 1 -1 4.9383 25 1 1 0 -1 3.3411 26 1 1 -1 -1 5.6326 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.20 4 C004 has 585 195 195 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 462 154 154 0.00 7 C007 has 732 244 244 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 90 30 30 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.23 Total of12975 atoms and 4316 groups and 4310 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.534" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.534" Parameter: BOX -> "33.534" Parameter: BOX -> "33.534" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.53400 B = 33.53400 C = 33.53400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4826 2 1 -1 0 -1 2.8791 3 1 -1 1 -1 6.1199 4 1 0 -1 -1 4.4470 5 1 0 0 -1 1.0897 6 1 0 1 -1 2.9750 7 1 -1 -1 0 4.9796 8 1 -1 0 0 1.7671 9 1 -1 1 0 5.6838 10 1 0 -1 0 2.3679 11 1 0 1 0 2.3679 12 1 -1 -1 1 4.9351 13 1 -1 0 1 3.3388 14 1 -1 1 1 5.6299 15 1 0 -1 1 2.9750 16 1 0 0 1 1.0897 17 1 0 1 1 4.4470 18 1 1 1 1 6.4826 19 1 1 0 1 2.8791 20 1 1 -1 1 6.1199 21 1 1 1 0 4.9796 22 1 1 0 0 1.7671 23 1 1 -1 0 5.6838 24 1 1 1 -1 4.9351 25 1 1 0 -1 3.3388 26 1 1 -1 -1 5.6299 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.20 4 C004 has 585 195 195 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 462 154 154 0.00 7 C007 has 732 244 244 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.23 Total of12978 atoms and 4317 groups and 4311 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.532" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.532" Parameter: BOX -> "33.532" Parameter: BOX -> "33.532" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.53200 B = 33.53200 C = 33.53200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4807 2 1 -1 0 -1 2.8764 3 1 -1 1 -1 6.1165 4 1 0 -1 -1 4.4484 5 1 0 0 -1 1.0880 6 1 0 1 -1 2.9739 7 1 -1 -1 0 4.9769 8 1 -1 0 0 1.7652 9 1 -1 1 0 5.6818 10 1 0 -1 0 2.3659 11 1 0 1 0 2.3659 12 1 -1 -1 1 4.9320 13 1 -1 0 1 3.3365 14 1 -1 1 1 5.6271 15 1 0 -1 1 2.9739 16 1 0 0 1 1.0880 17 1 0 1 1 4.4484 18 1 1 1 1 6.4807 19 1 1 0 1 2.8764 20 1 1 -1 1 6.1165 21 1 1 1 0 4.9769 22 1 1 0 0 1.7652 23 1 1 -1 0 5.6818 24 1 1 1 -1 4.9320 25 1 1 0 -1 3.3365 26 1 1 -1 -1 5.6271 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.20 4 C004 has 585 195 195 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 462 154 154 0.00 7 C007 has 732 244 244 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.23 Total of12981 atoms and 4318 groups and 4312 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.53" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.53" Parameter: BOX -> "33.53" Parameter: BOX -> "33.53" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.53000 B = 33.53000 C = 33.53000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4788 2 1 -1 0 -1 2.8736 3 1 -1 1 -1 6.1130 4 1 0 -1 -1 4.4499 5 1 0 0 -1 1.0862 6 1 0 1 -1 2.9727 7 1 -1 -1 0 4.9742 8 1 -1 0 0 1.7634 9 1 -1 1 0 5.6799 10 1 0 -1 0 2.3639 11 1 0 1 0 2.3639 12 1 -1 -1 1 4.9288 13 1 -1 0 1 3.3342 14 1 -1 1 1 5.6244 15 1 0 -1 1 2.9727 16 1 0 0 1 1.0862 17 1 0 1 1 4.4499 18 1 1 1 1 6.4788 19 1 1 0 1 2.8736 20 1 1 -1 1 6.1130 21 1 1 1 0 4.9742 22 1 1 0 0 1.7634 23 1 1 -1 0 5.6799 24 1 1 1 -1 4.9288 25 1 1 0 -1 3.3342 26 1 1 -1 -1 5.6244 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.19 4 C004 has 585 195 195 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 462 154 154 0.00 7 C007 has 732 244 244 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.23 Total of12981 atoms and 4318 groups and 4312 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.528" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.528" Parameter: BOX -> "33.528" Parameter: BOX -> "33.528" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.52800 B = 33.52800 C = 33.52800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4769 2 1 -1 0 -1 2.8709 3 1 -1 1 -1 6.1096 4 1 0 -1 -1 4.4513 5 1 0 0 -1 1.0845 6 1 0 1 -1 2.9715 7 1 -1 -1 0 4.9715 8 1 -1 0 0 1.7615 9 1 -1 1 0 5.6779 10 1 0 -1 0 2.3619 11 1 0 1 0 2.3619 12 1 -1 -1 1 4.9257 13 1 -1 0 1 3.3320 14 1 -1 1 1 5.6216 15 1 0 -1 1 2.9715 16 1 0 0 1 1.0845 17 1 0 1 1 4.4513 18 1 1 1 1 6.4769 19 1 1 0 1 2.8709 20 1 1 -1 1 6.1096 21 1 1 1 0 4.9715 22 1 1 0 0 1.7615 23 1 1 -1 0 5.6779 24 1 1 1 -1 4.9257 25 1 1 0 -1 3.3320 26 1 1 -1 -1 5.6216 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.19 4 C004 has 585 195 195 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 462 154 154 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.22 Total of12984 atoms and 4319 groups and 4313 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.526" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.526" Parameter: BOX -> "33.526" Parameter: BOX -> "33.526" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.52600 B = 33.52600 C = 33.52600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4750 2 1 -1 0 -1 2.8682 3 1 -1 1 -1 6.1061 4 1 0 -1 -1 4.4527 5 1 0 0 -1 1.0827 6 1 0 1 -1 2.9703 7 1 -1 -1 0 4.9688 8 1 -1 0 0 1.7596 9 1 -1 1 0 5.6760 10 1 0 -1 0 2.3599 11 1 0 1 0 2.3599 12 1 -1 -1 1 4.9225 13 1 -1 0 1 3.3297 14 1 -1 1 1 5.6189 15 1 0 -1 1 2.9703 16 1 0 0 1 1.0827 17 1 0 1 1 4.4527 18 1 1 1 1 6.4750 19 1 1 0 1 2.8682 20 1 1 -1 1 6.1061 21 1 1 1 0 4.9688 22 1 1 0 0 1.7596 23 1 1 -1 0 5.6760 24 1 1 1 -1 4.9225 25 1 1 0 -1 3.3297 26 1 1 -1 -1 5.6189 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.19 4 C004 has 585 195 195 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 462 154 154 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.22 Total of12984 atoms and 4319 groups and 4313 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.524" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.524" Parameter: BOX -> "33.524" Parameter: BOX -> "33.524" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.52400 B = 33.52400 C = 33.52400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4732 2 1 -1 0 -1 2.8655 3 1 -1 1 -1 6.1027 4 1 0 -1 -1 4.4542 5 1 0 0 -1 1.0810 6 1 0 1 -1 2.9692 7 1 -1 -1 0 4.9661 8 1 -1 0 0 1.7578 9 1 -1 1 0 5.6740 10 1 0 -1 0 2.3579 11 1 0 1 0 2.3579 12 1 -1 -1 1 4.9194 13 1 -1 0 1 3.3274 14 1 -1 1 1 5.6161 15 1 0 -1 1 2.9692 16 1 0 0 1 1.0810 17 1 0 1 1 4.4542 18 1 1 1 1 6.4732 19 1 1 0 1 2.8655 20 1 1 -1 1 6.1027 21 1 1 1 0 4.9661 22 1 1 0 0 1.7578 23 1 1 -1 0 5.6740 24 1 1 1 -1 4.9194 25 1 1 0 -1 3.3274 26 1 1 -1 -1 5.6161 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.19 4 C004 has 585 195 195 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 462 154 154 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.22 Total of12987 atoms and 4320 groups and 4314 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.522" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.522" Parameter: BOX -> "33.522" Parameter: BOX -> "33.522" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.52200 B = 33.52200 C = 33.52200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4713 2 1 -1 0 -1 2.8627 3 1 -1 1 -1 6.0993 4 1 0 -1 -1 4.4556 5 1 0 0 -1 1.0793 6 1 0 1 -1 2.9680 7 1 -1 -1 0 4.9635 8 1 -1 0 0 1.7559 9 1 -1 1 0 5.6720 10 1 0 -1 0 2.3559 11 1 0 1 0 2.3559 12 1 -1 -1 1 4.9162 13 1 -1 0 1 3.3251 14 1 -1 1 1 5.6134 15 1 0 -1 1 2.9680 16 1 0 0 1 1.0793 17 1 0 1 1 4.4556 18 1 1 1 1 6.4713 19 1 1 0 1 2.8627 20 1 1 -1 1 6.0993 21 1 1 1 0 4.9635 22 1 1 0 0 1.7559 23 1 1 -1 0 5.6720 24 1 1 1 -1 4.9162 25 1 1 0 -1 3.3251 26 1 1 -1 -1 5.6134 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.19 4 C004 has 585 195 195 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 462 154 154 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.22 Total of12993 atoms and 4322 groups and 4316 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.52" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.52" Parameter: BOX -> "33.52" Parameter: BOX -> "33.52" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.52000 B = 33.52000 C = 33.52000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4694 2 1 -1 0 -1 2.8600 3 1 -1 1 -1 6.0958 4 1 0 -1 -1 4.4570 5 1 0 0 -1 1.0775 6 1 0 1 -1 2.9668 7 1 -1 -1 0 4.9608 8 1 -1 0 0 1.7540 9 1 -1 1 0 5.6701 10 1 0 -1 0 2.3539 11 1 0 1 0 2.3539 12 1 -1 -1 1 4.9131 13 1 -1 0 1 3.3229 14 1 -1 1 1 5.6106 15 1 0 -1 1 2.9668 16 1 0 0 1 1.0775 17 1 0 1 1 4.4570 18 1 1 1 1 6.4694 19 1 1 0 1 2.8600 20 1 1 -1 1 6.0958 21 1 1 1 0 4.9608 22 1 1 0 0 1.7540 23 1 1 -1 0 5.6701 24 1 1 1 -1 4.9131 25 1 1 0 -1 3.3229 26 1 1 -1 -1 5.6106 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.18 4 C004 has 585 195 195 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 462 154 154 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.22 Total of12996 atoms and 4323 groups and 4317 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.518" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.518" Parameter: BOX -> "33.518" Parameter: BOX -> "33.518" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.51800 B = 33.51800 C = 33.51800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4675 2 1 -1 0 -1 2.8573 3 1 -1 1 -1 6.0924 4 1 0 -1 -1 4.4585 5 1 0 0 -1 1.0758 6 1 0 1 -1 2.9656 7 1 -1 -1 0 4.9581 8 1 -1 0 0 1.7522 9 1 -1 1 0 5.6681 10 1 0 -1 0 2.3519 11 1 0 1 0 2.3519 12 1 -1 -1 1 4.9099 13 1 -1 0 1 3.3206 14 1 -1 1 1 5.6079 15 1 0 -1 1 2.9656 16 1 0 0 1 1.0758 17 1 0 1 1 4.4585 18 1 1 1 1 6.4675 19 1 1 0 1 2.8573 20 1 1 -1 1 6.0924 21 1 1 1 0 4.9581 22 1 1 0 0 1.7522 23 1 1 -1 0 5.6681 24 1 1 1 -1 4.9099 25 1 1 0 -1 3.3206 26 1 1 -1 -1 5.6079 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.18 4 C004 has 585 195 195 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 462 154 154 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.21 Total of12996 atoms and 4323 groups and 4317 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.516" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.516" Parameter: BOX -> "33.516" Parameter: BOX -> "33.516" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.51600 B = 33.51600 C = 33.51600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4656 2 1 -1 0 -1 2.8546 3 1 -1 1 -1 6.0889 4 1 0 -1 -1 4.4599 5 1 0 0 -1 1.0740 6 1 0 1 -1 2.9645 7 1 -1 -1 0 4.9554 8 1 -1 0 0 1.7503 9 1 -1 1 0 5.6661 10 1 0 -1 0 2.3499 11 1 0 1 0 2.3499 12 1 -1 -1 1 4.9068 13 1 -1 0 1 3.3183 14 1 -1 1 1 5.6051 15 1 0 -1 1 2.9645 16 1 0 0 1 1.0740 17 1 0 1 1 4.4599 18 1 1 1 1 6.4656 19 1 1 0 1 2.8546 20 1 1 -1 1 6.0889 21 1 1 1 0 4.9554 22 1 1 0 0 1.7503 23 1 1 -1 0 5.6661 24 1 1 1 -1 4.9068 25 1 1 0 -1 3.3183 26 1 1 -1 -1 5.6051 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.18 4 C004 has 585 195 195 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 462 154 154 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.21 Total of12996 atoms and 4323 groups and 4317 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.514" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.514" Parameter: BOX -> "33.514" Parameter: BOX -> "33.514" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.51400 B = 33.51400 C = 33.51400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4637 2 1 -1 0 -1 2.8518 3 1 -1 1 -1 6.0855 4 1 0 -1 -1 4.4614 5 1 0 0 -1 1.0723 6 1 0 1 -1 2.9633 7 1 -1 -1 0 4.9527 8 1 -1 0 0 1.7485 9 1 -1 1 0 5.6642 10 1 0 -1 0 2.3479 11 1 0 1 0 2.3479 12 1 -1 -1 1 4.9036 13 1 -1 0 1 3.3160 14 1 -1 1 1 5.6024 15 1 0 -1 1 2.9633 16 1 0 0 1 1.0723 17 1 0 1 1 4.4614 18 1 1 1 1 6.4637 19 1 1 0 1 2.8518 20 1 1 -1 1 6.0855 21 1 1 1 0 4.9527 22 1 1 0 0 1.7485 23 1 1 -1 0 5.6642 24 1 1 1 -1 4.9036 25 1 1 0 -1 3.3160 26 1 1 -1 -1 5.6024 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.18 4 C004 has 588 196 196 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 462 154 154 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.21 Total of12999 atoms and 4324 groups and 4318 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.512" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.512" Parameter: BOX -> "33.512" Parameter: BOX -> "33.512" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.51200 B = 33.51200 C = 33.51200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4618 2 1 -1 0 -1 2.8491 3 1 -1 1 -1 6.0821 4 1 0 -1 -1 4.4628 5 1 0 0 -1 1.0706 6 1 0 1 -1 2.9622 7 1 -1 -1 0 4.9500 8 1 -1 0 0 1.7466 9 1 -1 1 0 5.6622 10 1 0 -1 0 2.3459 11 1 0 1 0 2.3459 12 1 -1 -1 1 4.9005 13 1 -1 0 1 3.3138 14 1 -1 1 1 5.5996 15 1 0 -1 1 2.9622 16 1 0 0 1 1.0706 17 1 0 1 1 4.4628 18 1 1 1 1 6.4618 19 1 1 0 1 2.8491 20 1 1 -1 1 6.0821 21 1 1 1 0 4.9500 22 1 1 0 0 1.7466 23 1 1 -1 0 5.6622 24 1 1 1 -1 4.9005 25 1 1 0 -1 3.3138 26 1 1 -1 -1 5.5996 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.18 4 C004 has 588 196 196 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 462 154 154 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.21 Total of12999 atoms and 4324 groups and 4318 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.51" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.51" Parameter: BOX -> "33.51" Parameter: BOX -> "33.51" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.51000 B = 33.51000 C = 33.51000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4600 2 1 -1 0 -1 2.8464 3 1 -1 1 -1 6.0786 4 1 0 -1 -1 4.4643 5 1 0 0 -1 1.0688 6 1 0 1 -1 2.9610 7 1 -1 -1 0 4.9473 8 1 -1 0 0 1.7447 9 1 -1 1 0 5.6603 10 1 0 -1 0 2.3439 11 1 0 1 0 2.3439 12 1 -1 -1 1 4.8973 13 1 -1 0 1 3.3115 14 1 -1 1 1 5.5969 15 1 0 -1 1 2.9610 16 1 0 0 1 1.0688 17 1 0 1 1 4.4643 18 1 1 1 1 6.4600 19 1 1 0 1 2.8464 20 1 1 -1 1 6.0786 21 1 1 1 0 4.9473 22 1 1 0 0 1.7447 23 1 1 -1 0 5.6603 24 1 1 1 -1 4.8973 25 1 1 0 -1 3.3115 26 1 1 -1 -1 5.5969 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.17 4 C004 has 588 196 196 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 465 155 155 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.21 Total of13002 atoms and 4325 groups and 4319 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.508" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.508" Parameter: BOX -> "33.508" Parameter: BOX -> "33.508" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.50800 B = 33.50800 C = 33.50800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4581 2 1 -1 0 -1 2.8437 3 1 -1 1 -1 6.0752 4 1 0 -1 -1 4.4657 5 1 0 0 -1 1.0671 6 1 0 1 -1 2.9599 7 1 -1 -1 0 4.9447 8 1 -1 0 0 1.7429 9 1 -1 1 0 5.6583 10 1 0 -1 0 2.3419 11 1 0 1 0 2.3419 12 1 -1 -1 1 4.8942 13 1 -1 0 1 3.3092 14 1 -1 1 1 5.5941 15 1 0 -1 1 2.9599 16 1 0 0 1 1.0671 17 1 0 1 1 4.4657 18 1 1 1 1 6.4581 19 1 1 0 1 2.8437 20 1 1 -1 1 6.0752 21 1 1 1 0 4.9447 22 1 1 0 0 1.7429 23 1 1 -1 0 5.6583 24 1 1 1 -1 4.8942 25 1 1 0 -1 3.3092 26 1 1 -1 -1 5.5941 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 735 245 245 0.00 3 C003 has 105 35 35 0.17 4 C004 has 588 196 196 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 465 155 155 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.20 Total of13002 atoms and 4325 groups and 4319 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.506" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.506" Parameter: BOX -> "33.506" Parameter: BOX -> "33.506" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.50600 B = 33.50600 C = 33.50600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4562 2 1 -1 0 -1 2.8409 3 1 -1 1 -1 6.0718 4 1 0 -1 -1 4.4672 5 1 0 0 -1 1.0654 6 1 0 1 -1 2.9587 7 1 -1 -1 0 4.9420 8 1 -1 0 0 1.7410 9 1 -1 1 0 5.6564 10 1 0 -1 0 2.3399 11 1 0 1 0 2.3399 12 1 -1 -1 1 4.8910 13 1 -1 0 1 3.3070 14 1 -1 1 1 5.5914 15 1 0 -1 1 2.9587 16 1 0 0 1 1.0654 17 1 0 1 1 4.4672 18 1 1 1 1 6.4562 19 1 1 0 1 2.8409 20 1 1 -1 1 6.0718 21 1 1 1 0 4.9420 22 1 1 0 0 1.7410 23 1 1 -1 0 5.6564 24 1 1 1 -1 4.8910 25 1 1 0 -1 3.3070 26 1 1 -1 -1 5.5914 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.17 4 C004 has 588 196 196 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 465 155 155 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1653 551 551 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.20 Total of13008 atoms and 4327 groups and 4321 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.504" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.504" Parameter: BOX -> "33.504" Parameter: BOX -> "33.504" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.50400 B = 33.50400 C = 33.50400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4543 2 1 -1 0 -1 2.8382 3 1 -1 1 -1 6.0683 4 1 0 -1 -1 4.4686 5 1 0 0 -1 1.0636 6 1 0 1 -1 2.9576 7 1 -1 -1 0 4.9393 8 1 -1 0 0 1.7391 9 1 -1 1 0 5.6544 10 1 0 -1 0 2.3379 11 1 0 1 0 2.3379 12 1 -1 -1 1 4.8879 13 1 -1 0 1 3.3047 14 1 -1 1 1 5.5886 15 1 0 -1 1 2.9576 16 1 0 0 1 1.0636 17 1 0 1 1 4.4686 18 1 1 1 1 6.4543 19 1 1 0 1 2.8382 20 1 1 -1 1 6.0683 21 1 1 1 0 4.9393 22 1 1 0 0 1.7391 23 1 1 -1 0 5.6544 24 1 1 1 -1 4.8879 25 1 1 0 -1 3.3047 26 1 1 -1 -1 5.5886 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.17 4 C004 has 591 197 197 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 465 155 155 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1653 551 551 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.20 Total of13011 atoms and 4328 groups and 4322 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.502" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.502" Parameter: BOX -> "33.502" Parameter: BOX -> "33.502" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.50200 B = 33.50200 C = 33.50200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4525 2 1 -1 0 -1 2.8355 3 1 -1 1 -1 6.0649 4 1 0 -1 -1 4.4701 5 1 0 0 -1 1.0619 6 1 0 1 -1 2.9564 7 1 -1 -1 0 4.9366 8 1 -1 0 0 1.7373 9 1 -1 1 0 5.6524 10 1 0 -1 0 2.3359 11 1 0 1 0 2.3359 12 1 -1 -1 1 4.8847 13 1 -1 0 1 3.3024 14 1 -1 1 1 5.5859 15 1 0 -1 1 2.9564 16 1 0 0 1 1.0619 17 1 0 1 1 4.4701 18 1 1 1 1 6.4525 19 1 1 0 1 2.8355 20 1 1 -1 1 6.0649 21 1 1 1 0 4.9366 22 1 1 0 0 1.7373 23 1 1 -1 0 5.6524 24 1 1 1 -1 4.8847 25 1 1 0 -1 3.3024 26 1 1 -1 -1 5.5859 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.17 4 C004 has 591 197 197 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 465 155 155 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1653 551 551 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.20 Total of13014 atoms and 4329 groups and 4323 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.5" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.5" Parameter: BOX -> "33.5" Parameter: BOX -> "33.5" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.50000 B = 33.50000 C = 33.50000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4506 2 1 -1 0 -1 2.8328 3 1 -1 1 -1 6.0614 4 1 0 -1 -1 4.4715 5 1 0 0 -1 1.0602 6 1 0 1 -1 2.9553 7 1 -1 -1 0 4.9339 8 1 -1 0 0 1.7354 9 1 -1 1 0 5.6505 10 1 0 -1 0 2.3339 11 1 0 1 0 2.3339 12 1 -1 -1 1 4.8816 13 1 -1 0 1 3.3002 14 1 -1 1 1 5.5831 15 1 0 -1 1 2.9553 16 1 0 0 1 1.0602 17 1 0 1 1 4.4715 18 1 1 1 1 6.4506 19 1 1 0 1 2.8328 20 1 1 -1 1 6.0614 21 1 1 1 0 4.9339 22 1 1 0 0 1.7354 23 1 1 -1 0 5.6505 24 1 1 1 -1 4.8816 25 1 1 0 -1 3.3002 26 1 1 -1 -1 5.5831 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.16 4 C004 has 591 197 197 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 465 155 155 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1653 551 551 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.20 Total of13014 atoms and 4329 groups and 4323 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.498" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.498" Parameter: BOX -> "33.498" Parameter: BOX -> "33.498" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.49800 B = 33.49800 C = 33.49800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4487 2 1 -1 0 -1 2.8301 3 1 -1 1 -1 6.0580 4 1 0 -1 -1 4.4730 5 1 0 0 -1 1.0585 6 1 0 1 -1 2.9541 7 1 -1 -1 0 4.9312 8 1 -1 0 0 1.7335 9 1 -1 1 0 5.6485 10 1 0 -1 0 2.3319 11 1 0 1 0 2.3319 12 1 -1 -1 1 4.8784 13 1 -1 0 1 3.2979 14 1 -1 1 1 5.5804 15 1 0 -1 1 2.9541 16 1 0 0 1 1.0585 17 1 0 1 1 4.4730 18 1 1 1 1 6.4487 19 1 1 0 1 2.8301 20 1 1 -1 1 6.0580 21 1 1 1 0 4.9312 22 1 1 0 0 1.7335 23 1 1 -1 0 5.6485 24 1 1 1 -1 4.8784 25 1 1 0 -1 3.2979 26 1 1 -1 -1 5.5804 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.16 4 C004 has 591 197 197 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 465 155 155 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1653 551 551 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.19 Total of13014 atoms and 4329 groups and 4323 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.496" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.496" Parameter: BOX -> "33.496" Parameter: BOX -> "33.496" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.49600 B = 33.49600 C = 33.49600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4468 2 1 -1 0 -1 2.8273 3 1 -1 1 -1 6.0546 4 1 0 -1 -1 4.4744 5 1 0 0 -1 1.0567 6 1 0 1 -1 2.9530 7 1 -1 -1 0 4.9286 8 1 -1 0 0 1.7317 9 1 -1 1 0 5.6466 10 1 0 -1 0 2.3299 11 1 0 1 0 2.3299 12 1 -1 -1 1 4.8753 13 1 -1 0 1 3.2956 14 1 -1 1 1 5.5777 15 1 0 -1 1 2.9530 16 1 0 0 1 1.0567 17 1 0 1 1 4.4744 18 1 1 1 1 6.4468 19 1 1 0 1 2.8273 20 1 1 -1 1 6.0546 21 1 1 1 0 4.9286 22 1 1 0 0 1.7317 23 1 1 -1 0 5.6466 24 1 1 1 -1 4.8753 25 1 1 0 -1 3.2956 26 1 1 -1 -1 5.5777 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.16 4 C004 has 594 198 198 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 465 155 155 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1653 551 551 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.19 Total of13020 atoms and 4331 groups and 4325 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.494" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.494" Parameter: BOX -> "33.494" Parameter: BOX -> "33.494" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.49400 B = 33.49400 C = 33.49400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4450 2 1 -1 0 -1 2.8246 3 1 -1 1 -1 6.0511 4 1 0 -1 -1 4.4759 5 1 0 0 -1 1.0550 6 1 0 1 -1 2.9518 7 1 -1 -1 0 4.9259 8 1 -1 0 0 1.7298 9 1 -1 1 0 5.6446 10 1 0 -1 0 2.3279 11 1 0 1 0 2.3279 12 1 -1 -1 1 4.8721 13 1 -1 0 1 3.2934 14 1 -1 1 1 5.5749 15 1 0 -1 1 2.9518 16 1 0 0 1 1.0550 17 1 0 1 1 4.4759 18 1 1 1 1 6.4450 19 1 1 0 1 2.8246 20 1 1 -1 1 6.0511 21 1 1 1 0 4.9259 22 1 1 0 0 1.7298 23 1 1 -1 0 5.6446 24 1 1 1 -1 4.8721 25 1 1 0 -1 3.2934 26 1 1 -1 -1 5.5749 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.16 4 C004 has 594 198 198 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 465 155 155 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1653 551 551 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.19 Total of13020 atoms and 4331 groups and 4325 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.492" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.492" Parameter: BOX -> "33.492" Parameter: BOX -> "33.492" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.49200 B = 33.49200 C = 33.49200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4431 2 1 -1 0 -1 2.8219 3 1 -1 1 -1 6.0477 4 1 0 -1 -1 4.4773 5 1 0 0 -1 1.0533 6 1 0 1 -1 2.9507 7 1 -1 -1 0 4.9232 8 1 -1 0 0 1.7280 9 1 -1 1 0 5.6427 10 1 0 -1 0 2.3259 11 1 0 1 0 2.3259 12 1 -1 -1 1 4.8690 13 1 -1 0 1 3.2911 14 1 -1 1 1 5.5722 15 1 0 -1 1 2.9507 16 1 0 0 1 1.0533 17 1 0 1 1 4.4773 18 1 1 1 1 6.4431 19 1 1 0 1 2.8219 20 1 1 -1 1 6.0477 21 1 1 1 0 4.9232 22 1 1 0 0 1.7280 23 1 1 -1 0 5.6427 24 1 1 1 -1 4.8690 25 1 1 0 -1 3.2911 26 1 1 -1 -1 5.5722 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.16 4 C004 has 594 198 198 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 468 156 156 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1653 551 551 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.19 Total of13023 atoms and 4332 groups and 4326 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.49" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.49" Parameter: BOX -> "33.49" Parameter: BOX -> "33.49" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.49000 B = 33.49000 C = 33.49000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4412 2 1 -1 0 -1 2.8192 3 1 -1 1 -1 6.0443 4 1 0 -1 -1 4.4788 5 1 0 0 -1 1.0515 6 1 0 1 -1 2.9496 7 1 -1 -1 0 4.9205 8 1 -1 0 0 1.7261 9 1 -1 1 0 5.6407 10 1 0 -1 0 2.3239 11 1 0 1 0 2.3239 12 1 -1 -1 1 4.8659 13 1 -1 0 1 3.2888 14 1 -1 1 1 5.5694 15 1 0 -1 1 2.9496 16 1 0 0 1 1.0515 17 1 0 1 1 4.4788 18 1 1 1 1 6.4412 19 1 1 0 1 2.8192 20 1 1 -1 1 6.0443 21 1 1 1 0 4.9205 22 1 1 0 0 1.7261 23 1 1 -1 0 5.6407 24 1 1 1 -1 4.8659 25 1 1 0 -1 3.2888 26 1 1 -1 -1 5.5694 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.15 4 C004 has 594 198 198 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 468 156 156 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.19 Total of13032 atoms and 4335 groups and 4329 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.488" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.488" Parameter: BOX -> "33.488" Parameter: BOX -> "33.488" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.48800 B = 33.48800 C = 33.48800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4394 2 1 -1 0 -1 2.8164 3 1 -1 1 -1 6.0408 4 1 0 -1 -1 4.4803 5 1 0 0 -1 1.0498 6 1 0 1 -1 2.9484 7 1 -1 -1 0 4.9178 8 1 -1 0 0 1.7242 9 1 -1 1 0 5.6388 10 1 0 -1 0 2.3219 11 1 0 1 0 2.3219 12 1 -1 -1 1 4.8627 13 1 -1 0 1 3.2866 14 1 -1 1 1 5.5667 15 1 0 -1 1 2.9484 16 1 0 0 1 1.0498 17 1 0 1 1 4.4803 18 1 1 1 1 6.4394 19 1 1 0 1 2.8164 20 1 1 -1 1 6.0408 21 1 1 1 0 4.9178 22 1 1 0 0 1.7242 23 1 1 -1 0 5.6388 24 1 1 1 -1 4.8627 25 1 1 0 -1 3.2866 26 1 1 -1 -1 5.5667 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.15 4 C004 has 594 198 198 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 468 156 156 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.18 Total of13032 atoms and 4335 groups and 4329 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.486" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.486" Parameter: BOX -> "33.486" Parameter: BOX -> "33.486" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.48600 B = 33.48600 C = 33.48600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4375 2 1 -1 0 -1 2.8137 3 1 -1 1 -1 6.0374 4 1 0 -1 -1 4.4817 5 1 0 0 -1 1.0481 6 1 0 1 -1 2.9473 7 1 -1 -1 0 4.9151 8 1 -1 0 0 1.7224 9 1 -1 1 0 5.6368 10 1 0 -1 0 2.3199 11 1 0 1 0 2.3199 12 1 -1 -1 1 4.8596 13 1 -1 0 1 3.2843 14 1 -1 1 1 5.5640 15 1 0 -1 1 2.9473 16 1 0 0 1 1.0481 17 1 0 1 1 4.4817 18 1 1 1 1 6.4375 19 1 1 0 1 2.8137 20 1 1 -1 1 6.0374 21 1 1 1 0 4.9151 22 1 1 0 0 1.7224 23 1 1 -1 0 5.6368 24 1 1 1 -1 4.8596 25 1 1 0 -1 3.2843 26 1 1 -1 -1 5.5640 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.15 4 C004 has 594 198 198 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 468 156 156 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.18 Total of13032 atoms and 4335 groups and 4329 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.484" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.484" Parameter: BOX -> "33.484" Parameter: BOX -> "33.484" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.48400 B = 33.48400 C = 33.48400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4356 2 1 -1 0 -1 2.8110 3 1 -1 1 -1 6.0339 4 1 0 -1 -1 4.4832 5 1 0 0 -1 1.0464 6 1 0 1 -1 2.9462 7 1 -1 -1 0 4.9125 8 1 -1 0 0 1.7205 9 1 -1 1 0 5.6349 10 1 0 -1 0 2.3179 11 1 0 1 0 2.3179 12 1 -1 -1 1 4.8564 13 1 -1 0 1 3.2820 14 1 -1 1 1 5.5612 15 1 0 -1 1 2.9462 16 1 0 0 1 1.0464 17 1 0 1 1 4.4832 18 1 1 1 1 6.4356 19 1 1 0 1 2.8110 20 1 1 -1 1 6.0339 21 1 1 1 0 4.9125 22 1 1 0 0 1.7205 23 1 1 -1 0 5.6349 24 1 1 1 -1 4.8564 25 1 1 0 -1 3.2820 26 1 1 -1 -1 5.5612 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.15 4 C004 has 594 198 198 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 468 156 156 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.18 Total of13032 atoms and 4335 groups and 4329 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.482" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.482" Parameter: BOX -> "33.482" Parameter: BOX -> "33.482" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.48200 B = 33.48200 C = 33.48200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4338 2 1 -1 0 -1 2.8083 3 1 -1 1 -1 6.0305 4 1 0 -1 -1 4.4846 5 1 0 0 -1 1.0447 6 1 0 1 -1 2.9451 7 1 -1 -1 0 4.9098 8 1 -1 0 0 1.7187 9 1 -1 1 0 5.6329 10 1 0 -1 0 2.3159 11 1 0 1 0 2.3159 12 1 -1 -1 1 4.8533 13 1 -1 0 1 3.2798 14 1 -1 1 1 5.5585 15 1 0 -1 1 2.9451 16 1 0 0 1 1.0447 17 1 0 1 1 4.4846 18 1 1 1 1 6.4338 19 1 1 0 1 2.8083 20 1 1 -1 1 6.0305 21 1 1 1 0 4.9098 22 1 1 0 0 1.7187 23 1 1 -1 0 5.6329 24 1 1 1 -1 4.8533 25 1 1 0 -1 3.2798 26 1 1 -1 -1 5.5585 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.15 4 C004 has 594 198 198 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 468 156 156 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.18 Total of13032 atoms and 4335 groups and 4329 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.48" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.48" Parameter: BOX -> "33.48" Parameter: BOX -> "33.48" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.48000 B = 33.48000 C = 33.48000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4319 2 1 -1 0 -1 2.8056 3 1 -1 1 -1 6.0271 4 1 0 -1 -1 4.4861 5 1 0 0 -1 1.0429 6 1 0 1 -1 2.9439 7 1 -1 -1 0 4.9071 8 1 -1 0 0 1.7168 9 1 -1 1 0 5.6310 10 1 0 -1 0 2.3139 11 1 0 1 0 2.3139 12 1 -1 -1 1 4.8501 13 1 -1 0 1 3.2775 14 1 -1 1 1 5.5558 15 1 0 -1 1 2.9439 16 1 0 0 1 1.0429 17 1 0 1 1 4.4861 18 1 1 1 1 6.4319 19 1 1 0 1 2.8056 20 1 1 -1 1 6.0271 21 1 1 1 0 4.9071 22 1 1 0 0 1.7168 23 1 1 -1 0 5.6310 24 1 1 1 -1 4.8501 25 1 1 0 -1 3.2775 26 1 1 -1 -1 5.5558 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.14 4 C004 has 594 198 198 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 468 156 156 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.18 Total of13032 atoms and 4335 groups and 4329 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.478" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.478" Parameter: BOX -> "33.478" Parameter: BOX -> "33.478" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.47800 B = 33.47800 C = 33.47800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4300 2 1 -1 0 -1 2.8028 3 1 -1 1 -1 6.0236 4 1 0 -1 -1 4.4876 5 1 0 0 -1 1.0412 6 1 0 1 -1 2.9428 7 1 -1 -1 0 4.9044 8 1 -1 0 0 1.7149 9 1 -1 1 0 5.6290 10 1 0 -1 0 2.3119 11 1 0 1 0 2.3119 12 1 -1 -1 1 4.8470 13 1 -1 0 1 3.2753 14 1 -1 1 1 5.5530 15 1 0 -1 1 2.9428 16 1 0 0 1 1.0412 17 1 0 1 1 4.4876 18 1 1 1 1 6.4300 19 1 1 0 1 2.8028 20 1 1 -1 1 6.0236 21 1 1 1 0 4.9044 22 1 1 0 0 1.7149 23 1 1 -1 0 5.6290 24 1 1 1 -1 4.8470 25 1 1 0 -1 3.2753 26 1 1 -1 -1 5.5530 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.14 4 C004 has 594 198 198 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 468 156 156 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.17 Total of13032 atoms and 4335 groups and 4329 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.476" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.476" Parameter: BOX -> "33.476" Parameter: BOX -> "33.476" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.47600 B = 33.47600 C = 33.47600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4282 2 1 -1 0 -1 2.8001 3 1 -1 1 -1 6.0202 4 1 0 -1 -1 4.4890 5 1 0 0 -1 1.0395 6 1 0 1 -1 2.9417 7 1 -1 -1 0 4.9017 8 1 -1 0 0 1.7131 9 1 -1 1 0 5.6271 10 1 0 -1 0 2.3099 11 1 0 1 0 2.3099 12 1 -1 -1 1 4.8439 13 1 -1 0 1 3.2730 14 1 -1 1 1 5.5503 15 1 0 -1 1 2.9417 16 1 0 0 1 1.0395 17 1 0 1 1 4.4890 18 1 1 1 1 6.4282 19 1 1 0 1 2.8001 20 1 1 -1 1 6.0202 21 1 1 1 0 4.9017 22 1 1 0 0 1.7131 23 1 1 -1 0 5.6271 24 1 1 1 -1 4.8439 25 1 1 0 -1 3.2730 26 1 1 -1 -1 5.5503 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.14 4 C004 has 594 198 198 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 468 156 156 0.00 7 C007 has 735 245 245 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.17 Total of13032 atoms and 4335 groups and 4329 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3776 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1247 Number of atoms = 3776 Number of groups = 1252 Number of bonds = 3769 Number of angles = 1351 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1249 Number of HB donors = 2476 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.474" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1247" Evaluating: 1247-7 Parameter: NUMWAT <- "1240" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1240" Comparing "1081" and "1240". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.474" Parameter: BOX -> "33.474" Parameter: BOX -> "33.474" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.47400 B = 33.47400 C = 33.47400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4263 2 1 -1 0 -1 2.7974 3 1 -1 1 -1 6.0168 4 1 0 -1 -1 4.4905 5 1 0 0 -1 1.0378 6 1 0 1 -1 2.9406 7 1 -1 -1 0 4.8990 8 1 -1 0 0 1.7112 9 1 -1 1 0 5.6251 10 1 0 -1 0 2.3079 11 1 0 1 0 2.3079 12 1 -1 -1 1 4.8407 13 1 -1 0 1 3.2708 14 1 -1 1 1 5.5476 15 1 0 -1 1 2.9406 16 1 0 0 1 1.0378 17 1 0 1 1 4.4905 18 1 1 1 1 6.4263 19 1 1 0 1 2.7974 20 1 1 -1 1 6.0168 21 1 1 1 0 4.8990 22 1 1 0 0 1.7112 23 1 1 -1 0 5.6251 24 1 1 1 -1 4.8407 25 1 1 0 -1 3.2708 26 1 1 -1 -1 5.5476 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3702 atoms have been selected out of 3776 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 782 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.14 4 C004 has 594 198 198 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 468 156 156 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.17 Total of13041 atoms and 4338 groups and 4332 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3776 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1246 Number of atoms = 3773 Number of groups = 1251 Number of bonds = 3766 Number of angles = 1350 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1248 Number of HB donors = 2474 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1246 Number of atoms = 3773 Number of groups = 1251 Number of bonds = 3766 Number of angles = 1350 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1248 Number of HB donors = 2474 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.472" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1246" Evaluating: 1246-7 Parameter: NUMWAT <- "1239" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1239" Comparing "1081" and "1239". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.472" Parameter: BOX -> "33.472" Parameter: BOX -> "33.472" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.47200 B = 33.47200 C = 33.47200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4245 2 1 -1 0 -1 2.7947 3 1 -1 1 -1 6.0133 4 1 0 -1 -1 4.4920 5 1 0 0 -1 1.0361 6 1 0 1 -1 2.9395 7 1 -1 -1 0 4.8964 8 1 -1 0 0 1.7094 9 1 -1 1 0 5.6232 10 1 0 -1 0 2.3059 11 1 0 1 0 2.3059 12 1 -1 -1 1 4.8376 13 1 -1 0 1 3.2685 14 1 -1 1 1 5.5448 15 1 0 -1 1 2.9395 16 1 0 0 1 1.0361 17 1 0 1 1 4.4920 18 1 1 1 1 6.4245 19 1 1 0 1 2.7947 20 1 1 -1 1 6.0133 21 1 1 1 0 4.8964 22 1 1 0 0 1.7094 23 1 1 -1 0 5.6232 24 1 1 1 -1 4.8376 25 1 1 0 -1 3.2685 26 1 1 -1 -1 5.5448 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3699 atoms have been selected out of 3773 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 738 246 246 0.00 3 C003 has 105 35 35 0.14 4 C004 has 597 199 199 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 468 156 156 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.17 Total of13032 atoms and 4335 groups and 4329 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3773 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1246 Number of atoms = 3773 Number of groups = 1251 Number of bonds = 3766 Number of angles = 1350 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1248 Number of HB donors = 2474 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1246 Number of atoms = 3773 Number of groups = 1251 Number of bonds = 3766 Number of angles = 1350 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1248 Number of HB donors = 2474 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.47" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1246" Evaluating: 1246-7 Parameter: NUMWAT <- "1239" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1239" Comparing "1081" and "1239". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.47" Parameter: BOX -> "33.47" Parameter: BOX -> "33.47" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.47000 B = 33.47000 C = 33.47000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4226 2 1 -1 0 -1 2.7920 3 1 -1 1 -1 6.0099 4 1 0 -1 -1 4.4935 5 1 0 0 -1 1.0343 6 1 0 1 -1 2.9384 7 1 -1 -1 0 4.8937 8 1 -1 0 0 1.7075 9 1 -1 1 0 5.6213 10 1 0 -1 0 2.3039 11 1 0 1 0 2.3039 12 1 -1 -1 1 4.8344 13 1 -1 0 1 3.2663 14 1 -1 1 1 5.5421 15 1 0 -1 1 2.9384 16 1 0 0 1 1.0343 17 1 0 1 1 4.4935 18 1 1 1 1 6.4226 19 1 1 0 1 2.7920 20 1 1 -1 1 6.0099 21 1 1 1 0 4.8937 22 1 1 0 0 1.7075 23 1 1 -1 0 5.6213 24 1 1 1 -1 4.8344 25 1 1 0 -1 3.2663 26 1 1 -1 -1 5.5421 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3699 atoms have been selected out of 3773 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.13 4 C004 has 597 199 199 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 468 156 156 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.17 Total of13035 atoms and 4336 groups and 4330 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3773 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1246 Number of atoms = 3773 Number of groups = 1251 Number of bonds = 3766 Number of angles = 1350 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1248 Number of HB donors = 2474 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1246 Number of atoms = 3773 Number of groups = 1251 Number of bonds = 3766 Number of angles = 1350 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1248 Number of HB donors = 2474 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.468" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1246" Evaluating: 1246-7 Parameter: NUMWAT <- "1239" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1239" Comparing "1081" and "1239". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.468" Parameter: BOX -> "33.468" Parameter: BOX -> "33.468" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.46800 B = 33.46800 C = 33.46800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4208 2 1 -1 0 -1 2.7892 3 1 -1 1 -1 6.0064 4 1 0 -1 -1 4.4949 5 1 0 0 -1 1.0326 6 1 0 1 -1 2.9372 7 1 -1 -1 0 4.8910 8 1 -1 0 0 1.7057 9 1 -1 1 0 5.6193 10 1 0 -1 0 2.3019 11 1 0 1 0 2.3019 12 1 -1 -1 1 4.8313 13 1 -1 0 1 3.2640 14 1 -1 1 1 5.5394 15 1 0 -1 1 2.9372 16 1 0 0 1 1.0326 17 1 0 1 1 4.4949 18 1 1 1 1 6.4208 19 1 1 0 1 2.7892 20 1 1 -1 1 6.0064 21 1 1 1 0 4.8910 22 1 1 0 0 1.7057 23 1 1 -1 0 5.6193 24 1 1 1 -1 4.8313 25 1 1 0 -1 3.2640 26 1 1 -1 -1 5.5394 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3699 atoms have been selected out of 3773 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.13 4 C004 has 600 200 200 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 468 156 156 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.16 Total of13038 atoms and 4337 groups and 4331 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3773 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1246 Number of atoms = 3773 Number of groups = 1251 Number of bonds = 3766 Number of angles = 1350 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1248 Number of HB donors = 2474 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1246 Number of atoms = 3773 Number of groups = 1251 Number of bonds = 3766 Number of angles = 1350 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1248 Number of HB donors = 2474 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.466" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1246" Evaluating: 1246-7 Parameter: NUMWAT <- "1239" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1239" Comparing "1081" and "1239". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.466" Parameter: BOX -> "33.466" Parameter: BOX -> "33.466" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.46600 B = 33.46600 C = 33.46600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4189 2 1 -1 0 -1 2.7865 3 1 -1 1 -1 6.0030 4 1 0 -1 -1 4.4964 5 1 0 0 -1 1.0309 6 1 0 1 -1 2.9361 7 1 -1 -1 0 4.8883 8 1 -1 0 0 1.7038 9 1 -1 1 0 5.6174 10 1 0 -1 0 2.2999 11 1 0 1 0 2.2999 12 1 -1 -1 1 4.8282 13 1 -1 0 1 3.2617 14 1 -1 1 1 5.5366 15 1 0 -1 1 2.9361 16 1 0 0 1 1.0309 17 1 0 1 1 4.4964 18 1 1 1 1 6.4189 19 1 1 0 1 2.7865 20 1 1 -1 1 6.0030 21 1 1 1 0 4.8883 22 1 1 0 0 1.7038 23 1 1 -1 0 5.6174 24 1 1 1 -1 4.8282 25 1 1 0 -1 3.2617 26 1 1 -1 -1 5.5366 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3699 atoms have been selected out of 3773 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.13 4 C004 has 600 200 200 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 468 156 156 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.16 Total of13041 atoms and 4338 groups and 4332 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3773 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1246 Number of atoms = 3773 Number of groups = 1251 Number of bonds = 3766 Number of angles = 1350 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1248 Number of HB donors = 2474 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1246 Number of atoms = 3773 Number of groups = 1251 Number of bonds = 3766 Number of angles = 1350 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1248 Number of HB donors = 2474 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.464" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1246" Evaluating: 1246-7 Parameter: NUMWAT <- "1239" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1239" Comparing "1081" and "1239". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.464" Parameter: BOX -> "33.464" Parameter: BOX -> "33.464" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.46400 B = 33.46400 C = 33.46400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4171 2 1 -1 0 -1 2.7838 3 1 -1 1 -1 5.9996 4 1 0 -1 -1 4.4979 5 1 0 0 -1 1.0292 6 1 0 1 -1 2.9350 7 1 -1 -1 0 4.8856 8 1 -1 0 0 1.7019 9 1 -1 1 0 5.6154 10 1 0 -1 0 2.2979 11 1 0 1 0 2.2979 12 1 -1 -1 1 4.8250 13 1 -1 0 1 3.2595 14 1 -1 1 1 5.5339 15 1 0 -1 1 2.9350 16 1 0 0 1 1.0292 17 1 0 1 1 4.4979 18 1 1 1 1 6.4171 19 1 1 0 1 2.7838 20 1 1 -1 1 5.9996 21 1 1 1 0 4.8856 22 1 1 0 0 1.7019 23 1 1 -1 0 5.6154 24 1 1 1 -1 4.8250 25 1 1 0 -1 3.2595 26 1 1 -1 -1 5.5339 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3699 atoms have been selected out of 3773 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.13 4 C004 has 600 200 200 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 468 156 156 0.00 7 C007 has 738 246 246 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.16 Total of13041 atoms and 4338 groups and 4332 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3773 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1246 Number of atoms = 3773 Number of groups = 1251 Number of bonds = 3766 Number of angles = 1350 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1248 Number of HB donors = 2474 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1246 Number of atoms = 3773 Number of groups = 1251 Number of bonds = 3766 Number of angles = 1350 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1248 Number of HB donors = 2474 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.462" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1246" Evaluating: 1246-7 Parameter: NUMWAT <- "1239" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1239" Comparing "1081" and "1239". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.462" Parameter: BOX -> "33.462" Parameter: BOX -> "33.462" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.46200 B = 33.46200 C = 33.46200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4152 2 1 -1 0 -1 2.7811 3 1 -1 1 -1 5.9961 4 1 0 -1 -1 4.4994 5 1 0 0 -1 1.0275 6 1 0 1 -1 2.9339 7 1 -1 -1 0 4.8830 8 1 -1 0 0 1.7001 9 1 -1 1 0 5.6135 10 1 0 -1 0 2.2959 11 1 0 1 0 2.2959 12 1 -1 -1 1 4.8219 13 1 -1 0 1 3.2572 14 1 -1 1 1 5.5312 15 1 0 -1 1 2.9339 16 1 0 0 1 1.0275 17 1 0 1 1 4.4994 18 1 1 1 1 6.4152 19 1 1 0 1 2.7811 20 1 1 -1 1 5.9961 21 1 1 1 0 4.8830 22 1 1 0 0 1.7001 23 1 1 -1 0 5.6135 24 1 1 1 -1 4.8219 25 1 1 0 -1 3.2572 26 1 1 -1 -1 5.5312 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3699 atoms have been selected out of 3773 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.13 4 C004 has 600 200 200 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 468 156 156 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.16 Total of13047 atoms and 4340 groups and 4334 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3773 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1246 Number of atoms = 3773 Number of groups = 1251 Number of bonds = 3766 Number of angles = 1350 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1248 Number of HB donors = 2474 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1246 Number of atoms = 3773 Number of groups = 1251 Number of bonds = 3766 Number of angles = 1350 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1248 Number of HB donors = 2474 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.46" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1246" Evaluating: 1246-7 Parameter: NUMWAT <- "1239" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1239" Comparing "1081" and "1239". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.46" Parameter: BOX -> "33.46" Parameter: BOX -> "33.46" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.46000 B = 33.46000 C = 33.46000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4134 2 1 -1 0 -1 2.7784 3 1 -1 1 -1 5.9927 4 1 0 -1 -1 4.5008 5 1 0 0 -1 1.0258 6 1 0 1 -1 2.9328 7 1 -1 -1 0 4.8803 8 1 -1 0 0 1.6982 9 1 -1 1 0 5.6116 10 1 0 -1 0 2.2939 11 1 0 1 0 2.2939 12 1 -1 -1 1 4.8188 13 1 -1 0 1 3.2550 14 1 -1 1 1 5.5285 15 1 0 -1 1 2.9328 16 1 0 0 1 1.0258 17 1 0 1 1 4.5008 18 1 1 1 1 6.4134 19 1 1 0 1 2.7784 20 1 1 -1 1 5.9927 21 1 1 1 0 4.8803 22 1 1 0 0 1.6982 23 1 1 -1 0 5.6116 24 1 1 1 -1 4.8188 25 1 1 0 -1 3.2550 26 1 1 -1 -1 5.5285 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3699 atoms have been selected out of 3773 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 744 248 248 0.00 3 C003 has 105 35 35 0.12 4 C004 has 600 200 200 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 468 156 156 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.16 Total of13050 atoms and 4341 groups and 4335 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3773 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1246 Number of atoms = 3773 Number of groups = 1251 Number of bonds = 3766 Number of angles = 1350 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1248 Number of HB donors = 2474 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1246 Number of atoms = 3773 Number of groups = 1251 Number of bonds = 3766 Number of angles = 1350 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1248 Number of HB donors = 2474 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.458" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1246" Evaluating: 1246-7 Parameter: NUMWAT <- "1239" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1239" Comparing "1081" and "1239". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.458" Parameter: BOX -> "33.458" Parameter: BOX -> "33.458" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.45800 B = 33.45800 C = 33.45800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4115 2 1 -1 0 -1 2.7756 3 1 -1 1 -1 5.9893 4 1 0 -1 -1 4.5023 5 1 0 0 -1 1.0241 6 1 0 1 -1 2.9317 7 1 -1 -1 0 4.8776 8 1 -1 0 0 1.6964 9 1 -1 1 0 5.6096 10 1 0 -1 0 2.2919 11 1 0 1 0 2.2919 12 1 -1 -1 1 4.8156 13 1 -1 0 1 3.2527 14 1 -1 1 1 5.5257 15 1 0 -1 1 2.9317 16 1 0 0 1 1.0241 17 1 0 1 1 4.5023 18 1 1 1 1 6.4115 19 1 1 0 1 2.7756 20 1 1 -1 1 5.9893 21 1 1 1 0 4.8776 22 1 1 0 0 1.6964 23 1 1 -1 0 5.6096 24 1 1 1 -1 4.8156 25 1 1 0 -1 3.2527 26 1 1 -1 -1 5.5257 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3699 atoms have been selected out of 3773 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 858 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 429 143 143 0.00 2 C002 has 744 248 248 0.00 3 C003 has 102 34 34 0.12 4 C004 has 603 201 201 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 465 155 155 0.00 7 C007 has 744 248 248 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.15 Total of13050 atoms and 4341 groups and 4335 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3773 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1245 Number of atoms = 3770 Number of groups = 1250 Number of bonds = 3763 Number of angles = 1349 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1247 Number of HB donors = 2472 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1245 Number of atoms = 3770 Number of groups = 1250 Number of bonds = 3763 Number of angles = 1349 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1247 Number of HB donors = 2472 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.456" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1245" Evaluating: 1245-7 Parameter: NUMWAT <- "1238" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1238" Comparing "1081" and "1238". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.456" Parameter: BOX -> "33.456" Parameter: BOX -> "33.456" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.45600 B = 33.45600 C = 33.45600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4097 2 1 -1 0 -1 2.7729 3 1 -1 1 -1 5.9858 4 1 0 -1 -1 4.5038 5 1 0 0 -1 1.0224 6 1 0 1 -1 2.9306 7 1 -1 -1 0 4.8749 8 1 -1 0 0 1.6945 9 1 -1 1 0 5.6077 10 1 0 -1 0 2.2899 11 1 0 1 0 2.2899 12 1 -1 -1 1 4.8125 13 1 -1 0 1 3.2505 14 1 -1 1 1 5.5230 15 1 0 -1 1 2.9306 16 1 0 0 1 1.0224 17 1 0 1 1 4.5038 18 1 1 1 1 6.4097 19 1 1 0 1 2.7729 20 1 1 -1 1 5.9858 21 1 1 1 0 4.8749 22 1 1 0 0 1.6945 23 1 1 -1 0 5.6077 24 1 1 1 -1 4.8125 25 1 1 0 -1 3.2505 26 1 1 -1 -1 5.5230 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3696 atoms have been selected out of 3770 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.12 4 C004 has 600 200 200 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 465 155 155 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 123 41 41 1.15 Total of13026 atoms and 4333 groups and 4327 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3770 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1245 Number of atoms = 3770 Number of groups = 1250 Number of bonds = 3763 Number of angles = 1349 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1247 Number of HB donors = 2472 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1245 Number of atoms = 3770 Number of groups = 1250 Number of bonds = 3763 Number of angles = 1349 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1247 Number of HB donors = 2472 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.454" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1245" Evaluating: 1245-7 Parameter: NUMWAT <- "1238" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1238" Comparing "1081" and "1238". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.454" Parameter: BOX -> "33.454" Parameter: BOX -> "33.454" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.45400 B = 33.45400 C = 33.45400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4078 2 1 -1 0 -1 2.7702 3 1 -1 1 -1 5.9824 4 1 0 -1 -1 4.5053 5 1 0 0 -1 1.0207 6 1 0 1 -1 2.9295 7 1 -1 -1 0 4.8722 8 1 -1 0 0 1.6927 9 1 -1 1 0 5.6057 10 1 0 -1 0 2.2879 11 1 0 1 0 2.2879 12 1 -1 -1 1 4.8093 13 1 -1 0 1 3.2483 14 1 -1 1 1 5.5203 15 1 0 -1 1 2.9295 16 1 0 0 1 1.0207 17 1 0 1 1 4.5053 18 1 1 1 1 6.4078 19 1 1 0 1 2.7702 20 1 1 -1 1 5.9824 21 1 1 1 0 4.8722 22 1 1 0 0 1.6927 23 1 1 -1 0 5.6057 24 1 1 1 -1 4.8093 25 1 1 0 -1 3.2483 26 1 1 -1 -1 5.5203 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3696 atoms have been selected out of 3770 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 21 OPERATED ON BY TRANSFORMATION C022 RESIDUE 637 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 426 142 142 0.00 2 C002 has 744 248 248 0.00 3 C003 has 105 35 35 0.12 4 C004 has 600 200 200 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 462 154 154 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 1.15 Total of13041 atoms and 4338 groups and 4332 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3770 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1243 Number of atoms = 3764 Number of groups = 1248 Number of bonds = 3757 Number of angles = 1347 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1245 Number of HB donors = 2468 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1243 Number of atoms = 3764 Number of groups = 1248 Number of bonds = 3757 Number of angles = 1347 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1245 Number of HB donors = 2468 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.452" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1243" Evaluating: 1243-7 Parameter: NUMWAT <- "1236" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1236" Comparing "1081" and "1236". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.452" Parameter: BOX -> "33.452" Parameter: BOX -> "33.452" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.45200 B = 33.45200 C = 33.45200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4060 2 1 -1 0 -1 2.7675 3 1 -1 1 -1 5.9789 4 1 0 -1 -1 4.5068 5 1 0 0 -1 1.0190 6 1 0 1 -1 2.9285 7 1 -1 -1 0 4.8695 8 1 -1 0 0 1.6908 9 1 -1 1 0 5.6038 10 1 0 -1 0 2.2859 11 1 0 1 0 2.2859 12 1 -1 -1 1 4.8062 13 1 -1 0 1 2.3167 14 1 -1 1 1 5.5176 15 1 0 -1 1 2.9285 16 1 0 0 1 1.0190 17 1 0 1 1 4.5068 18 1 1 1 1 6.4060 19 1 1 0 1 2.7675 20 1 1 -1 1 5.9789 21 1 1 1 0 4.8695 22 1 1 0 0 1.6908 23 1 1 -1 0 5.6038 24 1 1 1 -1 4.8062 25 1 1 0 -1 2.3167 26 1 1 -1 -1 5.5176 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3690 atoms have been selected out of 3764 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 429 143 143 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.12 4 C004 has 600 200 200 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 462 154 154 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 1.15 Total of13011 atoms and 4328 groups and 4322 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3764 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1243 Number of atoms = 3764 Number of groups = 1248 Number of bonds = 3757 Number of angles = 1347 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1245 Number of HB donors = 2468 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1243 Number of atoms = 3764 Number of groups = 1248 Number of bonds = 3757 Number of angles = 1347 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1245 Number of HB donors = 2468 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.45" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1243" Evaluating: 1243-7 Parameter: NUMWAT <- "1236" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1236" Comparing "1081" and "1236". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.45" Parameter: BOX -> "33.45" Parameter: BOX -> "33.45" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.45000 B = 33.45000 C = 33.45000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4042 2 1 -1 0 -1 2.7648 3 1 -1 1 -1 5.9755 4 1 0 -1 -1 4.5083 5 1 0 0 -1 1.0172 6 1 0 1 -1 2.9274 7 1 -1 -1 0 4.8669 8 1 -1 0 0 1.6890 9 1 -1 1 0 5.6019 10 1 0 -1 0 2.2839 11 1 0 1 0 2.2839 12 1 -1 -1 1 4.8031 13 1 -1 0 1 2.3154 14 1 -1 1 1 5.5148 15 1 0 -1 1 2.9274 16 1 0 0 1 1.0172 17 1 0 1 1 4.5083 18 1 1 1 1 6.4042 19 1 1 0 1 2.7648 20 1 1 -1 1 5.9755 21 1 1 1 0 4.8669 22 1 1 0 0 1.6890 23 1 1 -1 0 5.6019 24 1 1 1 -1 4.8031 25 1 1 0 -1 2.3154 26 1 1 -1 -1 5.5148 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3690 atoms have been selected out of 3764 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 429 143 143 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.11 4 C004 has 600 200 200 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 462 154 154 0.00 7 C007 has 741 247 247 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 1.15 Total of13014 atoms and 4329 groups and 4323 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3764 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1243 Number of atoms = 3764 Number of groups = 1248 Number of bonds = 3757 Number of angles = 1347 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1245 Number of HB donors = 2468 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1243 Number of atoms = 3764 Number of groups = 1248 Number of bonds = 3757 Number of angles = 1347 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1245 Number of HB donors = 2468 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.448" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1243" Evaluating: 1243-7 Parameter: NUMWAT <- "1236" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1236" Comparing "1081" and "1236". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.448" Parameter: BOX -> "33.448" Parameter: BOX -> "33.448" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.44800 B = 33.44800 C = 33.44800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4023 2 1 -1 0 -1 2.7621 3 1 -1 1 -1 5.9721 4 1 0 -1 -1 4.5097 5 1 0 0 -1 1.0155 6 1 0 1 -1 2.9263 7 1 -1 -1 0 4.8642 8 1 -1 0 0 1.6871 9 1 -1 1 0 5.5999 10 1 0 -1 0 2.2819 11 1 0 1 0 2.2819 12 1 -1 -1 1 4.7999 13 1 -1 0 1 2.3141 14 1 -1 1 1 5.5121 15 1 0 -1 1 2.9263 16 1 0 0 1 1.0155 17 1 0 1 1 4.5097 18 1 1 1 1 6.4023 19 1 1 0 1 2.7621 20 1 1 -1 1 5.9721 21 1 1 1 0 4.8642 22 1 1 0 0 1.6871 23 1 1 -1 0 5.5999 24 1 1 1 -1 4.7999 25 1 1 0 -1 2.3141 26 1 1 -1 -1 5.5121 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3690 atoms have been selected out of 3764 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 429 143 143 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.11 4 C004 has 600 200 200 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 462 154 154 0.00 7 C007 has 744 248 248 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 1.14 Total of13017 atoms and 4330 groups and 4324 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3764 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1243 Number of atoms = 3764 Number of groups = 1248 Number of bonds = 3757 Number of angles = 1347 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1245 Number of HB donors = 2468 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1243 Number of atoms = 3764 Number of groups = 1248 Number of bonds = 3757 Number of angles = 1347 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1245 Number of HB donors = 2468 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.446" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1243" Evaluating: 1243-7 Parameter: NUMWAT <- "1236" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1236" Comparing "1081" and "1236". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.446" Parameter: BOX -> "33.446" Parameter: BOX -> "33.446" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.44600 B = 33.44600 C = 33.44600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.4005 2 1 -1 0 -1 2.7593 3 1 -1 1 -1 5.9686 4 1 0 -1 -1 4.5112 5 1 0 0 -1 1.0138 6 1 0 1 -1 2.9252 7 1 -1 -1 0 4.8615 8 1 -1 0 0 1.6852 9 1 -1 1 0 5.5980 10 1 0 -1 0 2.2799 11 1 0 1 0 2.2799 12 1 -1 -1 1 4.7968 13 1 -1 0 1 2.3129 14 1 -1 1 1 5.5094 15 1 0 -1 1 2.9252 16 1 0 0 1 1.0138 17 1 0 1 1 4.5112 18 1 1 1 1 6.4005 19 1 1 0 1 2.7593 20 1 1 -1 1 5.9686 21 1 1 1 0 4.8615 22 1 1 0 0 1.6852 23 1 1 -1 0 5.5980 24 1 1 1 -1 4.7968 25 1 1 0 -1 2.3129 26 1 1 -1 -1 5.5094 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3690 atoms have been selected out of 3764 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 429 143 143 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.11 4 C004 has 600 200 200 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 462 154 154 0.00 7 C007 has 744 248 248 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 1.14 Total of13020 atoms and 4331 groups and 4325 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3764 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1243 Number of atoms = 3764 Number of groups = 1248 Number of bonds = 3757 Number of angles = 1347 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1245 Number of HB donors = 2468 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1243 Number of atoms = 3764 Number of groups = 1248 Number of bonds = 3757 Number of angles = 1347 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1245 Number of HB donors = 2468 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.444" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1243" Evaluating: 1243-7 Parameter: NUMWAT <- "1236" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1236" Comparing "1081" and "1236". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.444" Parameter: BOX -> "33.444" Parameter: BOX -> "33.444" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.44400 B = 33.44400 C = 33.44400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3986 2 1 -1 0 -1 2.7566 3 1 -1 1 -1 5.9652 4 1 0 -1 -1 4.5127 5 1 0 0 -1 1.0121 6 1 0 1 -1 2.9241 7 1 -1 -1 0 4.8588 8 1 -1 0 0 1.6834 9 1 -1 1 0 5.5961 10 1 0 -1 0 2.2779 11 1 0 1 0 2.2779 12 1 -1 -1 1 4.7937 13 1 -1 0 1 2.3116 14 1 -1 1 1 5.5067 15 1 0 -1 1 2.9241 16 1 0 0 1 1.0121 17 1 0 1 1 4.5127 18 1 1 1 1 6.3986 19 1 1 0 1 2.7566 20 1 1 -1 1 5.9652 21 1 1 1 0 4.8588 22 1 1 0 0 1.6834 23 1 1 -1 0 5.5961 24 1 1 1 -1 4.7937 25 1 1 0 -1 2.3116 26 1 1 -1 -1 5.5067 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3690 atoms have been selected out of 3764 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 429 143 143 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.11 4 C004 has 600 200 200 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 462 154 154 0.00 7 C007 has 744 248 248 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 1.14 Total of13020 atoms and 4331 groups and 4325 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3764 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1243 Number of atoms = 3764 Number of groups = 1248 Number of bonds = 3757 Number of angles = 1347 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1245 Number of HB donors = 2468 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1243 Number of atoms = 3764 Number of groups = 1248 Number of bonds = 3757 Number of angles = 1347 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1245 Number of HB donors = 2468 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.442" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1243" Evaluating: 1243-7 Parameter: NUMWAT <- "1236" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1236" Comparing "1081" and "1236". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.442" Parameter: BOX -> "33.442" Parameter: BOX -> "33.442" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.44200 B = 33.44200 C = 33.44200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3968 2 1 -1 0 -1 2.7539 3 1 -1 1 -1 5.9618 4 1 0 -1 -1 4.5142 5 1 0 0 -1 1.0104 6 1 0 1 -1 2.9230 7 1 -1 -1 0 4.8561 8 1 -1 0 0 1.6815 9 1 -1 1 0 5.5941 10 1 0 -1 0 2.2759 11 1 0 1 0 2.2759 12 1 -1 -1 1 4.7905 13 1 -1 0 1 2.3104 14 1 -1 1 1 5.5040 15 1 0 -1 1 2.9230 16 1 0 0 1 1.0104 17 1 0 1 1 4.5142 18 1 1 1 1 6.3968 19 1 1 0 1 2.7539 20 1 1 -1 1 5.9618 21 1 1 1 0 4.8561 22 1 1 0 0 1.6815 23 1 1 -1 0 5.5941 24 1 1 1 -1 4.7905 25 1 1 0 -1 2.3104 26 1 1 -1 -1 5.5040 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3690 atoms have been selected out of 3764 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 429 143 143 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.11 4 C004 has 600 200 200 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 462 154 154 0.00 7 C007 has 744 248 248 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 1.14 Total of13020 atoms and 4331 groups and 4325 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3764 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1243 Number of atoms = 3764 Number of groups = 1248 Number of bonds = 3757 Number of angles = 1347 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1245 Number of HB donors = 2468 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1243 Number of atoms = 3764 Number of groups = 1248 Number of bonds = 3757 Number of angles = 1347 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1245 Number of HB donors = 2468 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.44" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1243" Evaluating: 1243-7 Parameter: NUMWAT <- "1236" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1236" Comparing "1081" and "1236". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.44" Parameter: BOX -> "33.44" Parameter: BOX -> "33.44" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.44000 B = 33.44000 C = 33.44000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3950 2 1 -1 0 -1 2.7512 3 1 -1 1 -1 5.9583 4 1 0 -1 -1 4.5157 5 1 0 0 -1 1.0087 6 1 0 1 -1 2.9220 7 1 -1 -1 0 4.8535 8 1 -1 0 0 1.6797 9 1 -1 1 0 5.5922 10 1 0 -1 0 2.2739 11 1 0 1 0 2.2739 12 1 -1 -1 1 4.7874 13 1 -1 0 1 2.3091 14 1 -1 1 1 5.5013 15 1 0 -1 1 2.9220 16 1 0 0 1 1.0087 17 1 0 1 1 4.5157 18 1 1 1 1 6.3950 19 1 1 0 1 2.7512 20 1 1 -1 1 5.9583 21 1 1 1 0 4.8535 22 1 1 0 0 1.6797 23 1 1 -1 0 5.5922 24 1 1 1 -1 4.7874 25 1 1 0 -1 2.3091 26 1 1 -1 -1 5.5013 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3690 atoms have been selected out of 3764 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 432 144 144 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.10 4 C004 has 600 200 200 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 462 154 154 0.00 7 C007 has 744 248 248 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 1.14 Total of13026 atoms and 4333 groups and 4327 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3764 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1243 Number of atoms = 3764 Number of groups = 1248 Number of bonds = 3757 Number of angles = 1347 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1245 Number of HB donors = 2468 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1243 Number of atoms = 3764 Number of groups = 1248 Number of bonds = 3757 Number of angles = 1347 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1245 Number of HB donors = 2468 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.438" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1243" Evaluating: 1243-7 Parameter: NUMWAT <- "1236" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1236" Comparing "1081" and "1236". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.438" Parameter: BOX -> "33.438" Parameter: BOX -> "33.438" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.43800 B = 33.43800 C = 33.43800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3931 2 1 -1 0 -1 2.7485 3 1 -1 1 -1 5.9549 4 1 0 -1 -1 4.5172 5 1 0 0 -1 1.0070 6 1 0 1 -1 2.9209 7 1 -1 -1 0 4.8508 8 1 -1 0 0 1.6778 9 1 -1 1 0 5.5903 10 1 0 -1 0 2.2719 11 1 0 1 0 2.2719 12 1 -1 -1 1 4.7843 13 1 -1 0 1 2.3079 14 1 -1 1 1 5.4985 15 1 0 -1 1 2.9209 16 1 0 0 1 1.0070 17 1 0 1 1 4.5172 18 1 1 1 1 6.3931 19 1 1 0 1 2.7485 20 1 1 -1 1 5.9549 21 1 1 1 0 4.8508 22 1 1 0 0 1.6778 23 1 1 -1 0 5.5903 24 1 1 1 -1 4.7843 25 1 1 0 -1 2.3079 26 1 1 -1 -1 5.4985 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3690 atoms have been selected out of 3764 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 432 144 144 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.10 4 C004 has 600 200 200 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 462 154 154 0.00 7 C007 has 744 248 248 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 1.13 Total of13026 atoms and 4333 groups and 4327 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3764 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1243 Number of atoms = 3764 Number of groups = 1248 Number of bonds = 3757 Number of angles = 1347 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1245 Number of HB donors = 2468 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1243 Number of atoms = 3764 Number of groups = 1248 Number of bonds = 3757 Number of angles = 1347 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1245 Number of HB donors = 2468 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.436" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1243" Evaluating: 1243-7 Parameter: NUMWAT <- "1236" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1236" Comparing "1081" and "1236". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.436" Parameter: BOX -> "33.436" Parameter: BOX -> "33.436" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.43600 B = 33.43600 C = 33.43600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3913 2 1 -1 0 -1 2.7457 3 1 -1 1 -1 5.9514 4 1 0 -1 -1 4.5187 5 1 0 0 -1 1.0053 6 1 0 1 -1 2.9198 7 1 -1 -1 0 4.8481 8 1 -1 0 0 1.6760 9 1 -1 1 0 5.5883 10 1 0 -1 0 2.2699 11 1 0 1 0 2.2699 12 1 -1 -1 1 4.7811 13 1 -1 0 1 2.3066 14 1 -1 1 1 5.4958 15 1 0 -1 1 2.9198 16 1 0 0 1 1.0053 17 1 0 1 1 4.5187 18 1 1 1 1 6.3913 19 1 1 0 1 2.7457 20 1 1 -1 1 5.9514 21 1 1 1 0 4.8481 22 1 1 0 0 1.6760 23 1 1 -1 0 5.5883 24 1 1 1 -1 4.7811 25 1 1 0 -1 2.3066 26 1 1 -1 -1 5.4958 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3690 atoms have been selected out of 3764 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 432 144 144 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.10 4 C004 has 600 200 200 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 462 154 154 0.00 7 C007 has 744 248 248 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 1.13 Total of13026 atoms and 4333 groups and 4327 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3764 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1243 Number of atoms = 3764 Number of groups = 1248 Number of bonds = 3757 Number of angles = 1347 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1245 Number of HB donors = 2468 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1243 Number of atoms = 3764 Number of groups = 1248 Number of bonds = 3757 Number of angles = 1347 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1245 Number of HB donors = 2468 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.434" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1243" Evaluating: 1243-7 Parameter: NUMWAT <- "1236" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1236" Comparing "1081" and "1236". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.434" Parameter: BOX -> "33.434" Parameter: BOX -> "33.434" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.43400 B = 33.43400 C = 33.43400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3895 2 1 -1 0 -1 2.7430 3 1 -1 1 -1 5.9480 4 1 0 -1 -1 4.5202 5 1 0 0 -1 1.0036 6 1 0 1 -1 2.9187 7 1 -1 -1 0 4.8454 8 1 -1 0 0 1.6741 9 1 -1 1 0 5.5864 10 1 0 -1 0 2.2679 11 1 0 1 0 2.2679 12 1 -1 -1 1 4.7780 13 1 -1 0 1 2.3054 14 1 -1 1 1 5.4931 15 1 0 -1 1 2.9187 16 1 0 0 1 1.0036 17 1 0 1 1 4.5202 18 1 1 1 1 6.3895 19 1 1 0 1 2.7430 20 1 1 -1 1 5.9480 21 1 1 1 0 4.8454 22 1 1 0 0 1.6741 23 1 1 -1 0 5.5864 24 1 1 1 -1 4.7780 25 1 1 0 -1 2.3054 26 1 1 -1 -1 5.4931 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3690 atoms have been selected out of 3764 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 744 248 248 0.00 3 C003 has 102 34 34 0.10 4 C004 has 600 200 200 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 462 154 154 0.00 7 C007 has 744 248 248 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 1.13 Total of13035 atoms and 4336 groups and 4330 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3764 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1243 Number of atoms = 3764 Number of groups = 1248 Number of bonds = 3757 Number of angles = 1347 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1245 Number of HB donors = 2468 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1243 Number of atoms = 3764 Number of groups = 1248 Number of bonds = 3757 Number of angles = 1347 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1245 Number of HB donors = 2468 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.432" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1243" Evaluating: 1243-7 Parameter: NUMWAT <- "1236" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1236" Comparing "1081" and "1236". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.432" Parameter: BOX -> "33.432" Parameter: BOX -> "33.432" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.43200 B = 33.43200 C = 33.43200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3876 2 1 -1 0 -1 2.7403 3 1 -1 1 -1 5.9446 4 1 0 -1 -1 4.5217 5 1 0 0 -1 1.0020 6 1 0 1 -1 2.9177 7 1 -1 -1 0 4.8428 8 1 -1 0 0 1.6723 9 1 -1 1 0 5.5845 10 1 0 -1 0 2.2659 11 1 0 1 0 2.2659 12 1 -1 -1 1 4.7749 13 1 -1 0 1 2.3041 14 1 -1 1 1 5.4904 15 1 0 -1 1 2.9177 16 1 0 0 1 1.0020 17 1 0 1 1 4.5217 18 1 1 1 1 6.3876 19 1 1 0 1 2.7403 20 1 1 -1 1 5.9446 21 1 1 1 0 4.8428 22 1 1 0 0 1.6723 23 1 1 -1 0 5.5845 24 1 1 1 -1 4.7749 25 1 1 0 -1 2.3041 26 1 1 -1 -1 5.4904 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3690 atoms have been selected out of 3764 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 744 248 248 0.00 3 C003 has 102 34 34 0.10 4 C004 has 600 200 200 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 462 154 154 0.00 7 C007 has 747 249 249 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 474 158 158 0.00 14 C014 has 123 41 41 1.13 Total of13038 atoms and 4337 groups and 4331 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3764 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1243 Number of atoms = 3764 Number of groups = 1248 Number of bonds = 3757 Number of angles = 1347 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1245 Number of HB donors = 2468 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1243 Number of atoms = 3764 Number of groups = 1248 Number of bonds = 3757 Number of angles = 1347 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1245 Number of HB donors = 2468 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.43" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1243" Evaluating: 1243-7 Parameter: NUMWAT <- "1236" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1236" Comparing "1081" and "1236". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.43" Parameter: BOX -> "33.43" Parameter: BOX -> "33.43" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.43000 B = 33.43000 C = 33.43000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3858 2 1 -1 0 -1 2.7376 3 1 -1 1 -1 5.9411 4 1 0 -1 -1 4.5232 5 1 0 0 -1 1.0003 6 1 0 1 -1 2.9166 7 1 -1 -1 0 4.8401 8 1 -1 0 0 1.6704 9 1 -1 1 0 5.5826 10 1 0 -1 0 2.2639 11 1 0 1 0 2.2639 12 1 -1 -1 1 4.7717 13 1 -1 0 1 2.3029 14 1 -1 1 1 5.4877 15 1 0 -1 1 2.9166 16 1 0 0 1 1.0003 17 1 0 1 1 4.5232 18 1 1 1 1 6.3858 19 1 1 0 1 2.7376 20 1 1 -1 1 5.9411 21 1 1 1 0 4.8401 22 1 1 0 0 1.6704 23 1 1 -1 0 5.5826 24 1 1 1 -1 4.7717 25 1 1 0 -1 2.3029 26 1 1 -1 -1 5.4877 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3690 atoms have been selected out of 3764 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 140 OPERATED ON BY TRANSFORMATION C022 RESIDUE 446 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 744 248 248 0.00 3 C003 has 102 34 34 0.09 4 C004 has 600 200 200 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 462 154 154 0.00 7 C007 has 747 249 249 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 96 32 32 0.00 13 C013 has 483 161 161 0.00 14 C014 has 126 42 42 1.13 Total of13050 atoms and 4341 groups and 4335 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3764 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1241 Number of atoms = 3758 Number of groups = 1246 Number of bonds = 3751 Number of angles = 1345 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1243 Number of HB donors = 2464 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1241 Number of atoms = 3758 Number of groups = 1246 Number of bonds = 3751 Number of angles = 1345 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1243 Number of HB donors = 2464 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.428" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1241" Evaluating: 1241-7 Parameter: NUMWAT <- "1234" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1234" Comparing "1081" and "1234". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.428" Parameter: BOX -> "33.428" Parameter: BOX -> "33.428" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.42800 B = 33.42800 C = 33.42800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3840 2 1 -1 0 -1 2.7349 3 1 -1 1 -1 5.9377 4 1 0 -1 -1 4.5247 5 1 0 0 -1 0.9986 6 1 0 1 -1 2.9156 7 1 -1 -1 0 4.8374 8 1 -1 0 0 1.6686 9 1 -1 1 0 5.5806 10 1 0 -1 0 2.2619 11 1 0 1 0 2.2619 12 1 -1 -1 1 4.7686 13 1 -1 0 1 2.3017 14 1 -1 1 1 5.4850 15 1 0 -1 1 2.9156 16 1 0 0 1 0.9986 17 1 0 1 1 4.5247 18 1 1 1 1 6.3840 19 1 1 0 1 2.7349 20 1 1 -1 1 5.9377 21 1 1 1 0 4.8374 22 1 1 0 0 1.6686 23 1 1 -1 0 5.5806 24 1 1 1 -1 4.7686 25 1 1 0 -1 2.3017 26 1 1 -1 -1 5.4850 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3684 atoms have been selected out of 3758 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 744 248 248 0.00 3 C003 has 102 34 34 0.09 4 C004 has 600 200 200 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 462 154 154 0.00 7 C007 has 744 248 248 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 477 159 159 0.00 14 C014 has 123 41 41 1.12 Total of13020 atoms and 4331 groups and 4325 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3758 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1241 Number of atoms = 3758 Number of groups = 1246 Number of bonds = 3751 Number of angles = 1345 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1243 Number of HB donors = 2464 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1241 Number of atoms = 3758 Number of groups = 1246 Number of bonds = 3751 Number of angles = 1345 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1243 Number of HB donors = 2464 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.426" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1241" Evaluating: 1241-7 Parameter: NUMWAT <- "1234" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1234" Comparing "1081" and "1234". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.426" Parameter: BOX -> "33.426" Parameter: BOX -> "33.426" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.42600 B = 33.42600 C = 33.42600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3822 2 1 -1 0 -1 2.7322 3 1 -1 1 -1 5.9343 4 1 0 -1 -1 4.5262 5 1 0 0 -1 0.9969 6 1 0 1 -1 2.9145 7 1 -1 -1 0 4.8347 8 1 -1 0 0 1.6667 9 1 -1 1 0 5.5787 10 1 0 -1 0 2.2599 11 1 0 1 0 2.2599 12 1 -1 -1 1 4.7655 13 1 -1 0 1 2.3004 14 1 -1 1 1 5.4822 15 1 0 -1 1 2.9145 16 1 0 0 1 0.9969 17 1 0 1 1 4.5262 18 1 1 1 1 6.3822 19 1 1 0 1 2.7322 20 1 1 -1 1 5.9343 21 1 1 1 0 4.8347 22 1 1 0 0 1.6667 23 1 1 -1 0 5.5787 24 1 1 1 -1 4.7655 25 1 1 0 -1 2.3004 26 1 1 -1 -1 5.4822 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3684 atoms have been selected out of 3758 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 216 OPERATED ON BY TRANSFORMATION C008 RESIDUE 833 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 741 247 247 0.00 3 C003 has 99 33 33 0.09 4 C004 has 603 201 201 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 462 154 154 0.00 7 C007 has 747 249 249 0.00 8 C008 has 1756 583 582 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 492 164 164 0.00 14 C014 has 120 40 40 1.12 Total of13020 atoms and 4331 groups and 4325 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3758 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1239 Number of atoms = 3752 Number of groups = 1244 Number of bonds = 3745 Number of angles = 1343 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1241 Number of HB donors = 2460 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1239 Number of atoms = 3752 Number of groups = 1244 Number of bonds = 3745 Number of angles = 1343 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1241 Number of HB donors = 2460 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.424" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1239" Evaluating: 1239-7 Parameter: NUMWAT <- "1232" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1232" Comparing "1081" and "1232". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.424" Parameter: BOX -> "33.424" Parameter: BOX -> "33.424" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.42400 B = 33.42400 C = 33.42400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3803 2 1 -1 0 -1 2.7295 3 1 -1 1 -1 5.9308 4 1 0 -1 -1 4.5277 5 1 0 0 -1 0.9952 6 1 0 1 -1 2.9134 7 1 -1 -1 0 4.8320 8 1 -1 0 0 1.6649 9 1 -1 1 0 5.5768 10 1 0 -1 0 2.2579 11 1 0 1 0 2.2579 12 1 -1 -1 1 4.7624 13 1 -1 0 1 2.2992 14 1 -1 1 1 6.3291 15 1 0 -1 1 2.9134 16 1 0 0 1 0.9952 17 1 0 1 1 4.5277 18 1 1 1 1 6.3803 19 1 1 0 1 2.7295 20 1 1 -1 1 5.9308 21 1 1 1 0 4.8320 22 1 1 0 0 1.6649 23 1 1 -1 0 5.5768 24 1 1 1 -1 4.7624 25 1 1 0 -1 2.2992 26 1 1 -1 -1 6.3291 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3678 atoms have been selected out of 3752 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 741 247 247 0.00 3 C003 has 99 33 33 0.09 4 C004 has 603 201 201 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 459 153 153 0.00 7 C007 has 747 249 249 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 474 158 158 0.00 14 C014 has 120 40 40 1.12 Total of12987 atoms and 4320 groups and 4314 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3752 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1239 Number of atoms = 3752 Number of groups = 1244 Number of bonds = 3745 Number of angles = 1343 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1241 Number of HB donors = 2460 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1239 Number of atoms = 3752 Number of groups = 1244 Number of bonds = 3745 Number of angles = 1343 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1241 Number of HB donors = 2460 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.422" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1239" Evaluating: 1239-7 Parameter: NUMWAT <- "1232" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1232" Comparing "1081" and "1232". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.422" Parameter: BOX -> "33.422" Parameter: BOX -> "33.422" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.42200 B = 33.42200 C = 33.42200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3785 2 1 -1 0 -1 2.7267 3 1 -1 1 -1 5.9274 4 1 0 -1 -1 4.5292 5 1 0 0 -1 0.9935 6 1 0 1 -1 2.9124 7 1 -1 -1 0 4.8294 8 1 -1 0 0 1.6630 9 1 -1 1 0 5.5749 10 1 0 -1 0 2.2559 11 1 0 1 0 2.2559 12 1 -1 -1 1 4.7592 13 1 -1 0 1 2.2980 14 1 -1 1 1 6.3263 15 1 0 -1 1 2.9124 16 1 0 0 1 0.9935 17 1 0 1 1 4.5292 18 1 1 1 1 6.3785 19 1 1 0 1 2.7267 20 1 1 -1 1 5.9274 21 1 1 1 0 4.8294 22 1 1 0 0 1.6630 23 1 1 -1 0 5.5749 24 1 1 1 -1 4.7592 25 1 1 0 -1 2.2980 26 1 1 -1 -1 6.3263 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3678 atoms have been selected out of 3752 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 741 247 247 0.00 3 C003 has 99 33 33 0.09 4 C004 has 603 201 201 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 459 153 153 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 474 158 158 0.00 14 C014 has 120 40 40 1.12 Total of12990 atoms and 4321 groups and 4315 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3752 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1239 Number of atoms = 3752 Number of groups = 1244 Number of bonds = 3745 Number of angles = 1343 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1241 Number of HB donors = 2460 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1239 Number of atoms = 3752 Number of groups = 1244 Number of bonds = 3745 Number of angles = 1343 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1241 Number of HB donors = 2460 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.42" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1239" Evaluating: 1239-7 Parameter: NUMWAT <- "1232" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1232" Comparing "1081" and "1232". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.42" Parameter: BOX -> "33.42" Parameter: BOX -> "33.42" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.42000 B = 33.42000 C = 33.42000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3767 2 1 -1 0 -1 2.7240 3 1 -1 1 -1 5.9239 4 1 0 -1 -1 4.5307 5 1 0 0 -1 0.9918 6 1 0 1 -1 2.9113 7 1 -1 -1 0 4.8267 8 1 -1 0 0 1.6612 9 1 -1 1 0 5.5729 10 1 0 -1 0 2.2539 11 1 0 1 0 2.2539 12 1 -1 -1 1 4.7561 13 1 -1 0 1 2.2967 14 1 -1 1 1 6.3235 15 1 0 -1 1 2.9113 16 1 0 0 1 0.9918 17 1 0 1 1 4.5307 18 1 1 1 1 6.3767 19 1 1 0 1 2.7240 20 1 1 -1 1 5.9239 21 1 1 1 0 4.8267 22 1 1 0 0 1.6612 23 1 1 -1 0 5.5729 24 1 1 1 -1 4.7561 25 1 1 0 -1 2.2967 26 1 1 -1 -1 6.3235 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3678 atoms have been selected out of 3752 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 741 247 247 0.00 3 C003 has 99 33 33 0.08 4 C004 has 603 201 201 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 459 153 153 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 477 159 159 0.00 14 C014 has 120 40 40 1.12 Total of12993 atoms and 4322 groups and 4316 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3752 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1239 Number of atoms = 3752 Number of groups = 1244 Number of bonds = 3745 Number of angles = 1343 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1241 Number of HB donors = 2460 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1239 Number of atoms = 3752 Number of groups = 1244 Number of bonds = 3745 Number of angles = 1343 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1241 Number of HB donors = 2460 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.418" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1239" Evaluating: 1239-7 Parameter: NUMWAT <- "1232" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1232" Comparing "1081" and "1232". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.418" Parameter: BOX -> "33.418" Parameter: BOX -> "33.418" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.41800 B = 33.41800 C = 33.41800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3749 2 1 -1 0 -1 2.7213 3 1 -1 1 -1 5.9205 4 1 0 -1 -1 4.5322 5 1 0 0 -1 0.9901 6 1 0 1 -1 2.9103 7 1 -1 -1 0 4.8240 8 1 -1 0 0 1.6593 9 1 -1 1 0 5.5710 10 1 0 -1 0 2.2519 11 1 0 1 0 2.2519 12 1 -1 -1 1 4.7530 13 1 -1 0 1 2.2955 14 1 -1 1 1 6.3207 15 1 0 -1 1 2.9103 16 1 0 0 1 0.9901 17 1 0 1 1 4.5322 18 1 1 1 1 6.3749 19 1 1 0 1 2.7213 20 1 1 -1 1 5.9205 21 1 1 1 0 4.8240 22 1 1 0 0 1.6593 23 1 1 -1 0 5.5710 24 1 1 1 -1 4.7530 25 1 1 0 -1 2.2955 26 1 1 -1 -1 6.3207 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3678 atoms have been selected out of 3752 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 120 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 741 247 247 0.00 3 C003 has 99 33 33 0.08 4 C004 has 603 201 201 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 459 153 153 0.00 7 C007 has 750 250 250 0.00 8 C008 has 1756 583 582 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 120 40 40 1.11 Total of13002 atoms and 4325 groups and 4319 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3752 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.416" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.416" Parameter: BOX -> "33.416" Parameter: BOX -> "33.416" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.41600 B = 33.41600 C = 33.41600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3731 2 1 -1 0 -1 2.7186 3 1 -1 1 -1 5.9171 4 1 0 -1 -1 4.5337 5 1 0 0 -1 0.9884 6 1 0 1 -1 2.9092 7 1 -1 -1 0 4.8213 8 1 -1 0 0 1.6575 9 1 -1 1 0 5.5691 10 1 0 -1 0 2.2499 11 1 0 1 0 2.2499 12 1 -1 -1 1 4.7498 13 1 -1 0 1 2.2943 14 1 -1 1 1 6.3179 15 1 0 -1 1 2.9092 16 1 0 0 1 0.9884 17 1 0 1 1 4.5337 18 1 1 1 1 6.3731 19 1 1 0 1 2.7186 20 1 1 -1 1 5.9171 21 1 1 1 0 4.8213 22 1 1 0 0 1.6575 23 1 1 -1 0 5.5691 24 1 1 1 -1 4.7498 25 1 1 0 -1 2.2943 26 1 1 -1 -1 6.3179 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 741 247 247 0.00 3 C003 has 99 33 33 0.08 4 C004 has 603 201 201 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 459 153 153 0.00 7 C007 has 753 251 251 0.00 8 C008 has 1756 583 582 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 477 159 159 0.00 14 C014 has 120 40 40 1.11 Total of12996 atoms and 4323 groups and 4317 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3749 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.414" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.414" Parameter: BOX -> "33.414" Parameter: BOX -> "33.414" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.41400 B = 33.41400 C = 33.41400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3712 2 1 -1 0 -1 2.7159 3 1 -1 1 -1 5.9136 4 1 0 -1 -1 4.5352 5 1 0 0 -1 0.9867 6 1 0 1 -1 2.9082 7 1 -1 -1 0 4.8187 8 1 -1 0 0 1.6556 9 1 -1 1 0 5.5672 10 1 0 -1 0 2.2479 11 1 0 1 0 2.2479 12 1 -1 -1 1 4.7467 13 1 -1 0 1 2.2931 14 1 -1 1 1 6.3150 15 1 0 -1 1 2.9082 16 1 0 0 1 0.9867 17 1 0 1 1 4.5352 18 1 1 1 1 6.3712 19 1 1 0 1 2.7159 20 1 1 -1 1 5.9136 21 1 1 1 0 4.8187 22 1 1 0 0 1.6556 23 1 1 -1 0 5.5672 24 1 1 1 -1 4.7467 25 1 1 0 -1 2.2931 26 1 1 -1 -1 6.3150 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 741 247 247 0.00 3 C003 has 99 33 33 0.08 4 C004 has 603 201 201 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 459 153 153 0.00 7 C007 has 753 251 251 0.00 8 C008 has 1756 583 582 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 477 159 159 0.00 14 C014 has 120 40 40 1.11 Total of12996 atoms and 4323 groups and 4317 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3749 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.412" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.412" Parameter: BOX -> "33.412" Parameter: BOX -> "33.412" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.41200 B = 33.41200 C = 33.41200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3694 2 1 -1 0 -1 2.7132 3 1 -1 1 -1 5.9102 4 1 0 -1 -1 4.5367 5 1 0 0 -1 0.9851 6 1 0 1 -1 2.9071 7 1 -1 -1 0 4.8160 8 1 -1 0 0 1.6538 9 1 -1 1 0 5.5652 10 1 0 -1 0 2.2459 11 1 0 1 0 2.2459 12 1 -1 -1 1 4.7436 13 1 -1 0 1 2.2919 14 1 -1 1 1 6.3122 15 1 0 -1 1 2.9071 16 1 0 0 1 0.9851 17 1 0 1 1 4.5367 18 1 1 1 1 6.3694 19 1 1 0 1 2.7132 20 1 1 -1 1 5.9102 21 1 1 1 0 4.8160 22 1 1 0 0 1.6538 23 1 1 -1 0 5.5652 24 1 1 1 -1 4.7436 25 1 1 0 -1 2.2919 26 1 1 -1 -1 6.3122 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 741 247 247 0.00 3 C003 has 99 33 33 0.08 4 C004 has 603 201 201 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 459 153 153 0.00 7 C007 has 753 251 251 0.00 8 C008 has 1756 583 582 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 93 31 31 0.00 13 C013 has 477 159 159 0.00 14 C014 has 120 40 40 1.11 Total of12999 atoms and 4324 groups and 4318 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3749 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.41" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.41" Parameter: BOX -> "33.41" Parameter: BOX -> "33.41" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.41000 B = 33.41000 C = 33.41000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3676 2 1 -1 0 -1 2.7105 3 1 -1 1 -1 5.9068 4 1 0 -1 -1 4.5382 5 1 0 0 -1 0.9834 6 1 0 1 -1 2.9061 7 1 -1 -1 0 4.8133 8 1 -1 0 0 1.6519 9 1 -1 1 0 5.5633 10 1 0 -1 0 2.2439 11 1 0 1 0 2.2439 12 1 -1 -1 1 4.7405 13 1 -1 0 1 2.2907 14 1 -1 1 1 6.3094 15 1 0 -1 1 2.9061 16 1 0 0 1 0.9834 17 1 0 1 1 4.5382 18 1 1 1 1 6.3676 19 1 1 0 1 2.7105 20 1 1 -1 1 5.9068 21 1 1 1 0 4.8133 22 1 1 0 0 1.6519 23 1 1 -1 0 5.5633 24 1 1 1 -1 4.7405 25 1 1 0 -1 2.2907 26 1 1 -1 -1 6.3094 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.07 4 C004 has 603 201 201 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 459 153 153 0.00 7 C007 has 753 251 251 0.00 8 C008 has 1756 583 582 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 93 31 31 0.00 13 C013 has 477 159 159 0.00 14 C014 has 120 40 40 1.11 Total of13005 atoms and 4326 groups and 4320 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3749 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.408" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.408" Parameter: BOX -> "33.408" Parameter: BOX -> "33.408" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.40800 B = 33.40800 C = 33.40800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3658 2 1 -1 0 -1 2.7077 3 1 -1 1 -1 5.9033 4 1 0 -1 -1 4.5397 5 1 0 0 -1 0.9817 6 1 0 1 -1 2.9051 7 1 -1 -1 0 4.8106 8 1 -1 0 0 1.6501 9 1 -1 1 0 5.5614 10 1 0 -1 0 2.2419 11 1 0 1 0 2.2419 12 1 -1 -1 1 4.7373 13 1 -1 0 1 2.2895 14 1 -1 1 1 6.3066 15 1 0 -1 1 2.9051 16 1 0 0 1 0.9817 17 1 0 1 1 4.5397 18 1 1 1 1 6.3658 19 1 1 0 1 2.7077 20 1 1 -1 1 5.9033 21 1 1 1 0 4.8106 22 1 1 0 0 1.6501 23 1 1 -1 0 5.5614 24 1 1 1 -1 4.7373 25 1 1 0 -1 2.2895 26 1 1 -1 -1 6.3066 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.07 4 C004 has 603 201 201 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 459 153 153 0.00 7 C007 has 756 252 252 0.00 8 C008 has 1756 583 582 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 93 31 31 0.00 13 C013 has 477 159 159 0.00 14 C014 has 120 40 40 1.10 Total of13008 atoms and 4327 groups and 4321 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3749 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.406" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.406" Parameter: BOX -> "33.406" Parameter: BOX -> "33.406" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.40600 B = 33.40600 C = 33.40600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3640 2 1 -1 0 -1 2.7050 3 1 -1 1 -1 5.8999 4 1 0 -1 -1 4.5412 5 1 0 0 -1 0.9800 6 1 0 1 -1 2.9040 7 1 -1 -1 0 4.8079 8 1 -1 0 0 1.6482 9 1 -1 1 0 5.5595 10 1 0 -1 0 2.2399 11 1 0 1 0 2.2399 12 1 -1 -1 1 4.7342 13 1 -1 0 1 2.2883 14 1 -1 1 1 6.3038 15 1 0 -1 1 2.9040 16 1 0 0 1 0.9800 17 1 0 1 1 4.5412 18 1 1 1 1 6.3640 19 1 1 0 1 2.7050 20 1 1 -1 1 5.8999 21 1 1 1 0 4.8079 22 1 1 0 0 1.6482 23 1 1 -1 0 5.5595 24 1 1 1 -1 4.7342 25 1 1 0 -1 2.2883 26 1 1 -1 -1 6.3038 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.07 4 C004 has 606 202 202 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 459 153 153 0.00 7 C007 has 756 252 252 0.00 8 C008 has 1756 583 582 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 93 31 31 0.00 13 C013 has 477 159 159 0.00 14 C014 has 120 40 40 1.10 Total of13011 atoms and 4328 groups and 4322 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3749 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.404" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.404" Parameter: BOX -> "33.404" Parameter: BOX -> "33.404" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.40400 B = 33.40400 C = 33.40400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3622 2 1 -1 0 -1 2.7023 3 1 -1 1 -1 5.8965 4 1 0 -1 -1 4.5428 5 1 0 0 -1 0.9783 6 1 0 1 -1 2.9030 7 1 -1 -1 0 4.8053 8 1 -1 0 0 1.6464 9 1 -1 1 0 5.5576 10 1 0 -1 0 2.2379 11 1 0 1 0 2.2379 12 1 -1 -1 1 4.7311 13 1 -1 0 1 2.2871 14 1 -1 1 1 6.3010 15 1 0 -1 1 2.9030 16 1 0 0 1 0.9783 17 1 0 1 1 4.5428 18 1 1 1 1 6.3622 19 1 1 0 1 2.7023 20 1 1 -1 1 5.8965 21 1 1 1 0 4.8053 22 1 1 0 0 1.6464 23 1 1 -1 0 5.5576 24 1 1 1 -1 4.7311 25 1 1 0 -1 2.2871 26 1 1 -1 -1 6.3010 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.07 4 C004 has 606 202 202 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 459 153 153 0.00 7 C007 has 756 252 252 0.00 8 C008 has 1756 583 582 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 93 31 31 0.00 13 C013 has 477 159 159 0.00 14 C014 has 120 40 40 1.10 Total of13011 atoms and 4328 groups and 4322 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3749 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.402" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.402" Parameter: BOX -> "33.402" Parameter: BOX -> "33.402" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.40200 B = 33.40200 C = 33.40200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3604 2 1 -1 0 -1 2.6996 3 1 -1 1 -1 5.8930 4 1 0 -1 -1 4.5443 5 1 0 0 -1 0.9767 6 1 0 1 -1 2.9020 7 1 -1 -1 0 4.8026 8 1 -1 0 0 1.6445 9 1 -1 1 0 5.5556 10 1 0 -1 0 2.2359 11 1 0 1 0 2.2359 12 1 -1 -1 1 4.7280 13 1 -1 0 1 2.2859 14 1 -1 1 1 6.2982 15 1 0 -1 1 2.9020 16 1 0 0 1 0.9767 17 1 0 1 1 4.5443 18 1 1 1 1 6.3604 19 1 1 0 1 2.6996 20 1 1 -1 1 5.8930 21 1 1 1 0 4.8026 22 1 1 0 0 1.6445 23 1 1 -1 0 5.5556 24 1 1 1 -1 4.7280 25 1 1 0 -1 2.2859 26 1 1 -1 -1 6.2982 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.07 4 C004 has 606 202 202 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 459 153 153 0.00 7 C007 has 756 252 252 0.00 8 C008 has 1756 583 582 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 93 31 31 0.00 13 C013 has 477 159 159 0.00 14 C014 has 120 40 40 1.10 Total of13011 atoms and 4328 groups and 4322 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3749 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.4" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.4" Parameter: BOX -> "33.4" Parameter: BOX -> "33.4" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.40000 B = 33.40000 C = 33.40000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3586 2 1 -1 0 -1 2.6969 3 1 -1 1 -1 5.8896 4 1 0 -1 -1 4.5458 5 1 0 0 -1 0.9750 6 1 0 1 -1 2.9009 7 1 -1 -1 0 4.7999 8 1 -1 0 0 1.6427 9 1 -1 1 0 5.5537 10 1 0 -1 0 2.2339 11 1 0 1 0 2.2339 12 1 -1 -1 1 4.7248 13 1 -1 0 1 2.2847 14 1 -1 1 1 6.2953 15 1 0 -1 1 2.9009 16 1 0 0 1 0.9750 17 1 0 1 1 4.5458 18 1 1 1 1 6.3586 19 1 1 0 1 2.6969 20 1 1 -1 1 5.8896 21 1 1 1 0 4.7999 22 1 1 0 0 1.6427 23 1 1 -1 0 5.5537 24 1 1 1 -1 4.7248 25 1 1 0 -1 2.2847 26 1 1 -1 -1 6.2953 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.06 4 C004 has 606 202 202 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 459 153 153 0.00 7 C007 has 756 252 252 0.00 8 C008 has 1756 583 582 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 120 40 40 1.10 Total of13014 atoms and 4329 groups and 4323 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3749 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.398" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.398" Parameter: BOX -> "33.398" Parameter: BOX -> "33.398" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.39800 B = 33.39800 C = 33.39800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3568 2 1 -1 0 -1 2.6942 3 1 -1 1 -1 5.8861 4 1 0 -1 -1 4.5473 5 1 0 0 -1 0.9733 6 1 0 1 -1 2.8999 7 1 -1 -1 0 4.7972 8 1 -1 0 0 1.6409 9 1 -1 1 0 5.5518 10 1 0 -1 0 2.2319 11 1 0 1 0 2.2319 12 1 -1 -1 1 4.7217 13 1 -1 0 1 2.2835 14 1 -1 1 1 6.2925 15 1 0 -1 1 2.8999 16 1 0 0 1 0.9733 17 1 0 1 1 4.5473 18 1 1 1 1 6.3568 19 1 1 0 1 2.6942 20 1 1 -1 1 5.8861 21 1 1 1 0 4.7972 22 1 1 0 0 1.6409 23 1 1 -1 0 5.5518 24 1 1 1 -1 4.7217 25 1 1 0 -1 2.2835 26 1 1 -1 -1 6.2925 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.06 4 C004 has 606 202 202 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 459 153 153 0.00 7 C007 has 756 252 252 0.00 8 C008 has 1756 583 582 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 120 40 40 1.09 Total of13017 atoms and 4330 groups and 4324 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3749 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.396" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.396" Parameter: BOX -> "33.396" Parameter: BOX -> "33.396" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.39600 B = 33.39600 C = 33.39600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3550 2 1 -1 0 -1 2.6915 3 1 -1 1 -1 5.8827 4 1 0 -1 -1 4.5488 5 1 0 0 -1 0.9716 6 1 0 1 -1 2.8989 7 1 -1 -1 0 4.7946 8 1 -1 0 0 1.6390 9 1 -1 1 0 5.5499 10 1 0 -1 0 2.2299 11 1 0 1 0 2.2299 12 1 -1 -1 1 4.7186 13 1 -1 0 1 2.2823 14 1 -1 1 1 6.2897 15 1 0 -1 1 2.8989 16 1 0 0 1 0.9716 17 1 0 1 1 4.5488 18 1 1 1 1 6.3550 19 1 1 0 1 2.6915 20 1 1 -1 1 5.8827 21 1 1 1 0 4.7946 22 1 1 0 0 1.6390 23 1 1 -1 0 5.5499 24 1 1 1 -1 4.7186 25 1 1 0 -1 2.2823 26 1 1 -1 -1 6.2897 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.06 4 C004 has 606 202 202 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 459 153 153 0.00 7 C007 has 756 252 252 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 93 31 31 0.00 13 C013 has 480 160 160 0.00 14 C014 has 120 40 40 1.09 Total of13020 atoms and 4331 groups and 4325 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3749 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.394" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.394" Parameter: BOX -> "33.394" Parameter: BOX -> "33.394" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.39400 B = 33.39400 C = 33.39400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3532 2 1 -1 0 -1 2.6888 3 1 -1 1 -1 5.8793 4 1 0 -1 -1 4.5504 5 1 0 0 -1 0.9700 6 1 0 1 -1 2.8979 7 1 -1 -1 0 4.7919 8 1 -1 0 0 1.6372 9 1 -1 1 0 5.5480 10 1 0 -1 0 2.2279 11 1 0 1 0 2.2279 12 1 -1 -1 1 4.7155 13 1 -1 0 1 2.2811 14 1 -1 1 1 6.2869 15 1 0 -1 1 2.8979 16 1 0 0 1 0.9700 17 1 0 1 1 4.5504 18 1 1 1 1 6.3532 19 1 1 0 1 2.6888 20 1 1 -1 1 5.8793 21 1 1 1 0 4.7919 22 1 1 0 0 1.6372 23 1 1 -1 0 5.5480 24 1 1 1 -1 4.7155 25 1 1 0 -1 2.2811 26 1 1 -1 -1 6.2869 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.06 4 C004 has 606 202 202 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 459 153 153 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.09 Total of13026 atoms and 4333 groups and 4327 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3749 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.392" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.392" Parameter: BOX -> "33.392" Parameter: BOX -> "33.392" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.39200 B = 33.39200 C = 33.39200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3514 2 1 -1 0 -1 2.6861 3 1 -1 1 -1 5.8758 4 1 0 -1 -1 4.5519 5 1 0 0 -1 0.9683 6 1 0 1 -1 2.8968 7 1 -1 -1 0 4.7892 8 1 -1 0 0 1.6353 9 1 -1 1 0 5.5461 10 1 0 -1 0 2.2259 11 1 0 1 0 2.2259 12 1 -1 -1 1 4.7124 13 1 -1 0 1 2.2799 14 1 -1 1 1 6.2841 15 1 0 -1 1 2.8968 16 1 0 0 1 0.9683 17 1 0 1 1 4.5519 18 1 1 1 1 6.3514 19 1 1 0 1 2.6861 20 1 1 -1 1 5.8758 21 1 1 1 0 4.7892 22 1 1 0 0 1.6353 23 1 1 -1 0 5.5461 24 1 1 1 -1 4.7124 25 1 1 0 -1 2.2799 26 1 1 -1 -1 6.2841 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.06 4 C004 has 606 202 202 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 459 153 153 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.09 Total of13029 atoms and 4334 groups and 4328 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3749 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.39" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.39" Parameter: BOX -> "33.39" Parameter: BOX -> "33.39" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.39000 B = 33.39000 C = 33.39000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3496 2 1 -1 0 -1 2.6833 3 1 -1 1 -1 5.8724 4 1 0 -1 -1 4.5534 5 1 0 0 -1 0.9666 6 1 0 1 -1 2.8958 7 1 -1 -1 0 4.7865 8 1 -1 0 0 1.6335 9 1 -1 1 0 5.5442 10 1 0 -1 0 2.2239 11 1 0 1 0 2.2239 12 1 -1 -1 1 4.7092 13 1 -1 0 1 2.2787 14 1 -1 1 1 6.2813 15 1 0 -1 1 2.8958 16 1 0 0 1 0.9666 17 1 0 1 1 4.5534 18 1 1 1 1 6.3496 19 1 1 0 1 2.6833 20 1 1 -1 1 5.8724 21 1 1 1 0 4.7865 22 1 1 0 0 1.6335 23 1 1 -1 0 5.5442 24 1 1 1 -1 4.7092 25 1 1 0 -1 2.2787 26 1 1 -1 -1 6.2813 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.05 4 C004 has 609 203 203 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 459 153 153 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.09 Total of13032 atoms and 4335 groups and 4329 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3749 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.388" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.388" Parameter: BOX -> "33.388" Parameter: BOX -> "33.388" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.38800 B = 33.38800 C = 33.38800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3478 2 1 -1 0 -1 2.6806 3 1 -1 1 -1 5.8690 4 1 0 -1 -1 4.5549 5 1 0 0 -1 0.9650 6 1 0 1 -1 2.8948 7 1 -1 -1 0 4.7839 8 1 -1 0 0 1.6316 9 1 -1 1 0 5.5422 10 1 0 -1 0 2.2219 11 1 0 1 0 2.2219 12 1 -1 -1 1 4.7061 13 1 -1 0 1 2.2775 14 1 -1 1 1 6.2785 15 1 0 -1 1 2.8948 16 1 0 0 1 0.9650 17 1 0 1 1 4.5549 18 1 1 1 1 6.3478 19 1 1 0 1 2.6806 20 1 1 -1 1 5.8690 21 1 1 1 0 4.7839 22 1 1 0 0 1.6316 23 1 1 -1 0 5.5422 24 1 1 1 -1 4.7061 25 1 1 0 -1 2.2775 26 1 1 -1 -1 6.2785 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.05 4 C004 has 609 203 203 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 459 153 153 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.08 Total of13032 atoms and 4335 groups and 4329 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3749 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.386" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.386" Parameter: BOX -> "33.386" Parameter: BOX -> "33.386" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.38600 B = 33.38600 C = 33.38600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3460 2 1 -1 0 -1 2.6779 3 1 -1 1 -1 5.8655 4 1 0 -1 -1 4.5564 5 1 0 0 -1 0.9633 6 1 0 1 -1 2.8938 7 1 -1 -1 0 4.7812 8 1 -1 0 0 1.6298 9 1 -1 1 0 5.5403 10 1 0 -1 0 2.2199 11 1 0 1 0 2.2199 12 1 -1 -1 1 4.7030 13 1 -1 0 1 2.2764 14 1 -1 1 1 6.2757 15 1 0 -1 1 2.8938 16 1 0 0 1 0.9633 17 1 0 1 1 4.5564 18 1 1 1 1 6.3460 19 1 1 0 1 2.6779 20 1 1 -1 1 5.8655 21 1 1 1 0 4.7812 22 1 1 0 0 1.6298 23 1 1 -1 0 5.5403 24 1 1 1 -1 4.7030 25 1 1 0 -1 2.2764 26 1 1 -1 -1 6.2757 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.05 4 C004 has 609 203 203 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 459 153 153 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.08 Total of13032 atoms and 4335 groups and 4329 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3749 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.384" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.384" Parameter: BOX -> "33.384" Parameter: BOX -> "33.384" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.38400 B = 33.38400 C = 33.38400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3442 2 1 -1 0 -1 2.6752 3 1 -1 1 -1 5.8621 4 1 0 -1 -1 4.5580 5 1 0 0 -1 0.9616 6 1 0 1 -1 2.8928 7 1 -1 -1 0 4.7785 8 1 -1 0 0 1.6279 9 1 -1 1 0 5.5384 10 1 0 -1 0 2.2179 11 1 0 1 0 2.2179 12 1 -1 -1 1 4.6999 13 1 -1 0 1 2.2752 14 1 -1 1 1 6.2729 15 1 0 -1 1 2.8928 16 1 0 0 1 0.9616 17 1 0 1 1 4.5580 18 1 1 1 1 6.3442 19 1 1 0 1 2.6752 20 1 1 -1 1 5.8621 21 1 1 1 0 4.7785 22 1 1 0 0 1.6279 23 1 1 -1 0 5.5384 24 1 1 1 -1 4.6999 25 1 1 0 -1 2.2752 26 1 1 -1 -1 6.2729 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.05 4 C004 has 609 203 203 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 459 153 153 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.08 Total of13032 atoms and 4335 groups and 4329 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3749 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.382" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.382" Parameter: BOX -> "33.382" Parameter: BOX -> "33.382" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.38200 B = 33.38200 C = 33.38200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3424 2 1 -1 0 -1 2.6725 3 1 -1 1 -1 5.8587 4 1 0 -1 -1 4.5595 5 1 0 0 -1 0.9600 6 1 0 1 -1 2.8918 7 1 -1 -1 0 4.7758 8 1 -1 0 0 1.6261 9 1 -1 1 0 5.5365 10 1 0 -1 0 2.2159 11 1 0 1 0 2.2159 12 1 -1 -1 1 4.6968 13 1 -1 0 1 2.2740 14 1 -1 1 1 6.2701 15 1 0 -1 1 2.8918 16 1 0 0 1 0.9600 17 1 0 1 1 4.5595 18 1 1 1 1 6.3424 19 1 1 0 1 2.6725 20 1 1 -1 1 5.8587 21 1 1 1 0 4.7758 22 1 1 0 0 1.6261 23 1 1 -1 0 5.5365 24 1 1 1 -1 4.6968 25 1 1 0 -1 2.2740 26 1 1 -1 -1 6.2701 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.05 4 C004 has 609 203 203 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 459 153 153 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.08 Total of13032 atoms and 4335 groups and 4329 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3749 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.38" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.38" Parameter: BOX -> "33.38" Parameter: BOX -> "33.38" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.38000 B = 33.38000 C = 33.38000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3406 2 1 -1 0 -1 2.6698 3 1 -1 1 -1 5.8552 4 1 0 -1 -1 4.5610 5 1 0 0 -1 0.9583 6 1 0 1 -1 2.8908 7 1 -1 -1 0 4.7732 8 1 -1 0 0 1.6243 9 1 -1 1 0 5.5346 10 1 0 -1 0 2.2139 11 1 0 1 0 2.2139 12 1 -1 -1 1 4.6936 13 1 -1 0 1 2.2729 14 1 -1 1 1 6.2673 15 1 0 -1 1 2.8908 16 1 0 0 1 0.9583 17 1 0 1 1 4.5610 18 1 1 1 1 6.3406 19 1 1 0 1 2.6698 20 1 1 -1 1 5.8552 21 1 1 1 0 4.7732 22 1 1 0 0 1.6243 23 1 1 -1 0 5.5346 24 1 1 1 -1 4.6936 25 1 1 0 -1 2.2729 26 1 1 -1 -1 6.2673 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.04 4 C004 has 609 203 203 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 459 153 153 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.08 Total of13032 atoms and 4335 groups and 4329 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3749 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.378" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.378" Parameter: BOX -> "33.378" Parameter: BOX -> "33.378" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.37800 B = 33.37800 C = 33.37800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3388 2 1 -1 0 -1 2.6671 3 1 -1 1 -1 5.8518 4 1 0 -1 -1 4.5626 5 1 0 0 -1 0.9566 6 1 0 1 -1 2.8898 7 1 -1 -1 0 4.7705 8 1 -1 0 0 1.6224 9 1 -1 1 0 5.5327 10 1 0 -1 0 2.2119 11 1 0 1 0 2.2119 12 1 -1 -1 1 4.6905 13 1 -1 0 1 2.2717 14 1 -1 1 1 6.2645 15 1 0 -1 1 2.8898 16 1 0 0 1 0.9566 17 1 0 1 1 4.5626 18 1 1 1 1 6.3388 19 1 1 0 1 2.6671 20 1 1 -1 1 5.8518 21 1 1 1 0 4.7705 22 1 1 0 0 1.6224 23 1 1 -1 0 5.5327 24 1 1 1 -1 4.6905 25 1 1 0 -1 2.2717 26 1 1 -1 -1 6.2645 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.04 4 C004 has 609 203 203 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 459 153 153 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.07 Total of13035 atoms and 4336 groups and 4330 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3749 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.376" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.376" Parameter: BOX -> "33.376" Parameter: BOX -> "33.376" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.37600 B = 33.37600 C = 33.37600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3370 2 1 -1 0 -1 2.6644 3 1 -1 1 -1 5.8483 4 1 0 -1 -1 4.5641 5 1 0 0 -1 0.9550 6 1 0 1 -1 2.8888 7 1 -1 -1 0 4.7678 8 1 -1 0 0 1.6206 9 1 -1 1 0 5.5308 10 1 0 -1 0 2.2099 11 1 0 1 0 2.2099 12 1 -1 -1 1 4.6874 13 1 -1 0 1 2.2705 14 1 -1 1 1 6.2617 15 1 0 -1 1 2.8888 16 1 0 0 1 0.9550 17 1 0 1 1 4.5641 18 1 1 1 1 6.3370 19 1 1 0 1 2.6644 20 1 1 -1 1 5.8483 21 1 1 1 0 4.7678 22 1 1 0 0 1.6206 23 1 1 -1 0 5.5308 24 1 1 1 -1 4.6874 25 1 1 0 -1 2.2705 26 1 1 -1 -1 6.2617 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.04 4 C004 has 609 203 203 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 459 153 153 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1662 554 554 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.07 Total of13038 atoms and 4337 groups and 4331 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3749 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.374" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.374" Parameter: BOX -> "33.374" Parameter: BOX -> "33.374" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.37400 B = 33.37400 C = 33.37400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3352 2 1 -1 0 -1 2.6617 3 1 -1 1 -1 5.8449 4 1 0 -1 -1 4.5656 5 1 0 0 -1 0.9533 6 1 0 1 -1 2.8878 7 1 -1 -1 0 4.7651 8 1 -1 0 0 1.6187 9 1 -1 1 0 5.5289 10 1 0 -1 0 2.2079 11 1 0 1 0 2.2079 12 1 -1 -1 1 4.6843 13 1 -1 0 1 2.2694 14 1 -1 1 1 6.2589 15 1 0 -1 1 2.8878 16 1 0 0 1 0.9533 17 1 0 1 1 4.5656 18 1 1 1 1 6.3352 19 1 1 0 1 2.6617 20 1 1 -1 1 5.8449 21 1 1 1 0 4.7651 22 1 1 0 0 1.6187 23 1 1 -1 0 5.5289 24 1 1 1 -1 4.6843 25 1 1 0 -1 2.2694 26 1 1 -1 -1 6.2589 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 744 248 248 0.00 3 C003 has 102 34 34 0.04 4 C004 has 612 204 204 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 459 153 153 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1662 554 554 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.07 Total of13044 atoms and 4339 groups and 4333 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3749 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.372" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.372" Parameter: BOX -> "33.372" Parameter: BOX -> "33.372" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.37200 B = 33.37200 C = 33.37200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3334 2 1 -1 0 -1 2.6590 3 1 -1 1 -1 5.8415 4 1 0 -1 -1 4.5672 5 1 0 0 -1 0.9517 6 1 0 1 -1 2.8868 7 1 -1 -1 0 4.7625 8 1 -1 0 0 1.6169 9 1 -1 1 0 5.5270 10 1 0 -1 0 2.2059 11 1 0 1 0 2.2059 12 1 -1 -1 1 4.6812 13 1 -1 0 1 2.2682 14 1 -1 1 1 6.2560 15 1 0 -1 1 2.8868 16 1 0 0 1 0.9517 17 1 0 1 1 4.5672 18 1 1 1 1 6.3334 19 1 1 0 1 2.6590 20 1 1 -1 1 5.8415 21 1 1 1 0 4.7625 22 1 1 0 0 1.6169 23 1 1 -1 0 5.5270 24 1 1 1 -1 4.6812 25 1 1 0 -1 2.2682 26 1 1 -1 -1 6.2560 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 744 248 248 0.00 3 C003 has 102 34 34 0.04 4 C004 has 612 204 204 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 459 153 153 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1662 554 554 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.07 Total of13044 atoms and 4339 groups and 4333 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3749 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.37" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.37" Parameter: BOX -> "33.37" Parameter: BOX -> "33.37" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.37000 B = 33.37000 C = 33.37000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3316 2 1 -1 0 -1 2.6562 3 1 -1 1 -1 5.8380 4 1 0 -1 -1 4.5687 5 1 0 0 -1 0.9500 6 1 0 1 -1 2.8858 7 1 -1 -1 0 4.7598 8 1 -1 0 0 1.6151 9 1 -1 1 0 5.5251 10 1 0 -1 0 2.2039 11 1 0 1 0 2.2039 12 1 -1 -1 1 4.6780 13 1 -1 0 1 2.2671 14 1 -1 1 1 6.2532 15 1 0 -1 1 2.8858 16 1 0 0 1 0.9500 17 1 0 1 1 4.5687 18 1 1 1 1 6.3316 19 1 1 0 1 2.6562 20 1 1 -1 1 5.8380 21 1 1 1 0 4.7598 22 1 1 0 0 1.6151 23 1 1 -1 0 5.5251 24 1 1 1 -1 4.6780 25 1 1 0 -1 2.2671 26 1 1 -1 -1 6.2532 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 744 248 248 0.00 3 C003 has 102 34 34 0.03 4 C004 has 612 204 204 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 459 153 153 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1662 554 554 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.07 Total of13044 atoms and 4339 groups and 4333 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3749 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.368" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.368" Parameter: BOX -> "33.368" Parameter: BOX -> "33.368" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.36800 B = 33.36800 C = 33.36800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3298 2 1 -1 0 -1 2.6535 3 1 -1 1 -1 5.8346 4 1 0 -1 -1 4.5702 5 1 0 0 -1 0.9483 6 1 0 1 -1 2.8848 7 1 -1 -1 0 4.7571 8 1 -1 0 0 1.6132 9 1 -1 1 0 5.5232 10 1 0 -1 0 2.2019 11 1 0 1 0 2.2019 12 1 -1 -1 1 4.6749 13 1 -1 0 1 2.2659 14 1 -1 1 1 6.2504 15 1 0 -1 1 2.8848 16 1 0 0 1 0.9483 17 1 0 1 1 4.5702 18 1 1 1 1 6.3298 19 1 1 0 1 2.6535 20 1 1 -1 1 5.8346 21 1 1 1 0 4.7571 22 1 1 0 0 1.6132 23 1 1 -1 0 5.5232 24 1 1 1 -1 4.6749 25 1 1 0 -1 2.2659 26 1 1 -1 -1 6.2504 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 744 248 248 0.00 3 C003 has 102 34 34 0.03 4 C004 has 612 204 204 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 459 153 153 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.06 Total of13047 atoms and 4340 groups and 4334 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3749 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.366" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.366" Parameter: BOX -> "33.366" Parameter: BOX -> "33.366" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.36600 B = 33.36600 C = 33.36600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3281 2 1 -1 0 -1 2.6508 3 1 -1 1 -1 5.8312 4 1 0 -1 -1 4.5718 5 1 0 0 -1 0.9467 6 1 0 1 -1 2.8838 7 1 -1 -1 0 4.7545 8 1 -1 0 0 1.6114 9 1 -1 1 0 5.5213 10 1 0 -1 0 2.1999 11 1 0 1 0 2.1999 12 1 -1 -1 1 4.6718 13 1 -1 0 1 2.2648 14 1 -1 1 1 6.2476 15 1 0 -1 1 2.8838 16 1 0 0 1 0.9467 17 1 0 1 1 4.5718 18 1 1 1 1 6.3281 19 1 1 0 1 2.6508 20 1 1 -1 1 5.8312 21 1 1 1 0 4.7545 22 1 1 0 0 1.6114 23 1 1 -1 0 5.5213 24 1 1 1 -1 4.6718 25 1 1 0 -1 2.2648 26 1 1 -1 -1 6.2476 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 744 248 248 0.00 3 C003 has 102 34 34 0.03 4 C004 has 612 204 204 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 459 153 153 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.06 Total of13047 atoms and 4340 groups and 4334 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3749 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.364" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.364" Parameter: BOX -> "33.364" Parameter: BOX -> "33.364" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.36400 B = 33.36400 C = 33.36400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3263 2 1 -1 0 -1 2.6481 3 1 -1 1 -1 5.8277 4 1 0 -1 -1 4.5733 5 1 0 0 -1 0.9450 6 1 0 1 -1 2.8828 7 1 -1 -1 0 4.7518 8 1 -1 0 0 1.6095 9 1 -1 1 0 5.5194 10 1 0 -1 0 2.1979 11 1 0 1 0 2.1979 12 1 -1 -1 1 4.6687 13 1 -1 0 1 2.2636 14 1 -1 1 1 6.2448 15 1 0 -1 1 2.8828 16 1 0 0 1 0.9450 17 1 0 1 1 4.5733 18 1 1 1 1 6.3263 19 1 1 0 1 2.6481 20 1 1 -1 1 5.8277 21 1 1 1 0 4.7518 22 1 1 0 0 1.6095 23 1 1 -1 0 5.5194 24 1 1 1 -1 4.6687 25 1 1 0 -1 2.2636 26 1 1 -1 -1 6.2448 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 744 248 248 0.00 3 C003 has 102 34 34 0.03 4 C004 has 612 204 204 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 459 153 153 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.06 Total of13050 atoms and 4341 groups and 4335 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3749 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1238 Number of atoms = 3749 Number of groups = 1243 Number of bonds = 3742 Number of angles = 1342 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1240 Number of HB donors = 2458 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.362" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1238" Evaluating: 1238-7 Parameter: NUMWAT <- "1231" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1231" Comparing "1081" and "1231". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.362" Parameter: BOX -> "33.362" Parameter: BOX -> "33.362" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.36200 B = 33.36200 C = 33.36200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3245 2 1 -1 0 -1 2.6454 3 1 -1 1 -1 5.8243 4 1 0 -1 -1 4.5748 5 1 0 0 -1 0.9434 6 1 0 1 -1 2.8818 7 1 -1 -1 0 4.7491 8 1 -1 0 0 1.6077 9 1 -1 1 0 5.5175 10 1 0 -1 0 2.1959 11 1 0 1 0 2.1959 12 1 -1 -1 1 4.6656 13 1 -1 0 1 2.2625 14 1 -1 1 1 6.2420 15 1 0 -1 1 2.8818 16 1 0 0 1 0.9434 17 1 0 1 1 4.5748 18 1 1 1 1 6.3245 19 1 1 0 1 2.6454 20 1 1 -1 1 5.8243 21 1 1 1 0 4.7491 22 1 1 0 0 1.6077 23 1 1 -1 0 5.5175 24 1 1 1 -1 4.6656 25 1 1 0 -1 2.2625 26 1 1 -1 -1 6.2420 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3675 atoms have been selected out of 3749 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1145 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.03 4 C004 has 612 204 204 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 459 153 153 0.00 7 C007 has 756 252 252 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.06 Total of13047 atoms and 4340 groups and 4334 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3749 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1237 Number of atoms = 3746 Number of groups = 1242 Number of bonds = 3739 Number of angles = 1341 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1239 Number of HB donors = 2456 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1237 Number of atoms = 3746 Number of groups = 1242 Number of bonds = 3739 Number of angles = 1341 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1239 Number of HB donors = 2456 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.36" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1237" Evaluating: 1237-7 Parameter: NUMWAT <- "1230" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1230" Comparing "1081" and "1230". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.36" Parameter: BOX -> "33.36" Parameter: BOX -> "33.36" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.36000 B = 33.36000 C = 33.36000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3227 2 1 -1 0 -1 2.6427 3 1 -1 1 -1 5.8209 4 1 0 -1 -1 4.5764 5 1 0 0 -1 0.9417 6 1 0 1 -1 2.8809 7 1 -1 -1 0 4.7464 8 1 -1 0 0 1.6059 9 1 -1 1 0 5.5156 10 1 0 -1 0 2.1939 11 1 0 1 0 2.1939 12 1 -1 -1 1 4.6625 13 1 -1 0 1 2.2614 14 1 -1 1 1 6.2392 15 1 0 -1 1 2.8809 16 1 0 0 1 0.9417 17 1 0 1 1 4.5764 18 1 1 1 1 6.3227 19 1 1 0 1 2.6427 20 1 1 -1 1 5.8209 21 1 1 1 0 4.7464 22 1 1 0 0 1.6059 23 1 1 -1 0 5.5156 24 1 1 1 -1 4.6625 25 1 1 0 -1 2.2614 26 1 1 -1 -1 6.2392 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3672 atoms have been selected out of 3746 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.02 4 C004 has 609 203 203 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 459 153 153 0.00 7 C007 has 756 252 252 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1662 554 554 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.06 Total of13026 atoms and 4333 groups and 4327 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3746 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1237 Number of atoms = 3746 Number of groups = 1242 Number of bonds = 3739 Number of angles = 1341 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1239 Number of HB donors = 2456 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1237 Number of atoms = 3746 Number of groups = 1242 Number of bonds = 3739 Number of angles = 1341 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1239 Number of HB donors = 2456 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.358" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1237" Evaluating: 1237-7 Parameter: NUMWAT <- "1230" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1230" Comparing "1081" and "1230". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.358" Parameter: BOX -> "33.358" Parameter: BOX -> "33.358" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.35800 B = 33.35800 C = 33.35800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3209 2 1 -1 0 -1 2.6400 3 1 -1 1 -1 5.8174 4 1 0 -1 -1 4.5779 5 1 0 0 -1 0.9401 6 1 0 1 -1 2.8799 7 1 -1 -1 0 4.7438 8 1 -1 0 0 1.6040 9 1 -1 1 0 5.5137 10 1 0 -1 0 2.1919 11 1 0 1 0 2.1919 12 1 -1 -1 1 4.6594 13 1 -1 0 1 2.2602 14 1 -1 1 1 6.2364 15 1 0 -1 1 2.8799 16 1 0 0 1 0.9401 17 1 0 1 1 4.5779 18 1 1 1 1 6.3209 19 1 1 0 1 2.6400 20 1 1 -1 1 5.8174 21 1 1 1 0 4.7438 22 1 1 0 0 1.6040 23 1 1 -1 0 5.5137 24 1 1 1 -1 4.6594 25 1 1 0 -1 2.2602 26 1 1 -1 -1 6.2364 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3672 atoms have been selected out of 3746 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.02 4 C004 has 609 203 203 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 459 153 153 0.00 7 C007 has 756 252 252 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1662 554 554 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.05 Total of13026 atoms and 4333 groups and 4327 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3746 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1237 Number of atoms = 3746 Number of groups = 1242 Number of bonds = 3739 Number of angles = 1341 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1239 Number of HB donors = 2456 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1237 Number of atoms = 3746 Number of groups = 1242 Number of bonds = 3739 Number of angles = 1341 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1239 Number of HB donors = 2456 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.356" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1237" Evaluating: 1237-7 Parameter: NUMWAT <- "1230" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1230" Comparing "1081" and "1230". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.356" Parameter: BOX -> "33.356" Parameter: BOX -> "33.356" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.35600 B = 33.35600 C = 33.35600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3192 2 1 -1 0 -1 2.6373 3 1 -1 1 -1 5.8140 4 1 0 -1 -1 4.5795 5 1 0 0 -1 0.9384 6 1 0 1 -1 2.8789 7 1 -1 -1 0 4.7411 8 1 -1 0 0 1.6022 9 1 -1 1 0 5.5118 10 1 0 -1 0 2.1899 11 1 0 1 0 2.1899 12 1 -1 -1 1 4.6562 13 1 -1 0 1 2.2591 14 1 -1 1 1 6.2337 15 1 0 -1 1 2.8789 16 1 0 0 1 0.9384 17 1 0 1 1 4.5795 18 1 1 1 1 6.3192 19 1 1 0 1 2.6373 20 1 1 -1 1 5.8140 21 1 1 1 0 4.7411 22 1 1 0 0 1.6022 23 1 1 -1 0 5.5118 24 1 1 1 -1 4.6562 25 1 1 0 -1 2.2591 26 1 1 -1 -1 6.2337 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3672 atoms have been selected out of 3746 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.02 4 C004 has 609 203 203 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 459 153 153 0.00 7 C007 has 756 252 252 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1662 554 554 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.05 Total of13029 atoms and 4334 groups and 4328 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3746 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1237 Number of atoms = 3746 Number of groups = 1242 Number of bonds = 3739 Number of angles = 1341 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1239 Number of HB donors = 2456 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1237 Number of atoms = 3746 Number of groups = 1242 Number of bonds = 3739 Number of angles = 1341 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1239 Number of HB donors = 2456 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.354" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1237" Evaluating: 1237-7 Parameter: NUMWAT <- "1230" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1230" Comparing "1081" and "1230". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.354" Parameter: BOX -> "33.354" Parameter: BOX -> "33.354" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.35400 B = 33.35400 C = 33.35400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3174 2 1 -1 0 -1 2.6346 3 1 -1 1 -1 5.8106 4 1 0 -1 -1 4.5810 5 1 0 0 -1 0.9368 6 1 0 1 -1 2.8779 7 1 -1 -1 0 4.7384 8 1 -1 0 0 1.6004 9 1 -1 1 0 5.5099 10 1 0 -1 0 2.1879 11 1 0 1 0 2.1879 12 1 -1 -1 1 4.6531 13 1 -1 0 1 2.2580 14 1 -1 1 1 6.2309 15 1 0 -1 1 2.8779 16 1 0 0 1 0.9368 17 1 0 1 1 4.5810 18 1 1 1 1 6.3174 19 1 1 0 1 2.6346 20 1 1 -1 1 5.8106 21 1 1 1 0 4.7384 22 1 1 0 0 1.6004 23 1 1 -1 0 5.5099 24 1 1 1 -1 4.6531 25 1 1 0 -1 2.2580 26 1 1 -1 -1 6.2309 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3672 atoms have been selected out of 3746 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 425 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.02 4 C004 has 612 204 204 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 462 154 154 0.00 7 C007 has 756 252 252 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 93 31 31 0.00 13 C013 has 486 162 162 0.00 14 C014 has 120 40 40 1.05 Total of13041 atoms and 4338 groups and 4332 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3746 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1236 Number of atoms = 3743 Number of groups = 1241 Number of bonds = 3736 Number of angles = 1340 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1238 Number of HB donors = 2454 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1236 Number of atoms = 3743 Number of groups = 1241 Number of bonds = 3736 Number of angles = 1340 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1238 Number of HB donors = 2454 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.352" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1236" Evaluating: 1236-7 Parameter: NUMWAT <- "1229" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1229" Comparing "1081" and "1229". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.352" Parameter: BOX -> "33.352" Parameter: BOX -> "33.352" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.35200 B = 33.35200 C = 33.35200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3156 2 1 -1 0 -1 2.6319 3 1 -1 1 -1 5.8071 4 1 0 -1 -1 4.5826 5 1 0 0 -1 0.9351 6 1 0 1 -1 2.8770 7 1 -1 -1 0 4.7358 8 1 -1 0 0 1.5985 9 1 -1 1 0 5.5080 10 1 0 -1 0 2.1859 11 1 0 1 0 2.1859 12 1 -1 -1 1 4.6500 13 1 -1 0 1 2.2568 14 1 -1 1 1 6.2281 15 1 0 -1 1 2.8770 16 1 0 0 1 0.9351 17 1 0 1 1 4.5826 18 1 1 1 1 6.3156 19 1 1 0 1 2.6319 20 1 1 -1 1 5.8071 21 1 1 1 0 4.7358 22 1 1 0 0 1.5985 23 1 1 -1 0 5.5080 24 1 1 1 -1 4.6500 25 1 1 0 -1 2.2568 26 1 1 -1 -1 6.2281 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3669 atoms have been selected out of 3743 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.02 4 C004 has 609 203 203 0.00 5 C005 has 1578 526 526 0.00 6 C006 has 462 154 154 0.00 7 C007 has 756 252 252 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1662 554 554 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.05 Total of13026 atoms and 4333 groups and 4327 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3743 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1236 Number of atoms = 3743 Number of groups = 1241 Number of bonds = 3736 Number of angles = 1340 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1238 Number of HB donors = 2454 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1236 Number of atoms = 3743 Number of groups = 1241 Number of bonds = 3736 Number of angles = 1340 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1238 Number of HB donors = 2454 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.35" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1236" Evaluating: 1236-7 Parameter: NUMWAT <- "1229" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1229" Comparing "1081" and "1229". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.35" Parameter: BOX -> "33.35" Parameter: BOX -> "33.35" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.35000 B = 33.35000 C = 33.35000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3138 2 1 -1 0 -1 2.6292 3 1 -1 1 -1 5.8037 4 1 0 -1 -1 4.5841 5 1 0 0 -1 0.9335 6 1 0 1 -1 2.8760 7 1 -1 -1 0 4.7331 8 1 -1 0 0 1.5967 9 1 -1 1 0 5.5061 10 1 0 -1 0 2.1839 11 1 0 1 0 2.1839 12 1 -1 -1 1 4.6469 13 1 -1 0 1 2.2557 14 1 -1 1 1 6.2253 15 1 0 -1 1 2.8760 16 1 0 0 1 0.9335 17 1 0 1 1 4.5841 18 1 1 1 1 6.3138 19 1 1 0 1 2.6292 20 1 1 -1 1 5.8037 21 1 1 1 0 4.7331 22 1 1 0 0 1.5967 23 1 1 -1 0 5.5061 24 1 1 1 -1 4.6469 25 1 1 0 -1 2.2557 26 1 1 -1 -1 6.2253 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3669 atoms have been selected out of 3743 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.01 4 C004 has 609 203 203 0.00 5 C005 has 1578 526 526 0.00 6 C006 has 462 154 154 0.00 7 C007 has 756 252 252 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1662 554 554 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.05 Total of13026 atoms and 4333 groups and 4327 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3743 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1236 Number of atoms = 3743 Number of groups = 1241 Number of bonds = 3736 Number of angles = 1340 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1238 Number of HB donors = 2454 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1236 Number of atoms = 3743 Number of groups = 1241 Number of bonds = 3736 Number of angles = 1340 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1238 Number of HB donors = 2454 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.348" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1236" Evaluating: 1236-7 Parameter: NUMWAT <- "1229" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1229" Comparing "1081" and "1229". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.348" Parameter: BOX -> "33.348" Parameter: BOX -> "33.348" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.34800 B = 33.34800 C = 33.34800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3121 2 1 -1 0 -1 2.6265 3 1 -1 1 -1 5.8002 4 1 0 -1 -1 4.5857 5 1 0 0 -1 0.9319 6 1 0 1 -1 2.8750 7 1 -1 -1 0 4.7304 8 1 -1 0 0 1.5948 9 1 -1 1 0 5.5042 10 1 0 -1 0 2.1819 11 1 0 1 0 2.1819 12 1 -1 -1 1 4.6438 13 1 -1 0 1 2.2546 14 1 -1 1 1 6.2225 15 1 0 -1 1 2.8750 16 1 0 0 1 0.9319 17 1 0 1 1 4.5857 18 1 1 1 1 6.3121 19 1 1 0 1 2.6265 20 1 1 -1 1 5.8002 21 1 1 1 0 4.7304 22 1 1 0 0 1.5948 23 1 1 -1 0 5.5042 24 1 1 1 -1 4.6438 25 1 1 0 -1 2.2546 26 1 1 -1 -1 6.2225 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3669 atoms have been selected out of 3743 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.01 4 C004 has 609 203 203 0.00 5 C005 has 1578 526 526 0.00 6 C006 has 462 154 154 0.00 7 C007 has 756 252 252 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.04 Total of13029 atoms and 4334 groups and 4328 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3743 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1236 Number of atoms = 3743 Number of groups = 1241 Number of bonds = 3736 Number of angles = 1340 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1238 Number of HB donors = 2454 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1236 Number of atoms = 3743 Number of groups = 1241 Number of bonds = 3736 Number of angles = 1340 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1238 Number of HB donors = 2454 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.346" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1236" Evaluating: 1236-7 Parameter: NUMWAT <- "1229" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1229" Comparing "1081" and "1229". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.346" Parameter: BOX -> "33.346" Parameter: BOX -> "33.346" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.34600 B = 33.34600 C = 33.34600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3103 2 1 -1 0 -1 2.6238 3 1 -1 1 -1 5.7968 4 1 0 -1 -1 4.5872 5 1 0 0 -1 0.9302 6 1 0 1 -1 2.8741 7 1 -1 -1 0 4.7277 8 1 -1 0 0 1.5930 9 1 -1 1 0 5.5023 10 1 0 -1 0 2.1799 11 1 0 1 0 2.1799 12 1 -1 -1 1 4.6407 13 1 -1 0 1 2.2535 14 1 -1 1 1 6.2197 15 1 0 -1 1 2.8741 16 1 0 0 1 0.9302 17 1 0 1 1 4.5872 18 1 1 1 1 6.3103 19 1 1 0 1 2.6238 20 1 1 -1 1 5.7968 21 1 1 1 0 4.7277 22 1 1 0 0 1.5930 23 1 1 -1 0 5.5023 24 1 1 1 -1 4.6407 25 1 1 0 -1 2.2535 26 1 1 -1 -1 6.2197 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3669 atoms have been selected out of 3743 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.01 4 C004 has 609 203 203 0.00 5 C005 has 1578 526 526 0.00 6 C006 has 462 154 154 0.00 7 C007 has 756 252 252 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.04 Total of13029 atoms and 4334 groups and 4328 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3743 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1236 Number of atoms = 3743 Number of groups = 1241 Number of bonds = 3736 Number of angles = 1340 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1238 Number of HB donors = 2454 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1236 Number of atoms = 3743 Number of groups = 1241 Number of bonds = 3736 Number of angles = 1340 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1238 Number of HB donors = 2454 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.344" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1236" Evaluating: 1236-7 Parameter: NUMWAT <- "1229" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1229" Comparing "1081" and "1229". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.344" Parameter: BOX -> "33.344" Parameter: BOX -> "33.344" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.34400 B = 33.34400 C = 33.34400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3085 2 1 -1 0 -1 2.6211 3 1 -1 1 -1 5.7934 4 1 0 -1 -1 4.5888 5 1 0 0 -1 0.9286 6 1 0 1 -1 2.8731 7 1 -1 -1 0 4.7251 8 1 -1 0 0 1.5912 9 1 -1 1 0 5.5004 10 1 0 -1 0 2.1779 11 1 0 1 0 2.1779 12 1 -1 -1 1 4.6376 13 1 -1 0 1 2.2524 14 1 -1 1 1 6.2169 15 1 0 -1 1 2.8731 16 1 0 0 1 0.9286 17 1 0 1 1 4.5888 18 1 1 1 1 6.3085 19 1 1 0 1 2.6211 20 1 1 -1 1 5.7934 21 1 1 1 0 4.7251 22 1 1 0 0 1.5912 23 1 1 -1 0 5.5004 24 1 1 1 -1 4.6376 25 1 1 0 -1 2.2524 26 1 1 -1 -1 6.2169 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3669 atoms have been selected out of 3743 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.01 4 C004 has 609 203 203 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 462 154 154 0.00 7 C007 has 756 252 252 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.04 Total of13035 atoms and 4336 groups and 4330 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3743 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1236 Number of atoms = 3743 Number of groups = 1241 Number of bonds = 3736 Number of angles = 1340 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1238 Number of HB donors = 2454 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1236 Number of atoms = 3743 Number of groups = 1241 Number of bonds = 3736 Number of angles = 1340 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1238 Number of HB donors = 2454 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.342" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1236" Evaluating: 1236-7 Parameter: NUMWAT <- "1229" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1229" Comparing "1081" and "1229". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.342" Parameter: BOX -> "33.342" Parameter: BOX -> "33.342" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.34200 B = 33.34200 C = 33.34200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3068 2 1 -1 0 -1 2.6184 3 1 -1 1 -1 5.7899 4 1 0 -1 -1 4.5903 5 1 0 0 -1 0.9269 6 1 0 1 -1 2.8721 7 1 -1 -1 0 4.7224 8 1 -1 0 0 1.5893 9 1 -1 1 0 5.4985 10 1 0 -1 0 2.1759 11 1 0 1 0 2.1759 12 1 -1 -1 1 4.6345 13 1 -1 0 1 2.2513 14 1 -1 1 1 6.2141 15 1 0 -1 1 2.8721 16 1 0 0 1 0.9269 17 1 0 1 1 4.5903 18 1 1 1 1 6.3068 19 1 1 0 1 2.6184 20 1 1 -1 1 5.7899 21 1 1 1 0 4.7224 22 1 1 0 0 1.5893 23 1 1 -1 0 5.4985 24 1 1 1 -1 4.6345 25 1 1 0 -1 2.2513 26 1 1 -1 -1 6.2141 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3669 atoms have been selected out of 3743 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.01 4 C004 has 609 203 203 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 462 154 154 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.04 Total of13038 atoms and 4337 groups and 4331 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3743 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1236 Number of atoms = 3743 Number of groups = 1241 Number of bonds = 3736 Number of angles = 1340 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1238 Number of HB donors = 2454 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1236 Number of atoms = 3743 Number of groups = 1241 Number of bonds = 3736 Number of angles = 1340 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1238 Number of HB donors = 2454 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.34" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1236" Evaluating: 1236-7 Parameter: NUMWAT <- "1229" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1229" Comparing "1081" and "1229". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.34" Parameter: BOX -> "33.34" Parameter: BOX -> "33.34" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.34000 B = 33.34000 C = 33.34000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3050 2 1 -1 0 -1 2.6157 3 1 -1 1 -1 5.7865 4 1 0 -1 -1 4.5919 5 1 0 0 -1 0.9253 6 1 0 1 -1 2.8712 7 1 -1 -1 0 4.7197 8 1 -1 0 0 1.5875 9 1 -1 1 0 5.4966 10 1 0 -1 0 2.1739 11 1 0 1 0 2.1739 12 1 -1 -1 1 4.6314 13 1 -1 0 1 2.2502 14 1 -1 1 1 6.2113 15 1 0 -1 1 2.8712 16 1 0 0 1 0.9253 17 1 0 1 1 4.5919 18 1 1 1 1 6.3050 19 1 1 0 1 2.6157 20 1 1 -1 1 5.7865 21 1 1 1 0 4.7197 22 1 1 0 0 1.5875 23 1 1 -1 0 5.4966 24 1 1 1 -1 4.6314 25 1 1 0 -1 2.2502 26 1 1 -1 -1 6.2113 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3669 atoms have been selected out of 3743 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 462 154 154 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.04 Total of13038 atoms and 4337 groups and 4331 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3743 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1236 Number of atoms = 3743 Number of groups = 1241 Number of bonds = 3736 Number of angles = 1340 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1238 Number of HB donors = 2454 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1236 Number of atoms = 3743 Number of groups = 1241 Number of bonds = 3736 Number of angles = 1340 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1238 Number of HB donors = 2454 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.338" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1236" Evaluating: 1236-7 Parameter: NUMWAT <- "1229" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1229" Comparing "1081" and "1229". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.338" Parameter: BOX -> "33.338" Parameter: BOX -> "33.338" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.33800 B = 33.33800 C = 33.33800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3032 2 1 -1 0 -1 2.6129 3 1 -1 1 -1 5.7831 4 1 0 -1 -1 4.5934 5 1 0 0 -1 0.9237 6 1 0 1 -1 2.8702 7 1 -1 -1 0 4.7171 8 1 -1 0 0 1.5857 9 1 -1 1 0 5.4947 10 1 0 -1 0 2.1719 11 1 0 1 0 2.1719 12 1 -1 -1 1 4.6283 13 1 -1 0 1 2.2491 14 1 -1 1 1 6.2085 15 1 0 -1 1 2.8702 16 1 0 0 1 0.9237 17 1 0 1 1 4.5934 18 1 1 1 1 6.3032 19 1 1 0 1 2.6129 20 1 1 -1 1 5.7831 21 1 1 1 0 4.7171 22 1 1 0 0 1.5857 23 1 1 -1 0 5.4947 24 1 1 1 -1 4.6283 25 1 1 0 -1 2.2491 26 1 1 -1 -1 6.2085 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3669 atoms have been selected out of 3743 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 462 154 154 0.00 7 C007 has 759 253 253 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.03 Total of13038 atoms and 4337 groups and 4331 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3743 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1236 Number of atoms = 3743 Number of groups = 1241 Number of bonds = 3736 Number of angles = 1340 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1238 Number of HB donors = 2454 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1236 Number of atoms = 3743 Number of groups = 1241 Number of bonds = 3736 Number of angles = 1340 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1238 Number of HB donors = 2454 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.336" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1236" Evaluating: 1236-7 Parameter: NUMWAT <- "1229" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1229" Comparing "1081" and "1229". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.336" Parameter: BOX -> "33.336" Parameter: BOX -> "33.336" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.33600 B = 33.33600 C = 33.33600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.3015 2 1 -1 0 -1 2.6102 3 1 -1 1 -1 5.7796 4 1 0 -1 -1 4.5950 5 1 0 0 -1 0.9220 6 1 0 1 -1 2.8693 7 1 -1 -1 0 4.7144 8 1 -1 0 0 1.5838 9 1 -1 1 0 5.4928 10 1 0 -1 0 2.1699 11 1 0 1 0 2.1699 12 1 -1 -1 1 4.6251 13 1 -1 0 1 2.2480 14 1 -1 1 1 6.2057 15 1 0 -1 1 2.8693 16 1 0 0 1 0.9220 17 1 0 1 1 4.5950 18 1 1 1 1 6.3015 19 1 1 0 1 2.6102 20 1 1 -1 1 5.7796 21 1 1 1 0 4.7144 22 1 1 0 0 1.5838 23 1 1 -1 0 5.4928 24 1 1 1 -1 4.6251 25 1 1 0 -1 2.2480 26 1 1 -1 -1 6.2057 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3669 atoms have been selected out of 3743 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 744 248 248 0.00 3 C003 has 105 35 35 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 462 154 154 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.03 Total of13044 atoms and 4339 groups and 4333 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3743 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1236 Number of atoms = 3743 Number of groups = 1241 Number of bonds = 3736 Number of angles = 1340 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1238 Number of HB donors = 2454 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1236 Number of atoms = 3743 Number of groups = 1241 Number of bonds = 3736 Number of angles = 1340 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1238 Number of HB donors = 2454 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.334" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1236" Evaluating: 1236-7 Parameter: NUMWAT <- "1229" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1229" Comparing "1081" and "1229". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.334" Parameter: BOX -> "33.334" Parameter: BOX -> "33.334" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.33400 B = 33.33400 C = 33.33400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2997 2 1 -1 0 -1 2.6075 3 1 -1 1 -1 5.7762 4 1 0 -1 -1 4.5965 5 1 0 0 -1 0.9204 6 1 0 1 -1 2.8683 7 1 -1 -1 0 4.7117 8 1 -1 0 0 1.5820 9 1 -1 1 0 5.4909 10 1 0 -1 0 2.1679 11 1 0 1 0 2.1679 12 1 -1 -1 1 4.6220 13 1 -1 0 1 2.2469 14 1 -1 1 1 6.2029 15 1 0 -1 1 2.8683 16 1 0 0 1 0.9204 17 1 0 1 1 4.5965 18 1 1 1 1 6.2997 19 1 1 0 1 2.6075 20 1 1 -1 1 5.7762 21 1 1 1 0 4.7117 22 1 1 0 0 1.5820 23 1 1 -1 0 5.4909 24 1 1 1 -1 4.6220 25 1 1 0 -1 2.2469 26 1 1 -1 -1 6.2029 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3669 atoms have been selected out of 3743 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 143 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 747 249 249 0.00 3 C003 has 105 35 35 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 462 154 154 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1668 556 556 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.03 Total of13050 atoms and 4341 groups and 4335 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3743 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1235 Number of atoms = 3740 Number of groups = 1240 Number of bonds = 3733 Number of angles = 1339 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1237 Number of HB donors = 2452 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1235 Number of atoms = 3740 Number of groups = 1240 Number of bonds = 3733 Number of angles = 1339 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1237 Number of HB donors = 2452 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.332" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1235" Evaluating: 1235-7 Parameter: NUMWAT <- "1228" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1228" Comparing "1081" and "1228". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.332" Parameter: BOX -> "33.332" Parameter: BOX -> "33.332" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.33200 B = 33.33200 C = 33.33200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2980 2 1 -1 0 -1 2.6048 3 1 -1 1 -1 5.7728 4 1 0 -1 -1 4.5981 5 1 0 0 -1 0.9188 6 1 0 1 -1 2.8674 7 1 -1 -1 0 4.7090 8 1 -1 0 0 1.5802 9 1 -1 1 0 5.4890 10 1 0 -1 0 2.1659 11 1 0 1 0 2.1659 12 1 -1 -1 1 4.6189 13 1 -1 0 1 2.2458 14 1 -1 1 1 6.2001 15 1 0 -1 1 2.8674 16 1 0 0 1 0.9188 17 1 0 1 1 4.5981 18 1 1 1 1 6.2980 19 1 1 0 1 2.6048 20 1 1 -1 1 5.7728 21 1 1 1 0 4.7090 22 1 1 0 0 1.5802 23 1 1 -1 0 5.4890 24 1 1 1 -1 4.6189 25 1 1 0 -1 2.2458 26 1 1 -1 -1 6.2001 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3666 atoms have been selected out of 3740 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 747 249 249 0.00 3 C003 has 105 35 35 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 462 154 154 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.03 Total of13041 atoms and 4338 groups and 4332 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3740 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1235 Number of atoms = 3740 Number of groups = 1240 Number of bonds = 3733 Number of angles = 1339 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1237 Number of HB donors = 2452 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1235 Number of atoms = 3740 Number of groups = 1240 Number of bonds = 3733 Number of angles = 1339 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1237 Number of HB donors = 2452 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.33" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1235" Evaluating: 1235-7 Parameter: NUMWAT <- "1228" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1228" Comparing "1081" and "1228". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.33" Parameter: BOX -> "33.33" Parameter: BOX -> "33.33" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.33000 B = 33.33000 C = 33.33000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2962 2 1 -1 0 -1 2.6021 3 1 -1 1 -1 5.7693 4 1 0 -1 -1 4.5997 5 1 0 0 -1 0.9171 6 1 0 1 -1 2.8664 7 1 -1 -1 0 4.7064 8 1 -1 0 0 1.5783 9 1 -1 1 0 5.4871 10 1 0 -1 0 2.1639 11 1 0 1 0 2.1639 12 1 -1 -1 1 4.6158 13 1 -1 0 1 2.2447 14 1 -1 1 1 6.1973 15 1 0 -1 1 2.8664 16 1 0 0 1 0.9171 17 1 0 1 1 4.5997 18 1 1 1 1 6.2962 19 1 1 0 1 2.6021 20 1 1 -1 1 5.7693 21 1 1 1 0 4.7064 22 1 1 0 0 1.5783 23 1 1 -1 0 5.4871 24 1 1 1 -1 4.6158 25 1 1 0 -1 2.2447 26 1 1 -1 -1 6.1973 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3666 atoms have been selected out of 3740 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 750 250 250 0.00 3 C003 has 105 35 35 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 465 155 155 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.03 Total of13047 atoms and 4340 groups and 4334 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3740 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1235 Number of atoms = 3740 Number of groups = 1240 Number of bonds = 3733 Number of angles = 1339 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1237 Number of HB donors = 2452 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1235 Number of atoms = 3740 Number of groups = 1240 Number of bonds = 3733 Number of angles = 1339 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1237 Number of HB donors = 2452 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.328" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1235" Evaluating: 1235-7 Parameter: NUMWAT <- "1228" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1228" Comparing "1081" and "1228". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.328" Parameter: BOX -> "33.328" Parameter: BOX -> "33.328" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.32800 B = 33.32800 C = 33.32800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2944 2 1 -1 0 -1 2.5994 3 1 -1 1 -1 5.7659 4 1 0 -1 -1 4.6012 5 1 0 0 -1 0.9155 6 1 0 1 -1 2.8655 7 1 -1 -1 0 4.7037 8 1 -1 0 0 1.5765 9 1 -1 1 0 5.4853 10 1 0 -1 0 2.1619 11 1 0 1 0 2.1619 12 1 -1 -1 1 4.6127 13 1 -1 0 1 2.2436 14 1 -1 1 1 6.1946 15 1 0 -1 1 2.8655 16 1 0 0 1 0.9155 17 1 0 1 1 4.6012 18 1 1 1 1 6.2944 19 1 1 0 1 2.5994 20 1 1 -1 1 5.7659 21 1 1 1 0 4.7037 22 1 1 0 0 1.5765 23 1 1 -1 0 5.4853 24 1 1 1 -1 4.6127 25 1 1 0 -1 2.2436 26 1 1 -1 -1 6.1946 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3666 atoms have been selected out of 3740 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 750 250 250 0.00 3 C003 has 105 35 35 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 465 155 155 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.02 Total of13050 atoms and 4341 groups and 4335 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3740 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1235 Number of atoms = 3740 Number of groups = 1240 Number of bonds = 3733 Number of angles = 1339 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1237 Number of HB donors = 2452 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1235 Number of atoms = 3740 Number of groups = 1240 Number of bonds = 3733 Number of angles = 1339 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1237 Number of HB donors = 2452 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.326" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1235" Evaluating: 1235-7 Parameter: NUMWAT <- "1228" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1228" Comparing "1081" and "1228". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.326" Parameter: BOX -> "33.326" Parameter: BOX -> "33.326" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.32600 B = 33.32600 C = 33.32600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2927 2 1 -1 0 -1 2.5967 3 1 -1 1 -1 5.7625 4 1 0 -1 -1 4.6028 5 1 0 0 -1 0.9139 6 1 0 1 -1 2.8646 7 1 -1 -1 0 4.7010 8 1 -1 0 0 1.5747 9 1 -1 1 0 5.4834 10 1 0 -1 0 2.1599 11 1 0 1 0 2.1599 12 1 -1 -1 1 4.6096 13 1 -1 0 1 2.2425 14 1 -1 1 1 6.1918 15 1 0 -1 1 2.8646 16 1 0 0 1 0.9139 17 1 0 1 1 4.6028 18 1 1 1 1 6.2927 19 1 1 0 1 2.5967 20 1 1 -1 1 5.7625 21 1 1 1 0 4.7010 22 1 1 0 0 1.5747 23 1 1 -1 0 5.4834 24 1 1 1 -1 4.6096 25 1 1 0 -1 2.2425 26 1 1 -1 -1 6.1918 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3666 atoms have been selected out of 3740 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 465 155 155 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.02 Total of13056 atoms and 4343 groups and 4337 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3740 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1235 Number of atoms = 3740 Number of groups = 1240 Number of bonds = 3733 Number of angles = 1339 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1237 Number of HB donors = 2452 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1235 Number of atoms = 3740 Number of groups = 1240 Number of bonds = 3733 Number of angles = 1339 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1237 Number of HB donors = 2452 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.324" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1235" Evaluating: 1235-7 Parameter: NUMWAT <- "1228" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1228" Comparing "1081" and "1228". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.324" Parameter: BOX -> "33.324" Parameter: BOX -> "33.324" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.32400 B = 33.32400 C = 33.32400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2909 2 1 -1 0 -1 2.5940 3 1 -1 1 -1 5.7590 4 1 0 -1 -1 4.6043 5 1 0 0 -1 0.9123 6 1 0 1 -1 2.8636 7 1 -1 -1 0 4.6984 8 1 -1 0 0 1.5728 9 1 -1 1 0 5.4815 10 1 0 -1 0 2.1579 11 1 0 1 0 2.1579 12 1 -1 -1 1 4.6065 13 1 -1 0 1 2.2414 14 1 -1 1 1 6.1890 15 1 0 -1 1 2.8636 16 1 0 0 1 0.9123 17 1 0 1 1 4.6043 18 1 1 1 1 6.2909 19 1 1 0 1 2.5940 20 1 1 -1 1 5.7590 21 1 1 1 0 4.6984 22 1 1 0 0 1.5728 23 1 1 -1 0 5.4815 24 1 1 1 -1 4.6065 25 1 1 0 -1 2.2414 26 1 1 -1 -1 6.1890 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3666 atoms have been selected out of 3740 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 465 155 155 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.02 Total of13056 atoms and 4343 groups and 4337 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3740 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1235 Number of atoms = 3740 Number of groups = 1240 Number of bonds = 3733 Number of angles = 1339 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1237 Number of HB donors = 2452 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1235 Number of atoms = 3740 Number of groups = 1240 Number of bonds = 3733 Number of angles = 1339 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1237 Number of HB donors = 2452 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.322" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1235" Evaluating: 1235-7 Parameter: NUMWAT <- "1228" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1228" Comparing "1081" and "1228". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.322" Parameter: BOX -> "33.322" Parameter: BOX -> "33.322" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.32200 B = 33.32200 C = 33.32200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2892 2 1 -1 0 -1 2.5913 3 1 -1 1 -1 5.7556 4 1 0 -1 -1 4.6059 5 1 0 0 -1 0.9106 6 1 0 1 -1 2.8627 7 1 -1 -1 0 4.6957 8 1 -1 0 0 1.5710 9 1 -1 1 0 5.4796 10 1 0 -1 0 2.1559 11 1 0 1 0 2.1559 12 1 -1 -1 1 4.6034 13 1 -1 0 1 2.2403 14 1 -1 1 1 6.1862 15 1 0 -1 1 2.8627 16 1 0 0 1 0.9106 17 1 0 1 1 4.6059 18 1 1 1 1 6.2892 19 1 1 0 1 2.5913 20 1 1 -1 1 5.7556 21 1 1 1 0 4.6957 22 1 1 0 0 1.5710 23 1 1 -1 0 5.4796 24 1 1 1 -1 4.6034 25 1 1 0 -1 2.2403 26 1 1 -1 -1 6.1862 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3666 atoms have been selected out of 3740 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 688 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1578 526 526 0.00 6 C006 has 462 154 154 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.02 Total of13050 atoms and 4341 groups and 4335 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3740 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1234 Number of atoms = 3737 Number of groups = 1239 Number of bonds = 3730 Number of angles = 1338 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1236 Number of HB donors = 2450 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1234 Number of atoms = 3737 Number of groups = 1239 Number of bonds = 3730 Number of angles = 1338 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1236 Number of HB donors = 2450 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.32" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1234" Evaluating: 1234-7 Parameter: NUMWAT <- "1227" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1227" Comparing "1081" and "1227". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.32" Parameter: BOX -> "33.32" Parameter: BOX -> "33.32" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.32000 B = 33.32000 C = 33.32000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2874 2 1 -1 0 -1 2.5886 3 1 -1 1 -1 5.7521 4 1 0 -1 -1 4.6075 5 1 0 0 -1 0.9090 6 1 0 1 -1 2.8618 7 1 -1 -1 0 4.6930 8 1 -1 0 0 1.5692 9 1 -1 1 0 5.4777 10 1 0 -1 0 2.1539 11 1 0 1 0 2.1539 12 1 -1 -1 1 4.6003 13 1 -1 0 1 2.2393 14 1 -1 1 1 6.1834 15 1 0 -1 1 2.8618 16 1 0 0 1 0.9090 17 1 0 1 1 4.6075 18 1 1 1 1 6.2874 19 1 1 0 1 2.5886 20 1 1 -1 1 5.7521 21 1 1 1 0 4.6930 22 1 1 0 0 1.5692 23 1 1 -1 0 5.4777 24 1 1 1 -1 4.6003 25 1 1 0 -1 2.2393 26 1 1 -1 -1 6.1834 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3663 atoms have been selected out of 3737 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1578 526 526 0.00 6 C006 has 462 154 154 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.02 Total of13044 atoms and 4339 groups and 4333 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3737 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1234 Number of atoms = 3737 Number of groups = 1239 Number of bonds = 3730 Number of angles = 1338 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1236 Number of HB donors = 2450 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1234 Number of atoms = 3737 Number of groups = 1239 Number of bonds = 3730 Number of angles = 1338 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1236 Number of HB donors = 2450 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.318" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1234" Evaluating: 1234-7 Parameter: NUMWAT <- "1227" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1227" Comparing "1081" and "1227". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.318" Parameter: BOX -> "33.318" Parameter: BOX -> "33.318" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.31800 B = 33.31800 C = 33.31800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2857 2 1 -1 0 -1 2.5859 3 1 -1 1 -1 5.7487 4 1 0 -1 -1 4.6090 5 1 0 0 -1 0.9074 6 1 0 1 -1 2.8608 7 1 -1 -1 0 4.6904 8 1 -1 0 0 1.5674 9 1 -1 1 0 5.4758 10 1 0 -1 0 2.1519 11 1 0 1 0 2.1519 12 1 -1 -1 1 4.5972 13 1 -1 0 1 2.2382 14 1 -1 1 1 6.1806 15 1 0 -1 1 2.8608 16 1 0 0 1 0.9074 17 1 0 1 1 4.6090 18 1 1 1 1 6.2857 19 1 1 0 1 2.5859 20 1 1 -1 1 5.7487 21 1 1 1 0 4.6904 22 1 1 0 0 1.5674 23 1 1 -1 0 5.4758 24 1 1 1 -1 4.5972 25 1 1 0 -1 2.2382 26 1 1 -1 -1 6.1806 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3663 atoms have been selected out of 3737 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1578 526 526 0.00 6 C006 has 462 154 154 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.01 Total of13044 atoms and 4339 groups and 4333 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3737 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1234 Number of atoms = 3737 Number of groups = 1239 Number of bonds = 3730 Number of angles = 1338 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1236 Number of HB donors = 2450 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1234 Number of atoms = 3737 Number of groups = 1239 Number of bonds = 3730 Number of angles = 1338 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1236 Number of HB donors = 2450 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.316" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1234" Evaluating: 1234-7 Parameter: NUMWAT <- "1227" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1227" Comparing "1081" and "1227". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.316" Parameter: BOX -> "33.316" Parameter: BOX -> "33.316" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.31600 B = 33.31600 C = 33.31600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2839 2 1 -1 0 -1 2.5832 3 1 -1 1 -1 5.7453 4 1 0 -1 -1 4.6106 5 1 0 0 -1 0.9058 6 1 0 1 -1 2.8599 7 1 -1 -1 0 4.6877 8 1 -1 0 0 1.5655 9 1 -1 1 0 5.4739 10 1 0 -1 0 2.1499 11 1 0 1 0 2.1499 12 1 -1 -1 1 4.5941 13 1 -1 0 1 2.2371 14 1 -1 1 1 6.1778 15 1 0 -1 1 2.8599 16 1 0 0 1 0.9058 17 1 0 1 1 4.6106 18 1 1 1 1 6.2839 19 1 1 0 1 2.5832 20 1 1 -1 1 5.7453 21 1 1 1 0 4.6877 22 1 1 0 0 1.5655 23 1 1 -1 0 5.4739 24 1 1 1 -1 4.5941 25 1 1 0 -1 2.2371 26 1 1 -1 -1 6.1778 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3663 atoms have been selected out of 3737 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 462 154 154 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.01 Total of13047 atoms and 4340 groups and 4334 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3737 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1234 Number of atoms = 3737 Number of groups = 1239 Number of bonds = 3730 Number of angles = 1338 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1236 Number of HB donors = 2450 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1234 Number of atoms = 3737 Number of groups = 1239 Number of bonds = 3730 Number of angles = 1338 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1236 Number of HB donors = 2450 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.314" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1234" Evaluating: 1234-7 Parameter: NUMWAT <- "1227" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1227" Comparing "1081" and "1227". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.314" Parameter: BOX -> "33.314" Parameter: BOX -> "33.314" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.31400 B = 33.31400 C = 33.31400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2822 2 1 -1 0 -1 2.5805 3 1 -1 1 -1 5.7418 4 1 0 -1 -1 4.6122 5 1 0 0 -1 0.9042 6 1 0 1 -1 2.8590 7 1 -1 -1 0 4.6850 8 1 -1 0 0 1.5637 9 1 -1 1 0 5.4721 10 1 0 -1 0 2.1479 11 1 0 1 0 2.1479 12 1 -1 -1 1 4.5910 13 1 -1 0 1 2.2360 14 1 -1 1 1 6.1751 15 1 0 -1 1 2.8590 16 1 0 0 1 0.9042 17 1 0 1 1 4.6122 18 1 1 1 1 6.2822 19 1 1 0 1 2.5805 20 1 1 -1 1 5.7418 21 1 1 1 0 4.6850 22 1 1 0 0 1.5637 23 1 1 -1 0 5.4721 24 1 1 1 -1 4.5910 25 1 1 0 -1 2.2360 26 1 1 -1 -1 6.1751 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3663 atoms have been selected out of 3737 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 462 154 154 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.01 Total of13050 atoms and 4341 groups and 4335 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3737 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1234 Number of atoms = 3737 Number of groups = 1239 Number of bonds = 3730 Number of angles = 1338 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1236 Number of HB donors = 2450 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1234 Number of atoms = 3737 Number of groups = 1239 Number of bonds = 3730 Number of angles = 1338 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1236 Number of HB donors = 2450 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.312" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1234" Evaluating: 1234-7 Parameter: NUMWAT <- "1227" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1227" Comparing "1081" and "1227". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.312" Parameter: BOX -> "33.312" Parameter: BOX -> "33.312" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.31200 B = 33.31200 C = 33.31200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2804 2 1 -1 0 -1 2.5778 3 1 -1 1 -1 5.7384 4 1 0 -1 -1 4.6138 5 1 0 0 -1 0.9025 6 1 0 1 -1 2.8581 7 1 -1 -1 0 4.6824 8 1 -1 0 0 1.5619 9 1 -1 1 0 5.4702 10 1 0 -1 0 2.1459 11 1 0 1 0 2.1459 12 1 -1 -1 1 4.5879 13 1 -1 0 1 2.2350 14 1 -1 1 1 6.1723 15 1 0 -1 1 2.8581 16 1 0 0 1 0.9025 17 1 0 1 1 4.6138 18 1 1 1 1 6.2804 19 1 1 0 1 2.5778 20 1 1 -1 1 5.7384 21 1 1 1 0 4.6824 22 1 1 0 0 1.5619 23 1 1 -1 0 5.4702 24 1 1 1 -1 4.5879 25 1 1 0 -1 2.2350 26 1 1 -1 -1 6.1723 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3663 atoms have been selected out of 3737 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 73 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 462 154 154 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1674 558 558 0.00 12 C012 has 96 32 32 0.00 13 C013 has 483 161 161 0.00 14 C014 has 120 40 40 1.01 Total of13062 atoms and 4345 groups and 4339 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3737 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.31" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1233" Evaluating: 1233-7 Parameter: NUMWAT <- "1226" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1226" Comparing "1081" and "1226". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.31" Parameter: BOX -> "33.31" Parameter: BOX -> "33.31" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.31000 B = 33.31000 C = 33.31000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2787 2 1 -1 0 -1 2.5751 3 1 -1 1 -1 5.7350 4 1 0 -1 -1 4.6153 5 1 0 0 -1 0.9009 6 1 0 1 -1 2.8571 7 1 -1 -1 0 4.6797 8 1 -1 0 0 1.5600 9 1 -1 1 0 5.4683 10 1 0 -1 0 2.1439 11 1 0 1 0 2.1439 12 1 -1 -1 1 4.5848 13 1 -1 0 1 2.2339 14 1 -1 1 1 6.1695 15 1 0 -1 1 2.8571 16 1 0 0 1 0.9009 17 1 0 1 1 4.6153 18 1 1 1 1 6.2787 19 1 1 0 1 2.5751 20 1 1 -1 1 5.7350 21 1 1 1 0 4.6797 22 1 1 0 0 1.5600 23 1 1 -1 0 5.4683 24 1 1 1 -1 4.5848 25 1 1 0 -1 2.2339 26 1 1 -1 -1 6.1695 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3660 atoms have been selected out of 3734 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 462 154 154 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 96 32 32 0.00 13 C013 has 486 162 162 0.00 14 C014 has 120 40 40 1.01 Total of13059 atoms and 4344 groups and 4338 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3734 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.308" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1233" Evaluating: 1233-7 Parameter: NUMWAT <- "1226" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1226" Comparing "1081" and "1226". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.308" Parameter: BOX -> "33.308" Parameter: BOX -> "33.308" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.30800 B = 33.30800 C = 33.30800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2770 2 1 -1 0 -1 2.5724 3 1 -1 1 -1 5.7315 4 1 0 -1 -1 4.6169 5 1 0 0 -1 0.8993 6 1 0 1 -1 2.8562 7 1 -1 -1 0 4.6770 8 1 -1 0 0 1.5582 9 1 -1 1 0 5.4664 10 1 0 -1 0 2.1419 11 1 0 1 0 2.1419 12 1 -1 -1 1 4.5817 13 1 -1 0 1 2.2329 14 1 -1 1 1 6.1667 15 1 0 -1 1 2.8562 16 1 0 0 1 0.8993 17 1 0 1 1 4.6169 18 1 1 1 1 6.2770 19 1 1 0 1 2.5724 20 1 1 -1 1 5.7315 21 1 1 1 0 4.6770 22 1 1 0 0 1.5582 23 1 1 -1 0 5.4664 24 1 1 1 -1 4.5817 25 1 1 0 -1 2.2329 26 1 1 -1 -1 6.1667 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3660 atoms have been selected out of 3734 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 462 154 154 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 96 32 32 0.00 13 C013 has 486 162 162 0.00 14 C014 has 120 40 40 1.00 Total of13062 atoms and 4345 groups and 4339 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3734 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.306" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1233" Evaluating: 1233-7 Parameter: NUMWAT <- "1226" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1226" Comparing "1081" and "1226". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.306" Parameter: BOX -> "33.306" Parameter: BOX -> "33.306" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.30600 B = 33.30600 C = 33.30600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2752 2 1 -1 0 -1 2.5697 3 1 -1 1 -1 5.7281 4 1 0 -1 -1 4.6185 5 1 0 0 -1 0.8977 6 1 0 1 -1 2.8553 7 1 -1 -1 0 4.6744 8 1 -1 0 0 1.5564 9 1 -1 1 0 5.4645 10 1 0 -1 0 2.1399 11 1 0 1 0 2.1399 12 1 -1 -1 1 4.5786 13 1 -1 0 1 2.2318 14 1 -1 1 1 6.1639 15 1 0 -1 1 2.8553 16 1 0 0 1 0.8977 17 1 0 1 1 4.6185 18 1 1 1 1 6.2752 19 1 1 0 1 2.5697 20 1 1 -1 1 5.7281 21 1 1 1 0 4.6744 22 1 1 0 0 1.5564 23 1 1 -1 0 5.4645 24 1 1 1 -1 4.5786 25 1 1 0 -1 2.2318 26 1 1 -1 -1 6.1639 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3660 atoms have been selected out of 3734 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 462 154 154 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 96 32 32 0.00 13 C013 has 486 162 162 0.00 14 C014 has 120 40 40 1.00 Total of13062 atoms and 4345 groups and 4339 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3734 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.304" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1233" Evaluating: 1233-7 Parameter: NUMWAT <- "1226" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1226" Comparing "1081" and "1226". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.304" Parameter: BOX -> "33.304" Parameter: BOX -> "33.304" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.30400 B = 33.30400 C = 33.30400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2735 2 1 -1 0 -1 2.5670 3 1 -1 1 -1 5.7247 4 1 0 -1 -1 4.6201 5 1 0 0 -1 0.8961 6 1 0 1 -1 2.8544 7 1 -1 -1 0 4.6717 8 1 -1 0 0 1.5546 9 1 -1 1 0 5.4627 10 1 0 -1 0 2.1379 11 1 0 1 0 2.1379 12 1 -1 -1 1 4.5755 13 1 -1 0 1 2.2307 14 1 -1 1 1 6.1612 15 1 0 -1 1 2.8544 16 1 0 0 1 0.8961 17 1 0 1 1 4.6201 18 1 1 1 1 6.2735 19 1 1 0 1 2.5670 20 1 1 -1 1 5.7247 21 1 1 1 0 4.6717 22 1 1 0 0 1.5546 23 1 1 -1 0 5.4627 24 1 1 1 -1 4.5755 25 1 1 0 -1 2.2307 26 1 1 -1 -1 6.1612 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3660 atoms have been selected out of 3734 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 435 145 145 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 462 154 154 0.00 7 C007 has 762 254 254 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 96 32 32 0.00 13 C013 has 486 162 162 0.00 14 C014 has 120 40 40 1.00 Total of13062 atoms and 4345 groups and 4339 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3734 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.302" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1233" Evaluating: 1233-7 Parameter: NUMWAT <- "1226" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1226" Comparing "1081" and "1226". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.302" Parameter: BOX -> "33.302" Parameter: BOX -> "33.302" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.30200 B = 33.30200 C = 33.30200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2717 2 1 -1 0 -1 2.5643 3 1 -1 1 -1 5.7212 4 1 0 -1 -1 4.6216 5 1 0 0 -1 0.8945 6 1 0 1 -1 2.8535 7 1 -1 -1 0 4.6690 8 1 -1 0 0 1.5527 9 1 -1 1 0 5.4608 10 1 0 -1 0 2.1359 11 1 0 1 0 2.1359 12 1 -1 -1 1 4.5724 13 1 -1 0 1 2.2297 14 1 -1 1 1 6.1584 15 1 0 -1 1 2.8535 16 1 0 0 1 0.8945 17 1 0 1 1 4.6216 18 1 1 1 1 6.2717 19 1 1 0 1 2.5643 20 1 1 -1 1 5.7212 21 1 1 1 0 4.6690 22 1 1 0 0 1.5527 23 1 1 -1 0 5.4608 24 1 1 1 -1 4.5724 25 1 1 0 -1 2.2297 26 1 1 -1 -1 6.1584 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3660 atoms have been selected out of 3734 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 462 154 154 0.00 7 C007 has 765 255 255 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 96 32 32 0.00 13 C013 has 486 162 162 0.00 14 C014 has 120 40 40 1.00 Total of13068 atoms and 4347 groups and 4341 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3734 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.3" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1233" Evaluating: 1233-7 Parameter: NUMWAT <- "1226" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1226" Comparing "1081" and "1226". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.3" Parameter: BOX -> "33.3" Parameter: BOX -> "33.3" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.30000 B = 33.30000 C = 33.30000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2700 2 1 -1 0 -1 2.5616 3 1 -1 1 -1 5.7178 4 1 0 -1 -1 4.6232 5 1 0 0 -1 0.8929 6 1 0 1 -1 2.8526 7 1 -1 -1 0 4.6664 8 1 -1 0 0 1.5509 9 1 -1 1 0 5.4589 10 1 0 -1 0 2.1339 11 1 0 1 0 2.1339 12 1 -1 -1 1 4.5693 13 1 -1 0 1 2.2287 14 1 -1 1 1 6.1556 15 1 0 -1 1 2.8526 16 1 0 0 1 0.8929 17 1 0 1 1 4.6232 18 1 1 1 1 6.2700 19 1 1 0 1 2.5616 20 1 1 -1 1 5.7178 21 1 1 1 0 4.6664 22 1 1 0 0 1.5509 23 1 1 -1 0 5.4589 24 1 1 1 -1 4.5693 25 1 1 0 -1 2.2287 26 1 1 -1 -1 6.1556 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3660 atoms have been selected out of 3734 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 462 154 154 0.00 7 C007 has 765 255 255 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 96 32 32 0.00 13 C013 has 489 163 163 0.00 14 C014 has 120 40 40 1.00 Total of13074 atoms and 4349 groups and 4343 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3734 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.298" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1233" Evaluating: 1233-7 Parameter: NUMWAT <- "1226" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1226" Comparing "1081" and "1226". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.298" Parameter: BOX -> "33.298" Parameter: BOX -> "33.298" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.29800 B = 33.29800 C = 33.29800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2683 2 1 -1 0 -1 2.5589 3 1 -1 1 -1 5.7144 4 1 0 -1 -1 4.6248 5 1 0 0 -1 0.8913 6 1 0 1 -1 2.8517 7 1 -1 -1 0 4.6637 8 1 -1 0 0 1.5491 9 1 -1 1 0 5.4570 10 1 0 -1 0 2.1319 11 1 0 1 0 2.1319 12 1 -1 -1 1 4.5662 13 1 -1 0 1 2.2276 14 1 -1 1 1 6.1528 15 1 0 -1 1 2.8517 16 1 0 0 1 0.8913 17 1 0 1 1 4.6248 18 1 1 1 1 6.2683 19 1 1 0 1 2.5589 20 1 1 -1 1 5.7144 21 1 1 1 0 4.6637 22 1 1 0 0 1.5491 23 1 1 -1 0 5.4570 24 1 1 1 -1 4.5662 25 1 1 0 -1 2.2276 26 1 1 -1 -1 6.1528 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3660 atoms have been selected out of 3734 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 462 154 154 0.00 7 C007 has 765 255 255 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 96 32 32 0.00 13 C013 has 489 163 163 0.00 14 C014 has 120 40 40 0.99 Total of13074 atoms and 4349 groups and 4343 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3734 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.296" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1233" Evaluating: 1233-7 Parameter: NUMWAT <- "1226" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1226" Comparing "1081" and "1226". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.296" Parameter: BOX -> "33.296" Parameter: BOX -> "33.296" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.29600 B = 33.29600 C = 33.29600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2665 2 1 -1 0 -1 2.5562 3 1 -1 1 -1 5.7109 4 1 0 -1 -1 4.6264 5 1 0 0 -1 0.8897 6 1 0 1 -1 2.8508 7 1 -1 -1 0 4.6610 8 1 -1 0 0 1.5472 9 1 -1 1 0 5.4552 10 1 0 -1 0 2.1299 11 1 0 1 0 2.1299 12 1 -1 -1 1 4.5631 13 1 -1 0 1 2.2266 14 1 -1 1 1 6.1500 15 1 0 -1 1 2.8508 16 1 0 0 1 0.8897 17 1 0 1 1 4.6264 18 1 1 1 1 6.2665 19 1 1 0 1 2.5562 20 1 1 -1 1 5.7109 21 1 1 1 0 4.6610 22 1 1 0 0 1.5472 23 1 1 -1 0 5.4552 24 1 1 1 -1 4.5631 25 1 1 0 -1 2.2266 26 1 1 -1 -1 6.1500 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3660 atoms have been selected out of 3734 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 465 155 155 0.00 7 C007 has 765 255 255 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 96 32 32 0.00 13 C013 has 489 163 163 0.00 14 C014 has 120 40 40 0.99 Total of13077 atoms and 4350 groups and 4344 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3734 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.294" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1233" Evaluating: 1233-7 Parameter: NUMWAT <- "1226" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1226" Comparing "1081" and "1226". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.294" Parameter: BOX -> "33.294" Parameter: BOX -> "33.294" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.29400 B = 33.29400 C = 33.29400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2648 2 1 -1 0 -1 2.5535 3 1 -1 1 -1 5.7075 4 1 0 -1 -1 4.6279 5 1 0 0 -1 0.8881 6 1 0 1 -1 2.8499 7 1 -1 -1 0 4.6584 8 1 -1 0 0 1.5454 9 1 -1 1 0 5.4533 10 1 0 -1 0 2.1279 11 1 0 1 0 2.1279 12 1 -1 -1 1 4.5600 13 1 -1 0 1 2.2255 14 1 -1 1 1 6.1473 15 1 0 -1 1 2.8499 16 1 0 0 1 0.8881 17 1 0 1 1 4.6279 18 1 1 1 1 6.2648 19 1 1 0 1 2.5535 20 1 1 -1 1 5.7075 21 1 1 1 0 4.6584 22 1 1 0 0 1.5454 23 1 1 -1 0 5.4533 24 1 1 1 -1 4.5600 25 1 1 0 -1 2.2255 26 1 1 -1 -1 6.1473 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3660 atoms have been selected out of 3734 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 465 155 155 0.00 7 C007 has 765 255 255 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 96 32 32 0.00 13 C013 has 492 164 164 0.00 14 C014 has 120 40 40 0.99 Total of13083 atoms and 4352 groups and 4346 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3734 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.292" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1233" Evaluating: 1233-7 Parameter: NUMWAT <- "1226" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1226" Comparing "1081" and "1226". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.292" Parameter: BOX -> "33.292" Parameter: BOX -> "33.292" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.29200 B = 33.29200 C = 33.29200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2631 2 1 -1 0 -1 2.5508 3 1 -1 1 -1 5.7041 4 1 0 -1 -1 4.6295 5 1 0 0 -1 0.8865 6 1 0 1 -1 2.8490 7 1 -1 -1 0 4.6557 8 1 -1 0 0 1.5436 9 1 -1 1 0 5.4514 10 1 0 -1 0 2.1259 11 1 0 1 0 2.1259 12 1 -1 -1 1 4.5569 13 1 -1 0 1 2.2245 14 1 -1 1 1 6.1445 15 1 0 -1 1 2.8490 16 1 0 0 1 0.8865 17 1 0 1 1 4.6295 18 1 1 1 1 6.2631 19 1 1 0 1 2.5508 20 1 1 -1 1 5.7041 21 1 1 1 0 4.6557 22 1 1 0 0 1.5436 23 1 1 -1 0 5.4514 24 1 1 1 -1 4.5569 25 1 1 0 -1 2.2245 26 1 1 -1 -1 6.1445 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3660 atoms have been selected out of 3734 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 465 155 155 0.00 7 C007 has 765 255 255 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1674 558 558 0.00 12 C012 has 96 32 32 0.00 13 C013 has 492 164 164 0.00 14 C014 has 120 40 40 0.99 Total of13086 atoms and 4353 groups and 4347 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3734 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.29" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1233" Evaluating: 1233-7 Parameter: NUMWAT <- "1226" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1226" Comparing "1081" and "1226". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.29" Parameter: BOX -> "33.29" Parameter: BOX -> "33.29" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.29000 B = 33.29000 C = 33.29000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2613 2 1 -1 0 -1 2.5481 3 1 -1 1 -1 5.7006 4 1 0 -1 -1 4.6311 5 1 0 0 -1 0.8849 6 1 0 1 -1 2.8481 7 1 -1 -1 0 4.6530 8 1 -1 0 0 1.5418 9 1 -1 1 0 5.4495 10 1 0 -1 0 2.1239 11 1 0 1 0 2.1239 12 1 -1 -1 1 4.5538 13 1 -1 0 1 2.2235 14 1 -1 1 1 6.1417 15 1 0 -1 1 2.8481 16 1 0 0 1 0.8849 17 1 0 1 1 4.6311 18 1 1 1 1 6.2613 19 1 1 0 1 2.5481 20 1 1 -1 1 5.7006 21 1 1 1 0 4.6530 22 1 1 0 0 1.5418 23 1 1 -1 0 5.4495 24 1 1 1 -1 4.5538 25 1 1 0 -1 2.2235 26 1 1 -1 -1 6.1417 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3660 atoms have been selected out of 3734 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 465 155 155 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1674 558 558 0.00 12 C012 has 96 32 32 0.00 13 C013 has 492 164 164 0.00 14 C014 has 120 40 40 0.99 Total of13089 atoms and 4354 groups and 4348 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3734 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.288" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1233" Evaluating: 1233-7 Parameter: NUMWAT <- "1226" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1226" Comparing "1081" and "1226". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.288" Parameter: BOX -> "33.288" Parameter: BOX -> "33.288" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.28800 B = 33.28800 C = 33.28800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2596 2 1 -1 0 -1 2.5454 3 1 -1 1 -1 5.6972 4 1 0 -1 -1 4.6327 5 1 0 0 -1 0.8833 6 1 0 1 -1 2.8472 7 1 -1 -1 0 4.6504 8 1 -1 0 0 1.5400 9 1 -1 1 0 5.4477 10 1 0 -1 0 2.1219 11 1 0 1 0 2.1219 12 1 -1 -1 1 4.5507 13 1 -1 0 1 2.2224 14 1 -1 1 1 6.1389 15 1 0 -1 1 2.8472 16 1 0 0 1 0.8833 17 1 0 1 1 4.6327 18 1 1 1 1 6.2596 19 1 1 0 1 2.5454 20 1 1 -1 1 5.6972 21 1 1 1 0 4.6504 22 1 1 0 0 1.5400 23 1 1 -1 0 5.4477 24 1 1 1 -1 4.5507 25 1 1 0 -1 2.2224 26 1 1 -1 -1 6.1389 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3660 atoms have been selected out of 3734 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 465 155 155 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1677 559 559 0.00 12 C012 has 96 32 32 0.00 13 C013 has 492 164 164 0.00 14 C014 has 120 40 40 0.98 Total of13095 atoms and 4356 groups and 4350 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3734 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.286" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1233" Evaluating: 1233-7 Parameter: NUMWAT <- "1226" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1226" Comparing "1081" and "1226". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.286" Parameter: BOX -> "33.286" Parameter: BOX -> "33.286" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.28600 B = 33.28600 C = 33.28600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2579 2 1 -1 0 -1 2.5427 3 1 -1 1 -1 5.6938 4 1 0 -1 -1 4.6343 5 1 0 0 -1 0.8817 6 1 0 1 -1 2.8463 7 1 -1 -1 0 4.6477 8 1 -1 0 0 1.5381 9 1 -1 1 0 5.4458 10 1 0 -1 0 2.1199 11 1 0 1 0 2.1199 12 1 -1 -1 1 4.5476 13 1 -1 0 1 2.2214 14 1 -1 1 1 6.1362 15 1 0 -1 1 2.8463 16 1 0 0 1 0.8817 17 1 0 1 1 4.6343 18 1 1 1 1 6.2579 19 1 1 0 1 2.5427 20 1 1 -1 1 5.6938 21 1 1 1 0 4.6477 22 1 1 0 0 1.5381 23 1 1 -1 0 5.4458 24 1 1 1 -1 4.5476 25 1 1 0 -1 2.2214 26 1 1 -1 -1 6.1362 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3660 atoms have been selected out of 3734 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 468 156 156 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1677 559 559 0.00 12 C012 has 96 32 32 0.00 13 C013 has 495 165 165 0.00 14 C014 has 120 40 40 0.98 Total of13104 atoms and 4359 groups and 4353 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3734 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.284" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1233" Evaluating: 1233-7 Parameter: NUMWAT <- "1226" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1226" Comparing "1081" and "1226". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.284" Parameter: BOX -> "33.284" Parameter: BOX -> "33.284" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.28400 B = 33.28400 C = 33.28400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2562 2 1 -1 0 -1 2.5400 3 1 -1 1 -1 5.6903 4 1 0 -1 -1 4.6359 5 1 0 0 -1 0.8801 6 1 0 1 -1 2.8454 7 1 -1 -1 0 4.6450 8 1 -1 0 0 1.5363 9 1 -1 1 0 5.4439 10 1 0 -1 0 2.1179 11 1 0 1 0 2.1179 12 1 -1 -1 1 4.5445 13 1 -1 0 1 2.2204 14 1 -1 1 1 6.1334 15 1 0 -1 1 2.8454 16 1 0 0 1 0.8801 17 1 0 1 1 4.6359 18 1 1 1 1 6.2562 19 1 1 0 1 2.5400 20 1 1 -1 1 5.6903 21 1 1 1 0 4.6450 22 1 1 0 0 1.5363 23 1 1 -1 0 5.4439 24 1 1 1 -1 4.5445 25 1 1 0 -1 2.2204 26 1 1 -1 -1 6.1334 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3660 atoms have been selected out of 3734 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 468 156 156 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1677 559 559 0.00 12 C012 has 96 32 32 0.00 13 C013 has 495 165 165 0.00 14 C014 has 120 40 40 0.98 Total of13104 atoms and 4359 groups and 4353 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3734 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.282" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1233" Evaluating: 1233-7 Parameter: NUMWAT <- "1226" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1226" Comparing "1081" and "1226". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.282" Parameter: BOX -> "33.282" Parameter: BOX -> "33.282" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.28200 B = 33.28200 C = 33.28200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2544 2 1 -1 0 -1 2.5373 3 1 -1 1 -1 5.6869 4 1 0 -1 -1 4.6375 5 1 0 0 -1 0.8785 6 1 0 1 -1 2.8445 7 1 -1 -1 0 4.6424 8 1 -1 0 0 1.5345 9 1 -1 1 0 5.4421 10 1 0 -1 0 2.1159 11 1 0 1 0 2.1159 12 1 -1 -1 1 4.5414 13 1 -1 0 1 2.2194 14 1 -1 1 1 6.1306 15 1 0 -1 1 2.8445 16 1 0 0 1 0.8785 17 1 0 1 1 4.6375 18 1 1 1 1 6.2544 19 1 1 0 1 2.5373 20 1 1 -1 1 5.6869 21 1 1 1 0 4.6424 22 1 1 0 0 1.5345 23 1 1 -1 0 5.4421 24 1 1 1 -1 4.5414 25 1 1 0 -1 2.2194 26 1 1 -1 -1 6.1306 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3660 atoms have been selected out of 3734 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 468 156 156 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1677 559 559 0.00 12 C012 has 96 32 32 0.00 13 C013 has 495 165 165 0.00 14 C014 has 120 40 40 0.98 Total of13104 atoms and 4359 groups and 4353 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3734 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.28" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1233" Evaluating: 1233-7 Parameter: NUMWAT <- "1226" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1226" Comparing "1081" and "1226". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.28" Parameter: BOX -> "33.28" Parameter: BOX -> "33.28" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.28000 B = 33.28000 C = 33.28000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2527 2 1 -1 0 -1 2.5346 3 1 -1 1 -1 5.6835 4 1 0 -1 -1 4.6391 5 1 0 0 -1 0.8769 6 1 0 1 -1 2.8437 7 1 -1 -1 0 4.6397 8 1 -1 0 0 1.5327 9 1 -1 1 0 5.4402 10 1 0 -1 0 2.1139 11 1 0 1 0 2.1139 12 1 -1 -1 1 4.5383 13 1 -1 0 1 2.2184 14 1 -1 1 1 6.1279 15 1 0 -1 1 2.8437 16 1 0 0 1 0.8769 17 1 0 1 1 4.6391 18 1 1 1 1 6.2527 19 1 1 0 1 2.5346 20 1 1 -1 1 5.6835 21 1 1 1 0 4.6397 22 1 1 0 0 1.5327 23 1 1 -1 0 5.4402 24 1 1 1 -1 4.5383 25 1 1 0 -1 2.2184 26 1 1 -1 -1 6.1279 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3660 atoms have been selected out of 3734 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 468 156 156 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1677 559 559 0.00 12 C012 has 96 32 32 0.00 13 C013 has 495 165 165 0.00 14 C014 has 120 40 40 0.98 Total of13107 atoms and 4360 groups and 4354 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3734 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1233 Number of atoms = 3734 Number of groups = 1238 Number of bonds = 3727 Number of angles = 1337 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1235 Number of HB donors = 2448 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.278" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1233" Evaluating: 1233-7 Parameter: NUMWAT <- "1226" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1226" Comparing "1081" and "1226". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.278" Parameter: BOX -> "33.278" Parameter: BOX -> "33.278" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.27800 B = 33.27800 C = 33.27800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2510 2 1 -1 0 -1 2.5320 3 1 -1 1 -1 5.6800 4 1 0 -1 -1 4.6406 5 1 0 0 -1 0.8753 6 1 0 1 -1 2.8428 7 1 -1 -1 0 4.6370 8 1 -1 0 0 1.5308 9 1 -1 1 0 5.4383 10 1 0 -1 0 2.1119 11 1 0 1 0 2.1119 12 1 -1 -1 1 4.5352 13 1 -1 0 1 2.2174 14 1 -1 1 1 6.1251 15 1 0 -1 1 2.8428 16 1 0 0 1 0.8753 17 1 0 1 1 4.6406 18 1 1 1 1 6.2510 19 1 1 0 1 2.5320 20 1 1 -1 1 5.6800 21 1 1 1 0 4.6370 22 1 1 0 0 1.5308 23 1 1 -1 0 5.4383 24 1 1 1 -1 4.5352 25 1 1 0 -1 2.2174 26 1 1 -1 -1 6.1251 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3660 atoms have been selected out of 3734 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 108 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 471 157 157 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1677 559 559 0.00 12 C012 has 96 32 32 0.00 13 C013 has 495 165 165 0.00 14 C014 has 120 40 40 0.97 Total of13113 atoms and 4362 groups and 4356 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3734 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1232 Number of atoms = 3731 Number of groups = 1237 Number of bonds = 3724 Number of angles = 1336 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1234 Number of HB donors = 2446 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1232 Number of atoms = 3731 Number of groups = 1237 Number of bonds = 3724 Number of angles = 1336 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1234 Number of HB donors = 2446 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.276" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1232" Evaluating: 1232-7 Parameter: NUMWAT <- "1225" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1225" Comparing "1081" and "1225". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.276" Parameter: BOX -> "33.276" Parameter: BOX -> "33.276" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.27600 B = 33.27600 C = 33.27600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2493 2 1 -1 0 -1 2.5293 3 1 -1 1 -1 5.6766 4 1 0 -1 -1 4.6422 5 1 0 0 -1 0.8737 6 1 0 1 -1 2.8419 7 1 -1 -1 0 4.6344 8 1 -1 0 0 1.5290 9 1 -1 1 0 5.4365 10 1 0 -1 0 2.1099 11 1 0 1 0 2.1099 12 1 -1 -1 1 4.5321 13 1 -1 0 1 2.2163 14 1 -1 1 1 6.1223 15 1 0 -1 1 2.8419 16 1 0 0 1 0.8737 17 1 0 1 1 4.6422 18 1 1 1 1 6.2493 19 1 1 0 1 2.5293 20 1 1 -1 1 5.6766 21 1 1 1 0 4.6344 22 1 1 0 0 1.5290 23 1 1 -1 0 5.4365 24 1 1 1 -1 4.5321 25 1 1 0 -1 2.2163 26 1 1 -1 -1 6.1223 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3657 atoms have been selected out of 3731 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 468 156 156 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1677 559 559 0.00 12 C012 has 96 32 32 0.00 13 C013 has 495 165 165 0.00 14 C014 has 120 40 40 0.97 Total of13101 atoms and 4358 groups and 4352 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3731 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1232 Number of atoms = 3731 Number of groups = 1237 Number of bonds = 3724 Number of angles = 1336 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1234 Number of HB donors = 2446 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1232 Number of atoms = 3731 Number of groups = 1237 Number of bonds = 3724 Number of angles = 1336 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1234 Number of HB donors = 2446 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.274" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1232" Evaluating: 1232-7 Parameter: NUMWAT <- "1225" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1225" Comparing "1081" and "1225". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.274" Parameter: BOX -> "33.274" Parameter: BOX -> "33.274" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.27400 B = 33.27400 C = 33.27400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2476 2 1 -1 0 -1 2.5266 3 1 -1 1 -1 5.6731 4 1 0 -1 -1 4.6438 5 1 0 0 -1 0.8721 6 1 0 1 -1 2.8410 7 1 -1 -1 0 4.6317 8 1 -1 0 0 1.5272 9 1 -1 1 0 5.4346 10 1 0 -1 0 2.1079 11 1 0 1 0 2.1079 12 1 -1 -1 1 4.5291 13 1 -1 0 1 2.2153 14 1 -1 1 1 6.1195 15 1 0 -1 1 2.8410 16 1 0 0 1 0.8721 17 1 0 1 1 4.6438 18 1 1 1 1 6.2476 19 1 1 0 1 2.5266 20 1 1 -1 1 5.6731 21 1 1 1 0 4.6317 22 1 1 0 0 1.5272 23 1 1 -1 0 5.4346 24 1 1 1 -1 4.5291 25 1 1 0 -1 2.2153 26 1 1 -1 -1 6.1195 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3657 atoms have been selected out of 3731 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 468 156 156 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1680 560 560 0.00 12 C012 has 96 32 32 0.00 13 C013 has 495 165 165 0.00 14 C014 has 120 40 40 0.97 Total of13110 atoms and 4361 groups and 4355 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3731 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1232 Number of atoms = 3731 Number of groups = 1237 Number of bonds = 3724 Number of angles = 1336 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1234 Number of HB donors = 2446 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1232 Number of atoms = 3731 Number of groups = 1237 Number of bonds = 3724 Number of angles = 1336 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1234 Number of HB donors = 2446 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.272" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1232" Evaluating: 1232-7 Parameter: NUMWAT <- "1225" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1225" Comparing "1081" and "1225". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.272" Parameter: BOX -> "33.272" Parameter: BOX -> "33.272" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.27200 B = 33.27200 C = 33.27200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2458 2 1 -1 0 -1 2.5239 3 1 -1 1 -1 5.6697 4 1 0 -1 -1 4.6454 5 1 0 0 -1 0.8706 6 1 0 1 -1 2.8402 7 1 -1 -1 0 4.6290 8 1 -1 0 0 1.5254 9 1 -1 1 0 5.4327 10 1 0 -1 0 2.1059 11 1 0 1 0 2.1059 12 1 -1 -1 1 4.5260 13 1 -1 0 1 2.2143 14 1 -1 1 1 6.1168 15 1 0 -1 1 2.8402 16 1 0 0 1 0.8706 17 1 0 1 1 4.6454 18 1 1 1 1 6.2458 19 1 1 0 1 2.5239 20 1 1 -1 1 5.6697 21 1 1 1 0 4.6290 22 1 1 0 0 1.5254 23 1 1 -1 0 5.4327 24 1 1 1 -1 4.5260 25 1 1 0 -1 2.2143 26 1 1 -1 -1 6.1168 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3657 atoms have been selected out of 3731 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 468 156 156 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1680 560 560 0.00 12 C012 has 96 32 32 0.00 13 C013 has 495 165 165 0.00 14 C014 has 120 40 40 0.97 Total of13113 atoms and 4362 groups and 4356 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3731 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1232 Number of atoms = 3731 Number of groups = 1237 Number of bonds = 3724 Number of angles = 1336 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1234 Number of HB donors = 2446 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1232 Number of atoms = 3731 Number of groups = 1237 Number of bonds = 3724 Number of angles = 1336 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1234 Number of HB donors = 2446 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.27" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1232" Evaluating: 1232-7 Parameter: NUMWAT <- "1225" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1225" Comparing "1081" and "1225". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.27" Parameter: BOX -> "33.27" Parameter: BOX -> "33.27" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.27000 B = 33.27000 C = 33.27000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2441 2 1 -1 0 -1 2.5212 3 1 -1 1 -1 5.6663 4 1 0 -1 -1 4.6470 5 1 0 0 -1 0.8690 6 1 0 1 -1 2.8393 7 1 -1 -1 0 4.6264 8 1 -1 0 0 1.5236 9 1 -1 1 0 5.4309 10 1 0 -1 0 2.1039 11 1 0 1 0 2.1039 12 1 -1 -1 1 4.5229 13 1 -1 0 1 2.2133 14 1 -1 1 1 6.1140 15 1 0 -1 1 2.8393 16 1 0 0 1 0.8690 17 1 0 1 1 4.6470 18 1 1 1 1 6.2441 19 1 1 0 1 2.5212 20 1 1 -1 1 5.6663 21 1 1 1 0 4.6264 22 1 1 0 0 1.5236 23 1 1 -1 0 5.4309 24 1 1 1 -1 4.5229 25 1 1 0 -1 2.2133 26 1 1 -1 -1 6.1140 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3657 atoms have been selected out of 3731 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1599 533 533 0.00 6 C006 has 468 156 156 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1680 560 560 0.00 12 C012 has 96 32 32 0.00 13 C013 has 495 165 165 0.00 14 C014 has 120 40 40 0.97 Total of13119 atoms and 4364 groups and 4358 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3731 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1232 Number of atoms = 3731 Number of groups = 1237 Number of bonds = 3724 Number of angles = 1336 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1234 Number of HB donors = 2446 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1232 Number of atoms = 3731 Number of groups = 1237 Number of bonds = 3724 Number of angles = 1336 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1234 Number of HB donors = 2446 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.268" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1232" Evaluating: 1232-7 Parameter: NUMWAT <- "1225" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1225" Comparing "1081" and "1225". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.268" Parameter: BOX -> "33.268" Parameter: BOX -> "33.268" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.26800 B = 33.26800 C = 33.26800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2424 2 1 -1 0 -1 2.5185 3 1 -1 1 -1 5.6628 4 1 0 -1 -1 4.6486 5 1 0 0 -1 0.8674 6 1 0 1 -1 2.8384 7 1 -1 -1 0 4.6237 8 1 -1 0 0 1.5217 9 1 -1 1 0 5.4290 10 1 0 -1 0 2.1019 11 1 0 1 0 2.1019 12 1 -1 -1 1 4.5198 13 1 -1 0 1 2.2123 14 1 -1 1 1 6.1112 15 1 0 -1 1 2.8384 16 1 0 0 1 0.8674 17 1 0 1 1 4.6486 18 1 1 1 1 6.2424 19 1 1 0 1 2.5185 20 1 1 -1 1 5.6628 21 1 1 1 0 4.6237 22 1 1 0 0 1.5217 23 1 1 -1 0 5.4290 24 1 1 1 -1 4.5198 25 1 1 0 -1 2.2123 26 1 1 -1 -1 6.1112 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3657 atoms have been selected out of 3731 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1599 533 533 0.00 6 C006 has 468 156 156 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1680 560 560 0.00 12 C012 has 96 32 32 0.00 13 C013 has 495 165 165 0.00 14 C014 has 120 40 40 0.96 Total of13122 atoms and 4365 groups and 4359 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3731 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1232 Number of atoms = 3731 Number of groups = 1237 Number of bonds = 3724 Number of angles = 1336 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1234 Number of HB donors = 2446 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1232 Number of atoms = 3731 Number of groups = 1237 Number of bonds = 3724 Number of angles = 1336 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1234 Number of HB donors = 2446 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.266" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1232" Evaluating: 1232-7 Parameter: NUMWAT <- "1225" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1225" Comparing "1081" and "1225". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.266" Parameter: BOX -> "33.266" Parameter: BOX -> "33.266" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.26600 B = 33.26600 C = 33.26600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2407 2 1 -1 0 -1 2.5158 3 1 -1 1 -1 5.6594 4 1 0 -1 -1 4.6502 5 1 0 0 -1 0.8658 6 1 0 1 -1 2.8376 7 1 -1 -1 0 4.6210 8 1 -1 0 0 1.5199 9 1 -1 1 0 5.4271 10 1 0 -1 0 2.0999 11 1 0 1 0 2.0999 12 1 -1 -1 1 4.5167 13 1 -1 0 1 2.2114 14 1 -1 1 1 6.1085 15 1 0 -1 1 2.8376 16 1 0 0 1 0.8658 17 1 0 1 1 4.6502 18 1 1 1 1 6.2407 19 1 1 0 1 2.5158 20 1 1 -1 1 5.6594 21 1 1 1 0 4.6210 22 1 1 0 0 1.5199 23 1 1 -1 0 5.4271 24 1 1 1 -1 4.5167 25 1 1 0 -1 2.2114 26 1 1 -1 -1 6.1085 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3657 atoms have been selected out of 3731 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1599 533 533 0.00 6 C006 has 468 156 156 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1680 560 560 0.00 12 C012 has 96 32 32 0.00 13 C013 has 495 165 165 0.00 14 C014 has 120 40 40 0.96 Total of13125 atoms and 4366 groups and 4360 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3731 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1232 Number of atoms = 3731 Number of groups = 1237 Number of bonds = 3724 Number of angles = 1336 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1234 Number of HB donors = 2446 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1232 Number of atoms = 3731 Number of groups = 1237 Number of bonds = 3724 Number of angles = 1336 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1234 Number of HB donors = 2446 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.264" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1232" Evaluating: 1232-7 Parameter: NUMWAT <- "1225" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1225" Comparing "1081" and "1225". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.264" Parameter: BOX -> "33.264" Parameter: BOX -> "33.264" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.26400 B = 33.26400 C = 33.26400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2390 2 1 -1 0 -1 2.5131 3 1 -1 1 -1 5.6560 4 1 0 -1 -1 4.6518 5 1 0 0 -1 0.8642 6 1 0 1 -1 2.8367 7 1 -1 -1 0 4.6184 8 1 -1 0 0 1.5181 9 1 -1 1 0 5.4253 10 1 0 -1 0 2.0979 11 1 0 1 0 2.0979 12 1 -1 -1 1 4.5136 13 1 -1 0 1 2.2104 14 1 -1 1 1 6.1057 15 1 0 -1 1 2.8367 16 1 0 0 1 0.8642 17 1 0 1 1 4.6518 18 1 1 1 1 6.2390 19 1 1 0 1 2.5131 20 1 1 -1 1 5.6560 21 1 1 1 0 4.6184 22 1 1 0 0 1.5181 23 1 1 -1 0 5.4253 24 1 1 1 -1 4.5136 25 1 1 0 -1 2.2104 26 1 1 -1 -1 6.1057 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3657 atoms have been selected out of 3731 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 438 146 146 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1599 533 533 0.00 6 C006 has 468 156 156 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1680 560 560 0.00 12 C012 has 96 32 32 0.00 13 C013 has 495 165 165 0.00 14 C014 has 120 40 40 0.96 Total of13125 atoms and 4366 groups and 4360 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3731 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1232 Number of atoms = 3731 Number of groups = 1237 Number of bonds = 3724 Number of angles = 1336 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1234 Number of HB donors = 2446 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1232 Number of atoms = 3731 Number of groups = 1237 Number of bonds = 3724 Number of angles = 1336 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1234 Number of HB donors = 2446 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.262" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1232" Evaluating: 1232-7 Parameter: NUMWAT <- "1225" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1225" Comparing "1081" and "1225". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.262" Parameter: BOX -> "33.262" Parameter: BOX -> "33.262" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.26200 B = 33.26200 C = 33.26200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2373 2 1 -1 0 -1 2.5104 3 1 -1 1 -1 5.6525 4 1 0 -1 -1 4.6534 5 1 0 0 -1 0.8627 6 1 0 1 -1 2.8358 7 1 -1 -1 0 4.6157 8 1 -1 0 0 1.5163 9 1 -1 1 0 5.4234 10 1 0 -1 0 2.0959 11 1 0 1 0 2.0959 12 1 -1 -1 1 4.5105 13 1 -1 0 1 2.2094 14 1 -1 1 1 6.1029 15 1 0 -1 1 2.8358 16 1 0 0 1 0.8627 17 1 0 1 1 4.6534 18 1 1 1 1 6.2373 19 1 1 0 1 2.5104 20 1 1 -1 1 5.6525 21 1 1 1 0 4.6157 22 1 1 0 0 1.5163 23 1 1 -1 0 5.4234 24 1 1 1 -1 4.5105 25 1 1 0 -1 2.2094 26 1 1 -1 -1 6.1029 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3657 atoms have been selected out of 3731 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 441 147 147 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1599 533 533 0.00 6 C006 has 468 156 156 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1680 560 560 0.00 12 C012 has 96 32 32 0.00 13 C013 has 495 165 165 0.00 14 C014 has 120 40 40 0.96 Total of13131 atoms and 4368 groups and 4362 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3731 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1232 Number of atoms = 3731 Number of groups = 1237 Number of bonds = 3724 Number of angles = 1336 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1234 Number of HB donors = 2446 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1232 Number of atoms = 3731 Number of groups = 1237 Number of bonds = 3724 Number of angles = 1336 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1234 Number of HB donors = 2446 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.26" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1232" Evaluating: 1232-7 Parameter: NUMWAT <- "1225" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1225" Comparing "1081" and "1225". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.26" Parameter: BOX -> "33.26" Parameter: BOX -> "33.26" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.26000 B = 33.26000 C = 33.26000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2356 2 1 -1 0 -1 2.5077 3 1 -1 1 -1 5.6491 4 1 0 -1 -1 4.6550 5 1 0 0 -1 0.8611 6 1 0 1 -1 2.8350 7 1 -1 -1 0 4.6131 8 1 -1 0 0 1.5145 9 1 -1 1 0 5.4216 10 1 0 -1 0 2.0939 11 1 0 1 0 2.0939 12 1 -1 -1 1 4.5074 13 1 -1 0 1 2.2084 14 1 -1 1 1 6.1002 15 1 0 -1 1 2.8350 16 1 0 0 1 0.8611 17 1 0 1 1 4.6550 18 1 1 1 1 6.2356 19 1 1 0 1 2.5077 20 1 1 -1 1 5.6491 21 1 1 1 0 4.6131 22 1 1 0 0 1.5145 23 1 1 -1 0 5.4216 24 1 1 1 -1 4.5074 25 1 1 0 -1 2.2084 26 1 1 -1 -1 6.1002 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3657 atoms have been selected out of 3731 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 441 147 147 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1602 534 534 0.00 6 C006 has 468 156 156 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1680 560 560 0.00 12 C012 has 96 32 32 0.00 13 C013 has 495 165 165 0.00 14 C014 has 120 40 40 0.96 Total of13134 atoms and 4369 groups and 4363 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3731 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1232 Number of atoms = 3731 Number of groups = 1237 Number of bonds = 3724 Number of angles = 1336 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1234 Number of HB donors = 2446 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1232 Number of atoms = 3731 Number of groups = 1237 Number of bonds = 3724 Number of angles = 1336 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1234 Number of HB donors = 2446 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.258" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1232" Evaluating: 1232-7 Parameter: NUMWAT <- "1225" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1225" Comparing "1081" and "1225". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.258" Parameter: BOX -> "33.258" Parameter: BOX -> "33.258" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.25800 B = 33.25800 C = 33.25800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2339 2 1 -1 0 -1 2.5050 3 1 -1 1 -1 5.6457 4 1 0 -1 -1 4.6566 5 1 0 0 -1 0.8595 6 1 0 1 -1 2.8341 7 1 -1 -1 0 4.6104 8 1 -1 0 0 1.5127 9 1 -1 1 0 5.4197 10 1 0 -1 0 2.0919 11 1 0 1 0 2.0919 12 1 -1 -1 1 4.5043 13 1 -1 0 1 2.2074 14 1 -1 1 1 6.0974 15 1 0 -1 1 2.8341 16 1 0 0 1 0.8595 17 1 0 1 1 4.6566 18 1 1 1 1 6.2339 19 1 1 0 1 2.5050 20 1 1 -1 1 5.6457 21 1 1 1 0 4.6104 22 1 1 0 0 1.5127 23 1 1 -1 0 5.4197 24 1 1 1 -1 4.5043 25 1 1 0 -1 2.2074 26 1 1 -1 -1 6.0974 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3657 atoms have been selected out of 3731 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 441 147 147 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1602 534 534 0.00 6 C006 has 471 157 157 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1680 560 560 0.00 12 C012 has 96 32 32 0.00 13 C013 has 495 165 165 0.00 14 C014 has 120 40 40 0.95 Total of13137 atoms and 4370 groups and 4364 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3731 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1232 Number of atoms = 3731 Number of groups = 1237 Number of bonds = 3724 Number of angles = 1336 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1234 Number of HB donors = 2446 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1232 Number of atoms = 3731 Number of groups = 1237 Number of bonds = 3724 Number of angles = 1336 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1234 Number of HB donors = 2446 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.256" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1232" Evaluating: 1232-7 Parameter: NUMWAT <- "1225" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1225" Comparing "1081" and "1225". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.256" Parameter: BOX -> "33.256" Parameter: BOX -> "33.256" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.25600 B = 33.25600 C = 33.25600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2322 2 1 -1 0 -1 2.5023 3 1 -1 1 -1 5.6422 4 1 0 -1 -1 4.6582 5 1 0 0 -1 0.8579 6 1 0 1 -1 2.8333 7 1 -1 -1 0 4.6077 8 1 -1 0 0 1.5108 9 1 -1 1 0 5.4178 10 1 0 -1 0 2.0899 11 1 0 1 0 2.0899 12 1 -1 -1 1 4.5013 13 1 -1 0 1 2.2064 14 1 -1 1 1 6.0947 15 1 0 -1 1 2.8333 16 1 0 0 1 0.8579 17 1 0 1 1 4.6582 18 1 1 1 1 6.2322 19 1 1 0 1 2.5023 20 1 1 -1 1 5.6422 21 1 1 1 0 4.6077 22 1 1 0 0 1.5108 23 1 1 -1 0 5.4178 24 1 1 1 -1 4.5013 25 1 1 0 -1 2.2064 26 1 1 -1 -1 6.0947 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3657 atoms have been selected out of 3731 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 441 147 147 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1602 534 534 0.00 6 C006 has 471 157 157 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1680 560 560 0.00 12 C012 has 96 32 32 0.00 13 C013 has 495 165 165 0.00 14 C014 has 120 40 40 0.95 Total of13137 atoms and 4370 groups and 4364 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3731 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1232 Number of atoms = 3731 Number of groups = 1237 Number of bonds = 3724 Number of angles = 1336 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1234 Number of HB donors = 2446 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1232 Number of atoms = 3731 Number of groups = 1237 Number of bonds = 3724 Number of angles = 1336 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1234 Number of HB donors = 2446 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.254" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1232" Evaluating: 1232-7 Parameter: NUMWAT <- "1225" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1225" Comparing "1081" and "1225". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.254" Parameter: BOX -> "33.254" Parameter: BOX -> "33.254" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.25400 B = 33.25400 C = 33.25400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2305 2 1 -1 0 -1 2.4996 3 1 -1 1 -1 5.6388 4 1 0 -1 -1 4.6598 5 1 0 0 -1 0.8564 6 1 0 1 -1 2.8324 7 1 -1 -1 0 4.6051 8 1 -1 0 0 1.5090 9 1 -1 1 0 5.4160 10 1 0 -1 0 2.0879 11 1 0 1 0 2.0879 12 1 -1 -1 1 4.4982 13 1 -1 0 1 2.2055 14 1 -1 1 1 6.0919 15 1 0 -1 1 2.8324 16 1 0 0 1 0.8564 17 1 0 1 1 4.6598 18 1 1 1 1 6.2305 19 1 1 0 1 2.4996 20 1 1 -1 1 5.6388 21 1 1 1 0 4.6051 22 1 1 0 0 1.5090 23 1 1 -1 0 5.4160 24 1 1 1 -1 4.4982 25 1 1 0 -1 2.2055 26 1 1 -1 -1 6.0919 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3657 atoms have been selected out of 3731 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 413 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 441 147 147 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1602 534 534 0.00 6 C006 has 471 157 157 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1677 559 559 0.00 12 C012 has 96 32 32 0.00 13 C013 has 495 165 165 0.00 14 C014 has 120 40 40 1.12 Total of13134 atoms and 4369 groups and 4363 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3731 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1231 Number of atoms = 3728 Number of groups = 1236 Number of bonds = 3721 Number of angles = 1335 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1233 Number of HB donors = 2444 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1231 Number of atoms = 3728 Number of groups = 1236 Number of bonds = 3721 Number of angles = 1335 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1233 Number of HB donors = 2444 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.252" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1231" Evaluating: 1231-7 Parameter: NUMWAT <- "1224" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1224" Comparing "1081" and "1224". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.252" Parameter: BOX -> "33.252" Parameter: BOX -> "33.252" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.25200 B = 33.25200 C = 33.25200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2288 2 1 -1 0 -1 2.4969 3 1 -1 1 -1 5.6354 4 1 0 -1 -1 4.6614 5 1 0 0 -1 0.8548 6 1 0 1 -1 2.8316 7 1 -1 -1 0 4.6024 8 1 -1 0 0 1.5072 9 1 -1 1 0 5.4141 10 1 0 -1 0 2.0859 11 1 0 1 0 2.0859 12 1 -1 -1 1 4.4951 13 1 -1 0 1 2.2045 14 1 -1 1 1 6.0891 15 1 0 -1 1 2.8316 16 1 0 0 1 0.8548 17 1 0 1 1 4.6614 18 1 1 1 1 6.2288 19 1 1 0 1 2.4969 20 1 1 -1 1 5.6354 21 1 1 1 0 4.6024 22 1 1 0 0 1.5072 23 1 1 -1 0 5.4141 24 1 1 1 -1 4.4951 25 1 1 0 -1 2.2045 26 1 1 -1 -1 6.0891 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3654 atoms have been selected out of 3728 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 441 147 147 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1602 534 534 0.00 6 C006 has 471 157 157 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1677 559 559 0.00 12 C012 has 96 32 32 0.00 13 C013 has 495 165 165 0.00 14 C014 has 120 40 40 1.11 Total of13131 atoms and 4368 groups and 4362 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3728 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1231 Number of atoms = 3728 Number of groups = 1236 Number of bonds = 3721 Number of angles = 1335 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1233 Number of HB donors = 2444 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1231 Number of atoms = 3728 Number of groups = 1236 Number of bonds = 3721 Number of angles = 1335 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1233 Number of HB donors = 2444 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.25" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1231" Evaluating: 1231-7 Parameter: NUMWAT <- "1224" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1224" Comparing "1081" and "1224". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.25" Parameter: BOX -> "33.25" Parameter: BOX -> "33.25" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.25000 B = 33.25000 C = 33.25000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2271 2 1 -1 0 -1 2.4942 3 1 -1 1 -1 5.6319 4 1 0 -1 -1 4.6630 5 1 0 0 -1 0.8533 6 1 0 1 -1 2.8308 7 1 -1 -1 0 4.5997 8 1 -1 0 0 1.5054 9 1 -1 1 0 5.4123 10 1 0 -1 0 2.0839 11 1 0 1 0 2.0839 12 1 -1 -1 1 4.4920 13 1 -1 0 1 2.2035 14 1 -1 1 1 6.0864 15 1 0 -1 1 2.8308 16 1 0 0 1 0.8533 17 1 0 1 1 4.6630 18 1 1 1 1 6.2271 19 1 1 0 1 2.4942 20 1 1 -1 1 5.6319 21 1 1 1 0 4.5997 22 1 1 0 0 1.5054 23 1 1 -1 0 5.4123 24 1 1 1 -1 4.4920 25 1 1 0 -1 2.2035 26 1 1 -1 -1 6.0864 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3654 atoms have been selected out of 3728 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 282 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 441 147 147 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1602 534 534 0.00 6 C006 has 471 157 157 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1677 559 559 0.00 12 C012 has 99 33 33 0.00 13 C013 has 495 165 165 0.00 14 C014 has 117 39 39 1.02 Total of13131 atoms and 4368 groups and 4362 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3728 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.248" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1230" Evaluating: 1230-7 Parameter: NUMWAT <- "1223" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1223" Comparing "1081" and "1223". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.248" Parameter: BOX -> "33.248" Parameter: BOX -> "33.248" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.24800 B = 33.24800 C = 33.24800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2254 2 1 -1 0 -1 2.4915 3 1 -1 1 -1 5.6285 4 1 0 -1 -1 4.6646 5 1 0 0 -1 0.8517 6 1 0 1 -1 2.8299 7 1 -1 -1 0 4.5971 8 1 -1 0 0 1.5036 9 1 -1 1 0 5.4104 10 1 0 -1 0 2.0819 11 1 0 1 0 2.0819 12 1 -1 -1 1 4.4889 13 1 -1 0 1 2.2026 14 1 -1 1 1 6.0836 15 1 0 -1 1 2.8299 16 1 0 0 1 0.8517 17 1 0 1 1 4.6646 18 1 1 1 1 6.2254 19 1 1 0 1 2.4915 20 1 1 -1 1 5.6285 21 1 1 1 0 4.5971 22 1 1 0 0 1.5036 23 1 1 -1 0 5.4104 24 1 1 1 -1 4.4889 25 1 1 0 -1 2.2026 26 1 1 -1 -1 6.0836 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3651 atoms have been selected out of 3725 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 441 147 147 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1602 534 534 0.00 6 C006 has 471 157 157 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1674 558 558 0.00 12 C012 has 96 32 32 0.00 13 C013 has 492 164 164 0.00 14 C014 has 117 39 39 1.11 Total of13113 atoms and 4362 groups and 4356 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3725 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.246" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1230" Evaluating: 1230-7 Parameter: NUMWAT <- "1223" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1223" Comparing "1081" and "1223". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.246" Parameter: BOX -> "33.246" Parameter: BOX -> "33.246" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.24600 B = 33.24600 C = 33.24600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2237 2 1 -1 0 -1 2.4889 3 1 -1 1 -1 5.6251 4 1 0 -1 -1 4.6663 5 1 0 0 -1 0.8501 6 1 0 1 -1 2.8291 7 1 -1 -1 0 4.5944 8 1 -1 0 0 1.5018 9 1 -1 1 0 5.4086 10 1 0 -1 0 2.0799 11 1 0 1 0 2.0799 12 1 -1 -1 1 4.4858 13 1 -1 0 1 2.2016 14 1 -1 1 1 6.0809 15 1 0 -1 1 2.8291 16 1 0 0 1 0.8501 17 1 0 1 1 4.6663 18 1 1 1 1 6.2237 19 1 1 0 1 2.4889 20 1 1 -1 1 5.6251 21 1 1 1 0 4.5944 22 1 1 0 0 1.5018 23 1 1 -1 0 5.4086 24 1 1 1 -1 4.4858 25 1 1 0 -1 2.2016 26 1 1 -1 -1 6.0809 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3651 atoms have been selected out of 3725 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 441 147 147 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1605 535 535 0.00 6 C006 has 474 158 158 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1674 558 558 0.00 12 C012 has 96 32 32 0.00 13 C013 has 492 164 164 0.00 14 C014 has 117 39 39 1.11 Total of13119 atoms and 4364 groups and 4358 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3725 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.244" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1230" Evaluating: 1230-7 Parameter: NUMWAT <- "1223" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1223" Comparing "1081" and "1223". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.244" Parameter: BOX -> "33.244" Parameter: BOX -> "33.244" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.24400 B = 33.24400 C = 33.24400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2220 2 1 -1 0 -1 2.4862 3 1 -1 1 -1 5.6216 4 1 0 -1 -1 4.6679 5 1 0 0 -1 0.8486 6 1 0 1 -1 2.8282 7 1 -1 -1 0 4.5918 8 1 -1 0 0 1.4999 9 1 -1 1 0 5.4067 10 1 0 -1 0 2.0779 11 1 0 1 0 2.0779 12 1 -1 -1 1 4.4827 13 1 -1 0 1 2.2006 14 1 -1 1 1 6.0781 15 1 0 -1 1 2.8282 16 1 0 0 1 0.8486 17 1 0 1 1 4.6679 18 1 1 1 1 6.2220 19 1 1 0 1 2.4862 20 1 1 -1 1 5.6216 21 1 1 1 0 4.5918 22 1 1 0 0 1.4999 23 1 1 -1 0 5.4067 24 1 1 1 -1 4.4827 25 1 1 0 -1 2.2006 26 1 1 -1 -1 6.0781 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3651 atoms have been selected out of 3725 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 441 147 147 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1605 535 535 0.00 6 C006 has 474 158 158 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1674 558 558 0.00 12 C012 has 96 32 32 0.00 13 C013 has 492 164 164 0.00 14 C014 has 117 39 39 1.11 Total of13122 atoms and 4365 groups and 4359 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3725 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.242" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1230" Evaluating: 1230-7 Parameter: NUMWAT <- "1223" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1223" Comparing "1081" and "1223". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.242" Parameter: BOX -> "33.242" Parameter: BOX -> "33.242" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.24200 B = 33.24200 C = 33.24200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2203 2 1 -1 0 -1 2.4835 3 1 -1 1 -1 5.6182 4 1 0 -1 -1 4.6695 5 1 0 0 -1 0.8470 6 1 0 1 -1 2.8274 7 1 -1 -1 0 4.5891 8 1 -1 0 0 1.4981 9 1 -1 1 0 5.4049 10 1 0 -1 0 2.0759 11 1 0 1 0 2.0759 12 1 -1 -1 1 4.4797 13 1 -1 0 1 2.1997 14 1 -1 1 1 6.0753 15 1 0 -1 1 2.8274 16 1 0 0 1 0.8470 17 1 0 1 1 4.6695 18 1 1 1 1 6.2203 19 1 1 0 1 2.4835 20 1 1 -1 1 5.6182 21 1 1 1 0 4.5891 22 1 1 0 0 1.4981 23 1 1 -1 0 5.4049 24 1 1 1 -1 4.4797 25 1 1 0 -1 2.1997 26 1 1 -1 -1 6.0753 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3651 atoms have been selected out of 3725 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1605 535 535 0.00 6 C006 has 474 158 158 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1674 558 558 0.00 12 C012 has 96 32 32 0.00 13 C013 has 495 165 165 0.00 14 C014 has 117 39 39 1.10 Total of13128 atoms and 4367 groups and 4361 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3725 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.24" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1230" Evaluating: 1230-7 Parameter: NUMWAT <- "1223" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1223" Comparing "1081" and "1223". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.24" Parameter: BOX -> "33.24" Parameter: BOX -> "33.24" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.24000 B = 33.24000 C = 33.24000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2186 2 1 -1 0 -1 2.4808 3 1 -1 1 -1 5.6148 4 1 0 -1 -1 4.6711 5 1 0 0 -1 0.8455 6 1 0 1 -1 2.8266 7 1 -1 -1 0 4.5864 8 1 -1 0 0 1.4963 9 1 -1 1 0 5.4030 10 1 0 -1 0 2.0739 11 1 0 1 0 2.0739 12 1 -1 -1 1 4.4766 13 1 -1 0 1 2.1987 14 1 -1 1 1 6.0726 15 1 0 -1 1 2.8266 16 1 0 0 1 0.8455 17 1 0 1 1 4.6711 18 1 1 1 1 6.2186 19 1 1 0 1 2.4808 20 1 1 -1 1 5.6148 21 1 1 1 0 4.5864 22 1 1 0 0 1.4963 23 1 1 -1 0 5.4030 24 1 1 1 -1 4.4766 25 1 1 0 -1 2.1987 26 1 1 -1 -1 6.0726 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3651 atoms have been selected out of 3725 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1605 535 535 0.00 6 C006 has 474 158 158 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1674 558 558 0.00 12 C012 has 96 32 32 0.00 13 C013 has 495 165 165 0.00 14 C014 has 117 39 39 1.10 Total of13128 atoms and 4367 groups and 4361 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3725 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.238" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1230" Evaluating: 1230-7 Parameter: NUMWAT <- "1223" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1223" Comparing "1081" and "1223". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.238" Parameter: BOX -> "33.238" Parameter: BOX -> "33.238" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.23800 B = 33.23800 C = 33.23800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2169 2 1 -1 0 -1 2.4781 3 1 -1 1 -1 5.6113 4 1 0 -1 -1 4.6727 5 1 0 0 -1 0.8439 6 1 0 1 -1 2.8258 7 1 -1 -1 0 4.5838 8 1 -1 0 0 1.4945 9 1 -1 1 0 5.4012 10 1 0 -1 0 2.0719 11 1 0 1 0 2.0719 12 1 -1 -1 1 4.4735 13 1 -1 0 1 2.1978 14 1 -1 1 1 6.0698 15 1 0 -1 1 2.8258 16 1 0 0 1 0.8439 17 1 0 1 1 4.6727 18 1 1 1 1 6.2169 19 1 1 0 1 2.4781 20 1 1 -1 1 5.6113 21 1 1 1 0 4.5838 22 1 1 0 0 1.4945 23 1 1 -1 0 5.4012 24 1 1 1 -1 4.4735 25 1 1 0 -1 2.1978 26 1 1 -1 -1 6.0698 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3651 atoms have been selected out of 3725 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1605 535 535 0.00 6 C006 has 474 158 158 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1674 558 558 0.00 12 C012 has 96 32 32 0.00 13 C013 has 495 165 165 0.00 14 C014 has 117 39 39 1.10 Total of13128 atoms and 4367 groups and 4361 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3725 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.236" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1230" Evaluating: 1230-7 Parameter: NUMWAT <- "1223" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1223" Comparing "1081" and "1223". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.236" Parameter: BOX -> "33.236" Parameter: BOX -> "33.236" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.23600 B = 33.23600 C = 33.23600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2152 2 1 -1 0 -1 2.4754 3 1 -1 1 -1 5.6079 4 1 0 -1 -1 4.6743 5 1 0 0 -1 0.8424 6 1 0 1 -1 2.8249 7 1 -1 -1 0 4.5811 8 1 -1 0 0 1.4927 9 1 -1 1 0 5.3993 10 1 0 -1 0 2.0699 11 1 0 1 0 2.0699 12 1 -1 -1 1 4.4704 13 1 -1 0 1 2.1968 14 1 -1 1 1 6.0671 15 1 0 -1 1 2.8249 16 1 0 0 1 0.8424 17 1 0 1 1 4.6743 18 1 1 1 1 6.2152 19 1 1 0 1 2.4754 20 1 1 -1 1 5.6079 21 1 1 1 0 4.5811 22 1 1 0 0 1.4927 23 1 1 -1 0 5.3993 24 1 1 1 -1 4.4704 25 1 1 0 -1 2.1968 26 1 1 -1 -1 6.0671 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3651 atoms have been selected out of 3725 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1608 536 536 0.00 6 C006 has 474 158 158 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1674 558 558 0.00 12 C012 has 96 32 32 0.00 13 C013 has 495 165 165 0.00 14 C014 has 117 39 39 1.10 Total of13131 atoms and 4368 groups and 4362 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3725 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.234" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1230" Evaluating: 1230-7 Parameter: NUMWAT <- "1223" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1223" Comparing "1081" and "1223". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.234" Parameter: BOX -> "33.234" Parameter: BOX -> "33.234" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.23400 B = 33.23400 C = 33.23400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2135 2 1 -1 0 -1 2.4727 3 1 -1 1 -1 5.6045 4 1 0 -1 -1 4.6759 5 1 0 0 -1 0.8408 6 1 0 1 -1 2.8241 7 1 -1 -1 0 4.5785 8 1 -1 0 0 1.4909 9 1 -1 1 0 5.3975 10 1 0 -1 0 2.0679 11 1 0 1 0 2.0679 12 1 -1 -1 1 4.4673 13 1 -1 0 1 2.1959 14 1 -1 1 1 6.0643 15 1 0 -1 1 2.8241 16 1 0 0 1 0.8408 17 1 0 1 1 4.6759 18 1 1 1 1 6.2135 19 1 1 0 1 2.4727 20 1 1 -1 1 5.6045 21 1 1 1 0 4.5785 22 1 1 0 0 1.4909 23 1 1 -1 0 5.3975 24 1 1 1 -1 4.4673 25 1 1 0 -1 2.1959 26 1 1 -1 -1 6.0643 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3651 atoms have been selected out of 3725 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1608 536 536 0.00 6 C006 has 474 158 158 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1680 560 560 0.00 12 C012 has 96 32 32 0.00 13 C013 has 495 165 165 0.00 14 C014 has 117 39 39 1.10 Total of13137 atoms and 4370 groups and 4364 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3725 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.232" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1230" Evaluating: 1230-7 Parameter: NUMWAT <- "1223" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1223" Comparing "1081" and "1223". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.232" Parameter: BOX -> "33.232" Parameter: BOX -> "33.232" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.23200 B = 33.23200 C = 33.23200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2118 2 1 -1 0 -1 2.4700 3 1 -1 1 -1 5.6010 4 1 0 -1 -1 4.6776 5 1 0 0 -1 0.8393 6 1 0 1 -1 2.8233 7 1 -1 -1 0 4.5758 8 1 -1 0 0 1.4891 9 1 -1 1 0 5.3956 10 1 0 -1 0 2.0659 11 1 0 1 0 2.0659 12 1 -1 -1 1 4.4643 13 1 -1 0 1 2.1950 14 1 -1 1 1 6.0616 15 1 0 -1 1 2.8233 16 1 0 0 1 0.8393 17 1 0 1 1 4.6776 18 1 1 1 1 6.2118 19 1 1 0 1 2.4700 20 1 1 -1 1 5.6010 21 1 1 1 0 4.5758 22 1 1 0 0 1.4891 23 1 1 -1 0 5.3956 24 1 1 1 -1 4.4643 25 1 1 0 -1 2.1950 26 1 1 -1 -1 6.0616 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3651 atoms have been selected out of 3725 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1608 536 536 0.00 6 C006 has 474 158 158 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1680 560 560 0.00 12 C012 has 96 32 32 0.00 13 C013 has 495 165 165 0.00 14 C014 has 117 39 39 1.09 Total of13140 atoms and 4371 groups and 4365 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3725 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.23" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1230" Evaluating: 1230-7 Parameter: NUMWAT <- "1223" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1223" Comparing "1081" and "1223". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.23" Parameter: BOX -> "33.23" Parameter: BOX -> "33.23" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.23000 B = 33.23000 C = 33.23000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2101 2 1 -1 0 -1 2.4673 3 1 -1 1 -1 5.5976 4 1 0 -1 -1 4.6792 5 1 0 0 -1 0.8377 6 1 0 1 -1 2.8225 7 1 -1 -1 0 4.5731 8 1 -1 0 0 1.4873 9 1 -1 1 0 5.3938 10 1 0 -1 0 2.0639 11 1 0 1 0 2.0639 12 1 -1 -1 1 4.4612 13 1 -1 0 1 2.1940 14 1 -1 1 1 6.0588 15 1 0 -1 1 2.8225 16 1 0 0 1 0.8377 17 1 0 1 1 4.6792 18 1 1 1 1 6.2101 19 1 1 0 1 2.4673 20 1 1 -1 1 5.5976 21 1 1 1 0 4.5731 22 1 1 0 0 1.4873 23 1 1 -1 0 5.3938 24 1 1 1 -1 4.4612 25 1 1 0 -1 2.1940 26 1 1 -1 -1 6.0588 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3651 atoms have been selected out of 3725 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1608 536 536 0.00 6 C006 has 474 158 158 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1680 560 560 0.00 12 C012 has 96 32 32 0.00 13 C013 has 498 166 166 0.00 14 C014 has 117 39 39 1.09 Total of13143 atoms and 4372 groups and 4366 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3725 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.228" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1230" Evaluating: 1230-7 Parameter: NUMWAT <- "1223" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1223" Comparing "1081" and "1223". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.228" Parameter: BOX -> "33.228" Parameter: BOX -> "33.228" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.22800 B = 33.22800 C = 33.22800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2084 2 1 -1 0 -1 2.4646 3 1 -1 1 -1 5.5942 4 1 0 -1 -1 4.6808 5 1 0 0 -1 0.8362 6 1 0 1 -1 2.8217 7 1 -1 -1 0 4.5705 8 1 -1 0 0 1.4855 9 1 -1 1 0 5.3919 10 1 0 -1 0 2.0619 11 1 0 1 0 2.0619 12 1 -1 -1 1 4.4581 13 1 -1 0 1 2.1931 14 1 -1 1 1 6.0561 15 1 0 -1 1 2.8217 16 1 0 0 1 0.8362 17 1 0 1 1 4.6808 18 1 1 1 1 6.2084 19 1 1 0 1 2.4646 20 1 1 -1 1 5.5942 21 1 1 1 0 4.5705 22 1 1 0 0 1.4855 23 1 1 -1 0 5.3919 24 1 1 1 -1 4.4581 25 1 1 0 -1 2.1931 26 1 1 -1 -1 6.0561 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3651 atoms have been selected out of 3725 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1608 536 536 0.00 6 C006 has 474 158 158 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1680 560 560 0.00 12 C012 has 96 32 32 0.00 13 C013 has 498 166 166 0.00 14 C014 has 117 39 39 1.09 Total of13146 atoms and 4373 groups and 4367 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3725 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.226" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1230" Evaluating: 1230-7 Parameter: NUMWAT <- "1223" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1223" Comparing "1081" and "1223". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.226" Parameter: BOX -> "33.226" Parameter: BOX -> "33.226" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.22600 B = 33.22600 C = 33.22600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2068 2 1 -1 0 -1 2.4620 3 1 -1 1 -1 5.5907 4 1 0 -1 -1 4.6824 5 1 0 0 -1 0.8346 6 1 0 1 -1 2.8208 7 1 -1 -1 0 4.5678 8 1 -1 0 0 1.4836 9 1 -1 1 0 5.3901 10 1 0 -1 0 2.0599 11 1 0 1 0 2.0599 12 1 -1 -1 1 4.4550 13 1 -1 0 1 2.1922 14 1 -1 1 1 6.0533 15 1 0 -1 1 2.8208 16 1 0 0 1 0.8346 17 1 0 1 1 4.6824 18 1 1 1 1 6.2068 19 1 1 0 1 2.4620 20 1 1 -1 1 5.5907 21 1 1 1 0 4.5678 22 1 1 0 0 1.4836 23 1 1 -1 0 5.3901 24 1 1 1 -1 4.4550 25 1 1 0 -1 2.1922 26 1 1 -1 -1 6.0533 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3651 atoms have been selected out of 3725 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1608 536 536 0.00 6 C006 has 474 158 158 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1765 586 585 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1680 560 560 0.00 12 C012 has 96 32 32 0.00 13 C013 has 498 166 166 0.00 14 C014 has 117 39 39 1.09 Total of13146 atoms and 4373 groups and 4367 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3725 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.224" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1230" Evaluating: 1230-7 Parameter: NUMWAT <- "1223" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1223" Comparing "1081" and "1223". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.224" Parameter: BOX -> "33.224" Parameter: BOX -> "33.224" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.22400 B = 33.22400 C = 33.22400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2051 2 1 -1 0 -1 2.4593 3 1 -1 1 -1 5.5873 4 1 0 -1 -1 4.6840 5 1 0 0 -1 0.8331 6 1 0 1 -1 2.8200 7 1 -1 -1 0 4.5652 8 1 -1 0 0 1.4818 9 1 -1 1 0 5.3882 10 1 0 -1 0 2.0579 11 1 0 1 0 2.0579 12 1 -1 -1 1 4.4519 13 1 -1 0 1 2.1912 14 1 -1 1 1 6.0506 15 1 0 -1 1 2.8200 16 1 0 0 1 0.8331 17 1 0 1 1 4.6840 18 1 1 1 1 6.2051 19 1 1 0 1 2.4593 20 1 1 -1 1 5.5873 21 1 1 1 0 4.5652 22 1 1 0 0 1.4818 23 1 1 -1 0 5.3882 24 1 1 1 -1 4.4519 25 1 1 0 -1 2.1912 26 1 1 -1 -1 6.0506 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3651 atoms have been selected out of 3725 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1608 536 536 0.00 6 C006 has 474 158 158 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1680 560 560 0.00 12 C012 has 96 32 32 0.00 13 C013 has 498 166 166 0.00 14 C014 has 117 39 39 1.09 Total of13152 atoms and 4375 groups and 4369 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3725 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.222" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1230" Evaluating: 1230-7 Parameter: NUMWAT <- "1223" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1223" Comparing "1081" and "1223". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.222" Parameter: BOX -> "33.222" Parameter: BOX -> "33.222" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.22200 B = 33.22200 C = 33.22200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2034 2 1 -1 0 -1 2.4566 3 1 -1 1 -1 5.5839 4 1 0 -1 -1 4.6857 5 1 0 0 -1 0.8315 6 1 0 1 -1 2.8192 7 1 -1 -1 0 4.5625 8 1 -1 0 0 1.4800 9 1 -1 1 0 5.3864 10 1 0 -1 0 2.0559 11 1 0 1 0 2.0559 12 1 -1 -1 1 4.4489 13 1 -1 0 1 2.1903 14 1 -1 1 1 6.0478 15 1 0 -1 1 2.8192 16 1 0 0 1 0.8315 17 1 0 1 1 4.6857 18 1 1 1 1 6.2034 19 1 1 0 1 2.4566 20 1 1 -1 1 5.5839 21 1 1 1 0 4.5625 22 1 1 0 0 1.4800 23 1 1 -1 0 5.3864 24 1 1 1 -1 4.4489 25 1 1 0 -1 2.1903 26 1 1 -1 -1 6.0478 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3651 atoms have been selected out of 3725 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1608 536 536 0.00 6 C006 has 474 158 158 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1680 560 560 0.00 12 C012 has 96 32 32 0.00 13 C013 has 498 166 166 0.00 14 C014 has 117 39 39 1.08 Total of13152 atoms and 4375 groups and 4369 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3725 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.22" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1230" Evaluating: 1230-7 Parameter: NUMWAT <- "1223" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1223" Comparing "1081" and "1223". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.22" Parameter: BOX -> "33.22" Parameter: BOX -> "33.22" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.22000 B = 33.22000 C = 33.22000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2017 2 1 -1 0 -1 2.4539 3 1 -1 1 -1 5.5804 4 1 0 -1 -1 4.6873 5 1 0 0 -1 0.8300 6 1 0 1 -1 2.8184 7 1 -1 -1 0 4.5598 8 1 -1 0 0 1.4782 9 1 -1 1 0 5.3845 10 1 0 -1 0 2.0539 11 1 0 1 0 2.0539 12 1 -1 -1 1 4.4458 13 1 -1 0 1 2.1894 14 1 -1 1 1 6.0451 15 1 0 -1 1 2.8184 16 1 0 0 1 0.8300 17 1 0 1 1 4.6873 18 1 1 1 1 6.2017 19 1 1 0 1 2.4539 20 1 1 -1 1 5.5804 21 1 1 1 0 4.5598 22 1 1 0 0 1.4782 23 1 1 -1 0 5.3845 24 1 1 1 -1 4.4458 25 1 1 0 -1 2.1894 26 1 1 -1 -1 6.0451 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3651 atoms have been selected out of 3725 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1608 536 536 0.00 6 C006 has 477 159 159 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1680 560 560 0.00 12 C012 has 96 32 32 0.00 13 C013 has 498 166 166 0.00 14 C014 has 117 39 39 1.08 Total of13158 atoms and 4377 groups and 4371 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3725 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.218" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1230" Evaluating: 1230-7 Parameter: NUMWAT <- "1223" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1223" Comparing "1081" and "1223". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.218" Parameter: BOX -> "33.218" Parameter: BOX -> "33.218" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.21800 B = 33.21800 C = 33.21800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.2000 2 1 -1 0 -1 2.4512 3 1 -1 1 -1 5.5770 4 1 0 -1 -1 4.6889 5 1 0 0 -1 0.8285 6 1 0 1 -1 2.8176 7 1 -1 -1 0 4.5572 8 1 -1 0 0 1.4764 9 1 -1 1 0 5.3827 10 1 0 -1 0 2.0519 11 1 0 1 0 2.0519 12 1 -1 -1 1 4.4427 13 1 -1 0 1 2.1885 14 1 -1 1 1 6.0423 15 1 0 -1 1 2.8176 16 1 0 0 1 0.8285 17 1 0 1 1 4.6889 18 1 1 1 1 6.2000 19 1 1 0 1 2.4512 20 1 1 -1 1 5.5770 21 1 1 1 0 4.5572 22 1 1 0 0 1.4764 23 1 1 -1 0 5.3827 24 1 1 1 -1 4.4427 25 1 1 0 -1 2.1885 26 1 1 -1 -1 6.0423 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3651 atoms have been selected out of 3725 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1608 536 536 0.00 6 C006 has 477 159 159 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1680 560 560 0.00 12 C012 has 96 32 32 0.00 13 C013 has 498 166 166 0.00 14 C014 has 117 39 39 1.08 Total of13158 atoms and 4377 groups and 4371 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3725 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1230 Number of atoms = 3725 Number of groups = 1235 Number of bonds = 3718 Number of angles = 1334 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1232 Number of HB donors = 2442 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.216" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1230" Evaluating: 1230-7 Parameter: NUMWAT <- "1223" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1223" Comparing "1081" and "1223". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.216" Parameter: BOX -> "33.216" Parameter: BOX -> "33.216" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.21600 B = 33.21600 C = 33.21600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1984 2 1 -1 0 -1 2.4485 3 1 -1 1 -1 5.5736 4 1 0 -1 -1 4.6905 5 1 0 0 -1 0.8269 6 1 0 1 -1 2.8168 7 1 -1 -1 0 4.5545 8 1 -1 0 0 1.4746 9 1 -1 1 0 5.3808 10 1 0 -1 0 2.0499 11 1 0 1 0 2.0499 12 1 -1 -1 1 4.4396 13 1 -1 0 1 2.1876 14 1 -1 1 1 6.0396 15 1 0 -1 1 2.8168 16 1 0 0 1 0.8269 17 1 0 1 1 4.6905 18 1 1 1 1 6.1984 19 1 1 0 1 2.4485 20 1 1 -1 1 5.5736 21 1 1 1 0 4.5545 22 1 1 0 0 1.4746 23 1 1 -1 0 5.3808 24 1 1 1 -1 4.4396 25 1 1 0 -1 2.1876 26 1 1 -1 -1 6.0396 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3651 atoms have been selected out of 3725 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 657 OPERATED ON BY TRANSFORMATION C005 RESIDUE 964 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 753 251 251 0.00 3 C003 has 129 43 43 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1602 534 534 0.00 6 C006 has 486 162 162 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1680 560 560 0.00 12 C012 has 87 29 29 0.00 13 C013 has 492 164 164 0.00 14 C014 has 105 35 35 1.08 Total of13155 atoms and 4376 groups and 4370 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3725 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1228 Number of atoms = 3719 Number of groups = 1233 Number of bonds = 3712 Number of angles = 1332 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1230 Number of HB donors = 2438 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1228 Number of atoms = 3719 Number of groups = 1233 Number of bonds = 3712 Number of angles = 1332 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1230 Number of HB donors = 2438 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.214" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1228" Evaluating: 1228-7 Parameter: NUMWAT <- "1221" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1221" Comparing "1081" and "1221". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.214" Parameter: BOX -> "33.214" Parameter: BOX -> "33.214" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.21400 B = 33.21400 C = 33.21400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1967 2 1 -1 0 -1 2.4458 3 1 -1 1 -1 5.5701 4 1 0 -1 -1 4.8337 5 1 0 0 -1 0.8254 6 1 0 1 -1 2.8160 7 1 -1 -1 0 5.1687 8 1 -1 0 0 1.4728 9 1 -1 1 0 5.1976 10 1 0 -1 0 2.0479 11 1 0 1 0 2.0479 12 1 -1 -1 1 6.1583 13 1 -1 0 1 2.1867 14 1 -1 1 1 6.8772 15 1 0 -1 1 2.8160 16 1 0 0 1 0.8254 17 1 0 1 1 4.8337 18 1 1 1 1 6.1967 19 1 1 0 1 2.4458 20 1 1 -1 1 5.5701 21 1 1 1 0 5.1687 22 1 1 0 0 1.4728 23 1 1 -1 0 5.1976 24 1 1 1 -1 6.1583 25 1 1 0 -1 2.1867 26 1 1 -1 -1 6.8772 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3645 atoms have been selected out of 3719 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1602 534 534 0.00 6 C006 has 474 158 158 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1677 559 559 0.00 12 C012 has 87 29 29 0.00 13 C013 has 492 164 164 0.00 14 C014 has 105 35 35 1.08 Total of13116 atoms and 4363 groups and 4357 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3719 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1228 Number of atoms = 3719 Number of groups = 1233 Number of bonds = 3712 Number of angles = 1332 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1230 Number of HB donors = 2438 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1228 Number of atoms = 3719 Number of groups = 1233 Number of bonds = 3712 Number of angles = 1332 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1230 Number of HB donors = 2438 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.212" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1228" Evaluating: 1228-7 Parameter: NUMWAT <- "1221" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1221" Comparing "1081" and "1221". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.212" Parameter: BOX -> "33.212" Parameter: BOX -> "33.212" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.21200 B = 33.21200 C = 33.21200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1950 2 1 -1 0 -1 2.4432 3 1 -1 1 -1 5.5667 4 1 0 -1 -1 4.8339 5 1 0 0 -1 0.8239 6 1 0 1 -1 2.8152 7 1 -1 -1 0 5.1667 8 1 -1 0 0 1.4710 9 1 -1 1 0 5.1950 10 1 0 -1 0 2.0459 11 1 0 1 0 2.0459 12 1 -1 -1 1 6.1554 13 1 -1 0 1 2.1858 14 1 -1 1 1 6.8741 15 1 0 -1 1 2.8152 16 1 0 0 1 0.8239 17 1 0 1 1 4.8339 18 1 1 1 1 6.1950 19 1 1 0 1 2.4432 20 1 1 -1 1 5.5667 21 1 1 1 0 5.1667 22 1 1 0 0 1.4710 23 1 1 -1 0 5.1950 24 1 1 1 -1 6.1554 25 1 1 0 -1 2.1858 26 1 1 -1 -1 6.8741 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3645 atoms have been selected out of 3719 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1605 535 535 0.00 6 C006 has 474 158 158 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1677 559 559 0.00 12 C012 has 87 29 29 0.00 13 C013 has 492 164 164 0.00 14 C014 has 105 35 35 1.07 Total of13119 atoms and 4364 groups and 4358 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3719 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1228 Number of atoms = 3719 Number of groups = 1233 Number of bonds = 3712 Number of angles = 1332 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1230 Number of HB donors = 2438 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1228 Number of atoms = 3719 Number of groups = 1233 Number of bonds = 3712 Number of angles = 1332 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1230 Number of HB donors = 2438 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.21" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1228" Evaluating: 1228-7 Parameter: NUMWAT <- "1221" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1221" Comparing "1081" and "1221". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.21" Parameter: BOX -> "33.21" Parameter: BOX -> "33.21" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.21000 B = 33.21000 C = 33.21000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1933 2 1 -1 0 -1 2.4405 3 1 -1 1 -1 5.5633 4 1 0 -1 -1 4.8342 5 1 0 0 -1 0.8224 6 1 0 1 -1 2.8144 7 1 -1 -1 0 5.1646 8 1 -1 0 0 1.4692 9 1 -1 1 0 5.1925 10 1 0 -1 0 2.0439 11 1 0 1 0 2.0439 12 1 -1 -1 1 6.1525 13 1 -1 0 1 2.1849 14 1 -1 1 1 6.8711 15 1 0 -1 1 2.8144 16 1 0 0 1 0.8224 17 1 0 1 1 4.8342 18 1 1 1 1 6.1933 19 1 1 0 1 2.4405 20 1 1 -1 1 5.5633 21 1 1 1 0 5.1646 22 1 1 0 0 1.4692 23 1 1 -1 0 5.1925 24 1 1 1 -1 6.1525 25 1 1 0 -1 2.1849 26 1 1 -1 -1 6.8711 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3645 atoms have been selected out of 3719 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 331 OPERATED ON BY TRANSFORMATION C010 RESIDUE 558 OPERATED ON BY TRANSFORMATION C016 RESIDUE 928 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 759 253 253 0.00 3 C003 has 108 36 36 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 87 29 29 0.00 13 C013 has 492 164 164 0.00 14 C014 has 105 35 35 1.07 Total of13095 atoms and 4356 groups and 4350 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 9 atoms have been selected out of 3719 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 3 residues deleted. DELTIC: 9 bonds deleted DELTIC: 3 angles deleted DELTIC: 6 donors deleted DELTIC: 3 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.208" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1225" Evaluating: 1225-7 Parameter: NUMWAT <- "1218" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1218" Comparing "1081" and "1218". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.208" Parameter: BOX -> "33.208" Parameter: BOX -> "33.208" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.20800 B = 33.20800 C = 33.20800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1917 2 1 -1 0 -1 2.4378 3 1 -1 1 -1 5.5598 4 1 0 -1 -1 4.8344 5 1 0 0 -1 1.3278 6 1 0 1 -1 2.3785 7 1 -1 -1 0 5.1626 8 1 -1 0 0 1.4674 9 1 -1 1 0 5.1899 10 1 0 -1 0 1.1925 11 1 0 1 0 1.1925 12 1 -1 -1 1 6.1496 13 1 -1 0 1 2.1840 14 1 -1 1 1 6.8680 15 1 0 -1 1 2.3785 16 1 0 0 1 1.3278 17 1 0 1 1 4.8344 18 1 1 1 1 6.1917 19 1 1 0 1 2.4378 20 1 1 -1 1 5.5598 21 1 1 1 0 5.1626 22 1 1 0 0 1.4674 23 1 1 -1 0 5.1899 24 1 1 1 -1 6.1496 25 1 1 0 -1 2.1840 26 1 1 -1 -1 6.8680 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3636 atoms have been selected out of 3710 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 441 147 147 0.00 2 C002 has 756 252 252 0.00 3 C003 has 108 36 36 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 450 150 150 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1668 556 556 0.00 12 C012 has 90 30 30 0.00 13 C013 has 492 164 164 0.00 14 C014 has 108 36 36 1.07 Total of13056 atoms and 4343 groups and 4337 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3710 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.206" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1225" Evaluating: 1225-7 Parameter: NUMWAT <- "1218" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1218" Comparing "1081" and "1218". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.206" Parameter: BOX -> "33.206" Parameter: BOX -> "33.206" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.20600 B = 33.20600 C = 33.20600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1900 2 1 -1 0 -1 2.4351 3 1 -1 1 -1 5.5564 4 1 0 -1 -1 4.8346 5 1 0 0 -1 1.3259 6 1 0 1 -1 2.3758 7 1 -1 -1 0 5.1606 8 1 -1 0 0 1.4656 9 1 -1 1 0 5.1874 10 1 0 -1 0 1.1906 11 1 0 1 0 1.1906 12 1 -1 -1 1 6.1467 13 1 -1 0 1 2.1831 14 1 -1 1 1 6.8649 15 1 0 -1 1 2.3758 16 1 0 0 1 1.3259 17 1 0 1 1 4.8346 18 1 1 1 1 6.1900 19 1 1 0 1 2.4351 20 1 1 -1 1 5.5564 21 1 1 1 0 5.1606 22 1 1 0 0 1.4656 23 1 1 -1 0 5.1874 24 1 1 1 -1 6.1467 25 1 1 0 -1 2.1831 26 1 1 -1 -1 6.8649 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3636 atoms have been selected out of 3710 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 441 147 147 0.00 2 C002 has 756 252 252 0.00 3 C003 has 108 36 36 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 450 150 150 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1668 556 556 0.00 12 C012 has 90 30 30 0.00 13 C013 has 492 164 164 0.00 14 C014 has 108 36 36 1.07 Total of13056 atoms and 4343 groups and 4337 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3710 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.204" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1225" Evaluating: 1225-7 Parameter: NUMWAT <- "1218" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1218" Comparing "1081" and "1218". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.204" Parameter: BOX -> "33.204" Parameter: BOX -> "33.204" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.20400 B = 33.20400 C = 33.20400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1883 2 1 -1 0 -1 2.4324 3 1 -1 1 -1 5.5530 4 1 0 -1 -1 4.8348 5 1 0 0 -1 1.3241 6 1 0 1 -1 2.3731 7 1 -1 -1 0 5.1586 8 1 -1 0 0 1.4638 9 1 -1 1 0 5.1848 10 1 0 -1 0 1.1887 11 1 0 1 0 1.1887 12 1 -1 -1 1 6.1438 13 1 -1 0 1 2.1822 14 1 -1 1 1 6.8619 15 1 0 -1 1 2.3731 16 1 0 0 1 1.3241 17 1 0 1 1 4.8348 18 1 1 1 1 6.1883 19 1 1 0 1 2.4324 20 1 1 -1 1 5.5530 21 1 1 1 0 5.1586 22 1 1 0 0 1.4638 23 1 1 -1 0 5.1848 24 1 1 1 -1 6.1438 25 1 1 0 -1 2.1822 26 1 1 -1 -1 6.8619 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3636 atoms have been selected out of 3710 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 441 147 147 0.00 2 C002 has 756 252 252 0.00 3 C003 has 108 36 36 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 450 150 150 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1668 556 556 0.00 12 C012 has 90 30 30 0.00 13 C013 has 492 164 164 0.00 14 C014 has 108 36 36 1.07 Total of13056 atoms and 4343 groups and 4337 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3710 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.202" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1225" Evaluating: 1225-7 Parameter: NUMWAT <- "1218" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1218" Comparing "1081" and "1218". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.202" Parameter: BOX -> "33.202" Parameter: BOX -> "33.202" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.20200 B = 33.20200 C = 33.20200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1867 2 1 -1 0 -1 2.4297 3 1 -1 1 -1 5.5495 4 1 0 -1 -1 4.8351 5 1 0 0 -1 1.3222 6 1 0 1 -1 2.3704 7 1 -1 -1 0 5.1566 8 1 -1 0 0 1.4620 9 1 -1 1 0 5.1823 10 1 0 -1 0 1.1868 11 1 0 1 0 1.1868 12 1 -1 -1 1 6.1408 13 1 -1 0 1 2.1813 14 1 -1 1 1 6.8588 15 1 0 -1 1 2.3704 16 1 0 0 1 1.3222 17 1 0 1 1 4.8351 18 1 1 1 1 6.1867 19 1 1 0 1 2.4297 20 1 1 -1 1 5.5495 21 1 1 1 0 5.1566 22 1 1 0 0 1.4620 23 1 1 -1 0 5.1823 24 1 1 1 -1 6.1408 25 1 1 0 -1 2.1813 26 1 1 -1 -1 6.8588 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3636 atoms have been selected out of 3710 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 756 252 252 0.00 3 C003 has 108 36 36 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 90 30 30 0.00 13 C013 has 495 165 165 0.00 14 C014 has 108 36 36 1.06 Total of13071 atoms and 4348 groups and 4342 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3710 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.2" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1225" Evaluating: 1225-7 Parameter: NUMWAT <- "1218" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1218" Comparing "1081" and "1218". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.2" Parameter: BOX -> "33.2" Parameter: BOX -> "33.2" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.20000 B = 33.20000 C = 33.20000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1850 2 1 -1 0 -1 2.4270 3 1 -1 1 -1 5.5461 4 1 0 -1 -1 4.8353 5 1 0 0 -1 1.3204 6 1 0 1 -1 2.3677 7 1 -1 -1 0 5.1545 8 1 -1 0 0 1.4602 9 1 -1 1 0 5.1797 10 1 0 -1 0 1.1849 11 1 0 1 0 1.1849 12 1 -1 -1 1 6.1379 13 1 -1 0 1 2.1804 14 1 -1 1 1 6.8557 15 1 0 -1 1 2.3677 16 1 0 0 1 1.3204 17 1 0 1 1 4.8353 18 1 1 1 1 6.1850 19 1 1 0 1 2.4270 20 1 1 -1 1 5.5461 21 1 1 1 0 5.1545 22 1 1 0 0 1.4602 23 1 1 -1 0 5.1797 24 1 1 1 -1 6.1379 25 1 1 0 -1 2.1804 26 1 1 -1 -1 6.8557 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3636 atoms have been selected out of 3710 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 756 252 252 0.00 3 C003 has 108 36 36 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 90 30 30 0.00 13 C013 has 495 165 165 0.00 14 C014 has 108 36 36 1.06 Total of13071 atoms and 4348 groups and 4342 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3710 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.198" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1225" Evaluating: 1225-7 Parameter: NUMWAT <- "1218" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1218" Comparing "1081" and "1218". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.198" Parameter: BOX -> "33.198" Parameter: BOX -> "33.198" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.19800 B = 33.19800 C = 33.19800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1834 2 1 -1 0 -1 2.4244 3 1 -1 1 -1 5.5427 4 1 0 -1 -1 4.8355 5 1 0 0 -1 1.3185 6 1 0 1 -1 2.3650 7 1 -1 -1 0 5.1525 8 1 -1 0 0 1.4584 9 1 -1 1 0 5.1772 10 1 0 -1 0 1.1829 11 1 0 1 0 1.1829 12 1 -1 -1 1 6.1350 13 1 -1 0 1 2.1795 14 1 -1 1 1 6.8527 15 1 0 -1 1 2.3650 16 1 0 0 1 1.3185 17 1 0 1 1 4.8355 18 1 1 1 1 6.1834 19 1 1 0 1 2.4244 20 1 1 -1 1 5.5427 21 1 1 1 0 5.1525 22 1 1 0 0 1.4584 23 1 1 -1 0 5.1772 24 1 1 1 -1 6.1350 25 1 1 0 -1 2.1795 26 1 1 -1 -1 6.8527 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3636 atoms have been selected out of 3710 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 756 252 252 0.00 3 C003 has 108 36 36 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 90 30 30 0.00 13 C013 has 495 165 165 0.00 14 C014 has 108 36 36 1.06 Total of13071 atoms and 4348 groups and 4342 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3710 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.196" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1225" Evaluating: 1225-7 Parameter: NUMWAT <- "1218" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1218" Comparing "1081" and "1218". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.196" Parameter: BOX -> "33.196" Parameter: BOX -> "33.196" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.19600 B = 33.19600 C = 33.19600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1817 2 1 -1 0 -1 2.4217 3 1 -1 1 -1 5.5392 4 1 0 -1 -1 4.8358 5 1 0 0 -1 1.3167 6 1 0 1 -1 2.3623 7 1 -1 -1 0 5.1505 8 1 -1 0 0 1.4566 9 1 -1 1 0 5.1746 10 1 0 -1 0 1.1810 11 1 0 1 0 1.1810 12 1 -1 -1 1 6.1321 13 1 -1 0 1 2.1786 14 1 -1 1 1 6.8496 15 1 0 -1 1 2.3623 16 1 0 0 1 1.3167 17 1 0 1 1 4.8358 18 1 1 1 1 6.1817 19 1 1 0 1 2.4217 20 1 1 -1 1 5.5392 21 1 1 1 0 5.1505 22 1 1 0 0 1.4566 23 1 1 -1 0 5.1746 24 1 1 1 -1 6.1321 25 1 1 0 -1 2.1786 26 1 1 -1 -1 6.8496 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3636 atoms have been selected out of 3710 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 756 252 252 0.00 3 C003 has 108 36 36 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.06 Total of13074 atoms and 4349 groups and 4343 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3710 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.194" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1225" Evaluating: 1225-7 Parameter: NUMWAT <- "1218" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1218" Comparing "1081" and "1218". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.194" Parameter: BOX -> "33.194" Parameter: BOX -> "33.194" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.19400 B = 33.19400 C = 33.19400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1800 2 1 -1 0 -1 2.4190 3 1 -1 1 -1 5.5358 4 1 0 -1 -1 4.8360 5 1 0 0 -1 1.3148 6 1 0 1 -1 2.3596 7 1 -1 -1 0 5.1485 8 1 -1 0 0 1.4548 9 1 -1 1 0 5.1721 10 1 0 -1 0 1.1791 11 1 0 1 0 1.1791 12 1 -1 -1 1 6.1292 13 1 -1 0 1 2.1778 14 1 -1 1 1 6.8466 15 1 0 -1 1 2.3596 16 1 0 0 1 1.3148 17 1 0 1 1 4.8360 18 1 1 1 1 6.1800 19 1 1 0 1 2.4190 20 1 1 -1 1 5.5358 21 1 1 1 0 5.1485 22 1 1 0 0 1.4548 23 1 1 -1 0 5.1721 24 1 1 1 -1 6.1292 25 1 1 0 -1 2.1778 26 1 1 -1 -1 6.8466 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3636 atoms have been selected out of 3710 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 756 252 252 0.00 3 C003 has 108 36 36 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.06 Total of13077 atoms and 4350 groups and 4344 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3710 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.192" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1225" Evaluating: 1225-7 Parameter: NUMWAT <- "1218" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1218" Comparing "1081" and "1218". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.192" Parameter: BOX -> "33.192" Parameter: BOX -> "33.192" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.19200 B = 33.19200 C = 33.19200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1784 2 1 -1 0 -1 2.4163 3 1 -1 1 -1 5.5324 4 1 0 -1 -1 4.8362 5 1 0 0 -1 1.3130 6 1 0 1 -1 2.3570 7 1 -1 -1 0 5.1465 8 1 -1 0 0 1.4530 9 1 -1 1 0 5.1695 10 1 0 -1 0 1.1772 11 1 0 1 0 1.1772 12 1 -1 -1 1 6.1263 13 1 -1 0 1 2.1759 14 1 -1 1 1 6.8435 15 1 0 -1 1 2.3570 16 1 0 0 1 1.3130 17 1 0 1 1 4.8362 18 1 1 1 1 6.1784 19 1 1 0 1 2.4163 20 1 1 -1 1 5.5324 21 1 1 1 0 5.1465 22 1 1 0 0 1.4530 23 1 1 -1 0 5.1695 24 1 1 1 -1 6.1263 25 1 1 0 -1 2.1759 26 1 1 -1 -1 6.8435 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3636 atoms have been selected out of 3710 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 756 252 252 0.00 3 C003 has 108 36 36 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.05 Total of13080 atoms and 4351 groups and 4345 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3710 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.19" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1225" Evaluating: 1225-7 Parameter: NUMWAT <- "1218" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1218" Comparing "1081" and "1218". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.19" Parameter: BOX -> "33.19" Parameter: BOX -> "33.19" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.19000 B = 33.19000 C = 33.19000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1767 2 1 -1 0 -1 2.4136 3 1 -1 1 -1 5.5289 4 1 0 -1 -1 4.8365 5 1 0 0 -1 1.3112 6 1 0 1 -1 2.3543 7 1 -1 -1 0 5.1445 8 1 -1 0 0 1.4512 9 1 -1 1 0 5.1670 10 1 0 -1 0 1.1753 11 1 0 1 0 1.1753 12 1 -1 -1 1 6.1234 13 1 -1 0 1 2.1735 14 1 -1 1 1 6.8404 15 1 0 -1 1 2.3543 16 1 0 0 1 1.3112 17 1 0 1 1 4.8365 18 1 1 1 1 6.1767 19 1 1 0 1 2.4136 20 1 1 -1 1 5.5289 21 1 1 1 0 5.1445 22 1 1 0 0 1.4512 23 1 1 -1 0 5.1670 24 1 1 1 -1 6.1234 25 1 1 0 -1 2.1735 26 1 1 -1 -1 6.8404 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3636 atoms have been selected out of 3710 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.05 Total of13089 atoms and 4354 groups and 4348 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3710 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.188" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1225" Evaluating: 1225-7 Parameter: NUMWAT <- "1218" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1218" Comparing "1081" and "1218". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.188" Parameter: BOX -> "33.188" Parameter: BOX -> "33.188" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.18800 B = 33.18800 C = 33.18800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1751 2 1 -1 0 -1 2.4109 3 1 -1 1 -1 5.5255 4 1 0 -1 -1 4.8367 5 1 0 0 -1 1.3093 6 1 0 1 -1 2.3516 7 1 -1 -1 0 5.1425 8 1 -1 0 0 1.4494 9 1 -1 1 0 5.1644 10 1 0 -1 0 1.1734 11 1 0 1 0 1.1734 12 1 -1 -1 1 6.1204 13 1 -1 0 1 2.1711 14 1 -1 1 1 6.8374 15 1 0 -1 1 2.3516 16 1 0 0 1 1.3093 17 1 0 1 1 4.8367 18 1 1 1 1 6.1751 19 1 1 0 1 2.4109 20 1 1 -1 1 5.5255 21 1 1 1 0 5.1425 22 1 1 0 0 1.4494 23 1 1 -1 0 5.1644 24 1 1 1 -1 6.1204 25 1 1 0 -1 2.1711 26 1 1 -1 -1 6.8374 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3636 atoms have been selected out of 3710 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.05 Total of13089 atoms and 4354 groups and 4348 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3710 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.186" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1225" Evaluating: 1225-7 Parameter: NUMWAT <- "1218" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1218" Comparing "1081" and "1218". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.186" Parameter: BOX -> "33.186" Parameter: BOX -> "33.186" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.18600 B = 33.18600 C = 33.18600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1734 2 1 -1 0 -1 2.4083 3 1 -1 1 -1 5.5221 4 1 0 -1 -1 4.8370 5 1 0 0 -1 1.3075 6 1 0 1 -1 2.3489 7 1 -1 -1 0 5.1404 8 1 -1 0 0 1.4476 9 1 -1 1 0 5.1619 10 1 0 -1 0 1.1714 11 1 0 1 0 1.1714 12 1 -1 -1 1 6.1175 13 1 -1 0 1 2.1687 14 1 -1 1 1 6.8343 15 1 0 -1 1 2.3489 16 1 0 0 1 1.3075 17 1 0 1 1 4.8370 18 1 1 1 1 6.1734 19 1 1 0 1 2.4083 20 1 1 -1 1 5.5221 21 1 1 1 0 5.1404 22 1 1 0 0 1.4476 23 1 1 -1 0 5.1619 24 1 1 1 -1 6.1175 25 1 1 0 -1 2.1687 26 1 1 -1 -1 6.8343 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3636 atoms have been selected out of 3710 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.05 Total of13089 atoms and 4354 groups and 4348 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3710 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.184" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1225" Evaluating: 1225-7 Parameter: NUMWAT <- "1218" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1218" Comparing "1081" and "1218". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.184" Parameter: BOX -> "33.184" Parameter: BOX -> "33.184" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.18400 B = 33.18400 C = 33.18400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1718 2 1 -1 0 -1 2.4056 3 1 -1 1 -1 5.5186 4 1 0 -1 -1 4.8372 5 1 0 0 -1 1.3056 6 1 0 1 -1 2.3462 7 1 -1 -1 0 5.1384 8 1 -1 0 0 1.4458 9 1 -1 1 0 5.1593 10 1 0 -1 0 1.1695 11 1 0 1 0 1.1695 12 1 -1 -1 1 6.1146 13 1 -1 0 1 2.1663 14 1 -1 1 1 6.8313 15 1 0 -1 1 2.3462 16 1 0 0 1 1.3056 17 1 0 1 1 4.8372 18 1 1 1 1 6.1718 19 1 1 0 1 2.4056 20 1 1 -1 1 5.5186 21 1 1 1 0 5.1384 22 1 1 0 0 1.4458 23 1 1 -1 0 5.1593 24 1 1 1 -1 6.1146 25 1 1 0 -1 2.1663 26 1 1 -1 -1 6.8313 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3636 atoms have been selected out of 3710 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.05 Total of13089 atoms and 4354 groups and 4348 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3710 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.182" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1225" Evaluating: 1225-7 Parameter: NUMWAT <- "1218" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1218" Comparing "1081" and "1218". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.182" Parameter: BOX -> "33.182" Parameter: BOX -> "33.182" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.18200 B = 33.18200 C = 33.18200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1701 2 1 -1 0 -1 2.4029 3 1 -1 1 -1 5.5152 4 1 0 -1 -1 4.8374 5 1 0 0 -1 1.3038 6 1 0 1 -1 2.3435 7 1 -1 -1 0 5.1364 8 1 -1 0 0 1.4440 9 1 -1 1 0 5.1568 10 1 0 -1 0 1.1676 11 1 0 1 0 1.1676 12 1 -1 -1 1 6.1117 13 1 -1 0 1 2.1638 14 1 -1 1 1 6.8282 15 1 0 -1 1 2.3435 16 1 0 0 1 1.3038 17 1 0 1 1 4.8374 18 1 1 1 1 6.1701 19 1 1 0 1 2.4029 20 1 1 -1 1 5.5152 21 1 1 1 0 5.1364 22 1 1 0 0 1.4440 23 1 1 -1 0 5.1568 24 1 1 1 -1 6.1117 25 1 1 0 -1 2.1638 26 1 1 -1 -1 6.8282 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3636 atoms have been selected out of 3710 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.04 Total of13089 atoms and 4354 groups and 4348 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3710 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.18" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1225" Evaluating: 1225-7 Parameter: NUMWAT <- "1218" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1218" Comparing "1081" and "1218". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.18" Parameter: BOX -> "33.18" Parameter: BOX -> "33.18" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.18000 B = 33.18000 C = 33.18000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1685 2 1 -1 0 -1 2.4002 3 1 -1 1 -1 5.5118 4 1 0 -1 -1 4.8377 5 1 0 0 -1 1.3019 6 1 0 1 -1 2.3408 7 1 -1 -1 0 5.1344 8 1 -1 0 0 1.4422 9 1 -1 1 0 5.1542 10 1 0 -1 0 1.1657 11 1 0 1 0 1.1657 12 1 -1 -1 1 6.1088 13 1 -1 0 1 2.1614 14 1 -1 1 1 6.8252 15 1 0 -1 1 2.3408 16 1 0 0 1 1.3019 17 1 0 1 1 4.8377 18 1 1 1 1 6.1685 19 1 1 0 1 2.4002 20 1 1 -1 1 5.5118 21 1 1 1 0 5.1344 22 1 1 0 0 1.4422 23 1 1 -1 0 5.1542 24 1 1 1 -1 6.1088 25 1 1 0 -1 2.1614 26 1 1 -1 -1 6.8252 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3636 atoms have been selected out of 3710 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1674 558 558 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.04 Total of13092 atoms and 4355 groups and 4349 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3710 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1225 Number of atoms = 3710 Number of groups = 1230 Number of bonds = 3703 Number of angles = 1329 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1227 Number of HB donors = 2432 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.178" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1225" Evaluating: 1225-7 Parameter: NUMWAT <- "1218" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1218" Comparing "1081" and "1218". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.178" Parameter: BOX -> "33.178" Parameter: BOX -> "33.178" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.17800 B = 33.17800 C = 33.17800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1668 2 1 -1 0 -1 2.3975 3 1 -1 1 -1 5.5083 4 1 0 -1 -1 4.8379 5 1 0 0 -1 1.3001 6 1 0 1 -1 2.3381 7 1 -1 -1 0 5.1324 8 1 -1 0 0 1.4404 9 1 -1 1 0 5.1517 10 1 0 -1 0 1.1638 11 1 0 1 0 1.1638 12 1 -1 -1 1 6.1059 13 1 -1 0 1 2.1590 14 1 -1 1 1 6.8221 15 1 0 -1 1 2.3381 16 1 0 0 1 1.3001 17 1 0 1 1 4.8379 18 1 1 1 1 6.1668 19 1 1 0 1 2.3975 20 1 1 -1 1 5.5083 21 1 1 1 0 5.1324 22 1 1 0 0 1.4404 23 1 1 -1 0 5.1517 24 1 1 1 -1 6.1059 25 1 1 0 -1 2.1590 26 1 1 -1 -1 6.8221 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3636 atoms have been selected out of 3710 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 566 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 444 148 148 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1674 558 558 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.04 Total of13092 atoms and 4355 groups and 4349 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3710 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1224 Number of atoms = 3707 Number of groups = 1229 Number of bonds = 3700 Number of angles = 1328 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1226 Number of HB donors = 2430 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1224 Number of atoms = 3707 Number of groups = 1229 Number of bonds = 3700 Number of angles = 1328 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1226 Number of HB donors = 2430 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.176" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1224" Evaluating: 1224-7 Parameter: NUMWAT <- "1217" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1217" Comparing "1081" and "1217". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.176" Parameter: BOX -> "33.176" Parameter: BOX -> "33.176" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.17600 B = 33.17600 C = 33.17600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1652 2 1 -1 0 -1 2.3949 3 1 -1 1 -1 5.5049 4 1 0 -1 -1 4.8382 5 1 0 0 -1 1.2982 6 1 0 1 -1 2.3354 7 1 -1 -1 0 5.1304 8 1 -1 0 0 1.4386 9 1 -1 1 0 5.1491 10 1 0 -1 0 1.1619 11 1 0 1 0 1.1619 12 1 -1 -1 1 6.1030 13 1 -1 0 1 2.1566 14 1 -1 1 1 6.8190 15 1 0 -1 1 2.3354 16 1 0 0 1 1.2982 17 1 0 1 1 4.8382 18 1 1 1 1 6.1652 19 1 1 0 1 2.3949 20 1 1 -1 1 5.5049 21 1 1 1 0 5.1304 22 1 1 0 0 1.4386 23 1 1 -1 0 5.1491 24 1 1 1 -1 6.1030 25 1 1 0 -1 2.1566 26 1 1 -1 -1 6.8190 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3633 atoms have been selected out of 3707 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 447 149 149 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.04 Total of13083 atoms and 4352 groups and 4346 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3707 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1224 Number of atoms = 3707 Number of groups = 1229 Number of bonds = 3700 Number of angles = 1328 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1226 Number of HB donors = 2430 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1224 Number of atoms = 3707 Number of groups = 1229 Number of bonds = 3700 Number of angles = 1328 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1226 Number of HB donors = 2430 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.174" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1224" Evaluating: 1224-7 Parameter: NUMWAT <- "1217" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1217" Comparing "1081" and "1217". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.174" Parameter: BOX -> "33.174" Parameter: BOX -> "33.174" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.17400 B = 33.17400 C = 33.17400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1635 2 1 -1 0 -1 2.3922 3 1 -1 1 -1 5.5015 4 1 0 -1 -1 4.8384 5 1 0 0 -1 1.2964 6 1 0 1 -1 2.3328 7 1 -1 -1 0 5.1284 8 1 -1 0 0 1.4368 9 1 -1 1 0 5.1466 10 1 0 -1 0 1.1599 11 1 0 1 0 1.1599 12 1 -1 -1 1 6.1001 13 1 -1 0 1 2.1542 14 1 -1 1 1 6.8160 15 1 0 -1 1 2.3328 16 1 0 0 1 1.2964 17 1 0 1 1 4.8384 18 1 1 1 1 6.1635 19 1 1 0 1 2.3922 20 1 1 -1 1 5.5015 21 1 1 1 0 5.1284 22 1 1 0 0 1.4368 23 1 1 -1 0 5.1466 24 1 1 1 -1 6.1001 25 1 1 0 -1 2.1542 26 1 1 -1 -1 6.8160 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3633 atoms have been selected out of 3707 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 447 149 149 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1674 558 558 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.04 Total of13086 atoms and 4353 groups and 4347 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3707 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1224 Number of atoms = 3707 Number of groups = 1229 Number of bonds = 3700 Number of angles = 1328 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1226 Number of HB donors = 2430 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1224 Number of atoms = 3707 Number of groups = 1229 Number of bonds = 3700 Number of angles = 1328 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1226 Number of HB donors = 2430 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.172" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1224" Evaluating: 1224-7 Parameter: NUMWAT <- "1217" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1217" Comparing "1081" and "1217". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.172" Parameter: BOX -> "33.172" Parameter: BOX -> "33.172" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.17200 B = 33.17200 C = 33.17200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1619 2 1 -1 0 -1 2.3895 3 1 -1 1 -1 5.4980 4 1 0 -1 -1 4.8387 5 1 0 0 -1 1.2946 6 1 0 1 -1 2.3301 7 1 -1 -1 0 5.1264 8 1 -1 0 0 1.4350 9 1 -1 1 0 5.1440 10 1 0 -1 0 1.1580 11 1 0 1 0 1.1580 12 1 -1 -1 1 6.0972 13 1 -1 0 1 2.1518 14 1 -1 1 1 6.8129 15 1 0 -1 1 2.3301 16 1 0 0 1 1.2946 17 1 0 1 1 4.8387 18 1 1 1 1 6.1619 19 1 1 0 1 2.3895 20 1 1 -1 1 5.4980 21 1 1 1 0 5.1264 22 1 1 0 0 1.4350 23 1 1 -1 0 5.1440 24 1 1 1 -1 6.0972 25 1 1 0 -1 2.1518 26 1 1 -1 -1 6.8129 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3633 atoms have been selected out of 3707 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 447 149 149 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1677 559 559 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.03 Total of13089 atoms and 4354 groups and 4348 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3707 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1224 Number of atoms = 3707 Number of groups = 1229 Number of bonds = 3700 Number of angles = 1328 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1226 Number of HB donors = 2430 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1224 Number of atoms = 3707 Number of groups = 1229 Number of bonds = 3700 Number of angles = 1328 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1226 Number of HB donors = 2430 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.17" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1224" Evaluating: 1224-7 Parameter: NUMWAT <- "1217" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1217" Comparing "1081" and "1217". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.17" Parameter: BOX -> "33.17" Parameter: BOX -> "33.17" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.17000 B = 33.17000 C = 33.17000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1602 2 1 -1 0 -1 2.3868 3 1 -1 1 -1 5.4946 4 1 0 -1 -1 4.8389 5 1 0 0 -1 1.2927 6 1 0 1 -1 2.3274 7 1 -1 -1 0 5.1244 8 1 -1 0 0 1.4332 9 1 -1 1 0 5.1415 10 1 0 -1 0 1.1561 11 1 0 1 0 1.1561 12 1 -1 -1 1 6.0943 13 1 -1 0 1 2.1494 14 1 -1 1 1 6.8099 15 1 0 -1 1 2.3274 16 1 0 0 1 1.2927 17 1 0 1 1 4.8389 18 1 1 1 1 6.1602 19 1 1 0 1 2.3868 20 1 1 -1 1 5.4946 21 1 1 1 0 5.1244 22 1 1 0 0 1.4332 23 1 1 -1 0 5.1415 24 1 1 1 -1 6.0943 25 1 1 0 -1 2.1494 26 1 1 -1 -1 6.8099 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3633 atoms have been selected out of 3707 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 447 149 149 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1677 559 559 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.03 Total of13089 atoms and 4354 groups and 4348 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3707 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1224 Number of atoms = 3707 Number of groups = 1229 Number of bonds = 3700 Number of angles = 1328 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1226 Number of HB donors = 2430 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1224 Number of atoms = 3707 Number of groups = 1229 Number of bonds = 3700 Number of angles = 1328 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1226 Number of HB donors = 2430 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.168" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1224" Evaluating: 1224-7 Parameter: NUMWAT <- "1217" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1217" Comparing "1081" and "1217". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.168" Parameter: BOX -> "33.168" Parameter: BOX -> "33.168" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.16800 B = 33.16800 C = 33.16800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1586 2 1 -1 0 -1 2.3841 3 1 -1 1 -1 5.4912 4 1 0 -1 -1 4.8392 5 1 0 0 -1 1.2909 6 1 0 1 -1 2.3247 7 1 -1 -1 0 5.1224 8 1 -1 0 0 1.4314 9 1 -1 1 0 5.1389 10 1 0 -1 0 1.1542 11 1 0 1 0 1.1542 12 1 -1 -1 1 6.0914 13 1 -1 0 1 2.1470 14 1 -1 1 1 6.8068 15 1 0 -1 1 2.3247 16 1 0 0 1 1.2909 17 1 0 1 1 4.8392 18 1 1 1 1 6.1586 19 1 1 0 1 2.3841 20 1 1 -1 1 5.4912 21 1 1 1 0 5.1224 22 1 1 0 0 1.4314 23 1 1 -1 0 5.1389 24 1 1 1 -1 6.0914 25 1 1 0 -1 2.1470 26 1 1 -1 -1 6.8068 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3633 atoms have been selected out of 3707 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 447 149 149 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1677 559 559 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.03 Total of13095 atoms and 4356 groups and 4350 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3707 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1224 Number of atoms = 3707 Number of groups = 1229 Number of bonds = 3700 Number of angles = 1328 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1226 Number of HB donors = 2430 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1224 Number of atoms = 3707 Number of groups = 1229 Number of bonds = 3700 Number of angles = 1328 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1226 Number of HB donors = 2430 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.166" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1224" Evaluating: 1224-7 Parameter: NUMWAT <- "1217" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1217" Comparing "1081" and "1217". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.166" Parameter: BOX -> "33.166" Parameter: BOX -> "33.166" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.16600 B = 33.16600 C = 33.16600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1570 2 1 -1 0 -1 2.3815 3 1 -1 1 -1 5.4878 4 1 0 -1 -1 4.8395 5 1 0 0 -1 1.2890 6 1 0 1 -1 2.3220 7 1 -1 -1 0 5.1204 8 1 -1 0 0 1.4296 9 1 -1 1 0 5.1364 10 1 0 -1 0 1.1523 11 1 0 1 0 1.1523 12 1 -1 -1 1 6.0885 13 1 -1 0 1 2.1446 14 1 -1 1 1 6.8038 15 1 0 -1 1 2.3220 16 1 0 0 1 1.2890 17 1 0 1 1 4.8395 18 1 1 1 1 6.1570 19 1 1 0 1 2.3815 20 1 1 -1 1 5.4878 21 1 1 1 0 5.1204 22 1 1 0 0 1.4296 23 1 1 -1 0 5.1364 24 1 1 1 -1 6.0885 25 1 1 0 -1 2.1446 26 1 1 -1 -1 6.8038 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3633 atoms have been selected out of 3707 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 447 149 149 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1677 559 559 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.03 Total of13101 atoms and 4358 groups and 4352 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3707 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1224 Number of atoms = 3707 Number of groups = 1229 Number of bonds = 3700 Number of angles = 1328 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1226 Number of HB donors = 2430 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1224 Number of atoms = 3707 Number of groups = 1229 Number of bonds = 3700 Number of angles = 1328 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1226 Number of HB donors = 2430 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.164" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1224" Evaluating: 1224-7 Parameter: NUMWAT <- "1217" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1217" Comparing "1081" and "1217". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.164" Parameter: BOX -> "33.164" Parameter: BOX -> "33.164" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.16400 B = 33.16400 C = 33.16400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1553 2 1 -1 0 -1 2.3788 3 1 -1 1 -1 5.4843 4 1 0 -1 -1 4.8397 5 1 0 0 -1 1.2872 6 1 0 1 -1 2.3193 7 1 -1 -1 0 5.1184 8 1 -1 0 0 1.4278 9 1 -1 1 0 5.1338 10 1 0 -1 0 1.1504 11 1 0 1 0 1.1504 12 1 -1 -1 1 6.0855 13 1 -1 0 1 2.1422 14 1 -1 1 1 6.8007 15 1 0 -1 1 2.3193 16 1 0 0 1 1.2872 17 1 0 1 1 4.8397 18 1 1 1 1 6.1553 19 1 1 0 1 2.3788 20 1 1 -1 1 5.4843 21 1 1 1 0 5.1184 22 1 1 0 0 1.4278 23 1 1 -1 0 5.1338 24 1 1 1 -1 6.0855 25 1 1 0 -1 2.1422 26 1 1 -1 -1 6.8007 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3633 atoms have been selected out of 3707 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 447 149 149 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1677 559 559 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.03 Total of13101 atoms and 4358 groups and 4352 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3707 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1224 Number of atoms = 3707 Number of groups = 1229 Number of bonds = 3700 Number of angles = 1328 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1226 Number of HB donors = 2430 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1224 Number of atoms = 3707 Number of groups = 1229 Number of bonds = 3700 Number of angles = 1328 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1226 Number of HB donors = 2430 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.162" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1224" Evaluating: 1224-7 Parameter: NUMWAT <- "1217" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1217" Comparing "1081" and "1217". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.162" Parameter: BOX -> "33.162" Parameter: BOX -> "33.162" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.16200 B = 33.16200 C = 33.16200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1537 2 1 -1 0 -1 2.3761 3 1 -1 1 -1 5.4809 4 1 0 -1 -1 4.8400 5 1 0 0 -1 1.2854 6 1 0 1 -1 2.3166 7 1 -1 -1 0 5.1163 8 1 -1 0 0 1.4260 9 1 -1 1 0 5.1313 10 1 0 -1 0 1.1484 11 1 0 1 0 1.1484 12 1 -1 -1 1 6.0826 13 1 -1 0 1 2.1398 14 1 -1 1 1 6.7977 15 1 0 -1 1 2.3166 16 1 0 0 1 1.2854 17 1 0 1 1 4.8400 18 1 1 1 1 6.1537 19 1 1 0 1 2.3761 20 1 1 -1 1 5.4809 21 1 1 1 0 5.1163 22 1 1 0 0 1.4260 23 1 1 -1 0 5.1313 24 1 1 1 -1 6.0826 25 1 1 0 -1 2.1398 26 1 1 -1 -1 6.7977 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3633 atoms have been selected out of 3707 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 450 150 150 0.00 2 C002 has 762 254 254 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1677 559 559 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.02 Total of13107 atoms and 4360 groups and 4354 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3707 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1224 Number of atoms = 3707 Number of groups = 1229 Number of bonds = 3700 Number of angles = 1328 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1226 Number of HB donors = 2430 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1224 Number of atoms = 3707 Number of groups = 1229 Number of bonds = 3700 Number of angles = 1328 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1226 Number of HB donors = 2430 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.16" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1224" Evaluating: 1224-7 Parameter: NUMWAT <- "1217" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1217" Comparing "1081" and "1217". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.16" Parameter: BOX -> "33.16" Parameter: BOX -> "33.16" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.16000 B = 33.16000 C = 33.16000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1521 2 1 -1 0 -1 2.3734 3 1 -1 1 -1 5.4775 4 1 0 -1 -1 4.8402 5 1 0 0 -1 1.2835 6 1 0 1 -1 2.3139 7 1 -1 -1 0 5.1143 8 1 -1 0 0 1.4242 9 1 -1 1 0 5.1288 10 1 0 -1 0 1.1465 11 1 0 1 0 1.1465 12 1 -1 -1 1 6.0797 13 1 -1 0 1 2.1374 14 1 -1 1 1 6.7946 15 1 0 -1 1 2.3139 16 1 0 0 1 1.2835 17 1 0 1 1 4.8402 18 1 1 1 1 6.1521 19 1 1 0 1 2.3734 20 1 1 -1 1 5.4775 21 1 1 1 0 5.1143 22 1 1 0 0 1.4242 23 1 1 -1 0 5.1288 24 1 1 1 -1 6.0797 25 1 1 0 -1 2.1374 26 1 1 -1 -1 6.7946 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3633 atoms have been selected out of 3707 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 450 150 150 0.00 2 C002 has 762 254 254 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1677 559 559 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.02 Total of13107 atoms and 4360 groups and 4354 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3707 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1224 Number of atoms = 3707 Number of groups = 1229 Number of bonds = 3700 Number of angles = 1328 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1226 Number of HB donors = 2430 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1224 Number of atoms = 3707 Number of groups = 1229 Number of bonds = 3700 Number of angles = 1328 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1226 Number of HB donors = 2430 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.158" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1224" Evaluating: 1224-7 Parameter: NUMWAT <- "1217" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1217" Comparing "1081" and "1217". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.158" Parameter: BOX -> "33.158" Parameter: BOX -> "33.158" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.15800 B = 33.15800 C = 33.15800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1504 2 1 -1 0 -1 2.3708 3 1 -1 1 -1 5.4740 4 1 0 -1 -1 4.8405 5 1 0 0 -1 1.2817 6 1 0 1 -1 2.3113 7 1 -1 -1 0 5.1123 8 1 -1 0 0 1.4224 9 1 -1 1 0 5.1262 10 1 0 -1 0 1.1446 11 1 0 1 0 1.1446 12 1 -1 -1 1 6.0768 13 1 -1 0 1 2.1350 14 1 -1 1 1 6.7916 15 1 0 -1 1 2.3113 16 1 0 0 1 1.2817 17 1 0 1 1 4.8405 18 1 1 1 1 6.1504 19 1 1 0 1 2.3708 20 1 1 -1 1 5.4740 21 1 1 1 0 5.1123 22 1 1 0 0 1.4224 23 1 1 -1 0 5.1262 24 1 1 1 -1 6.0768 25 1 1 0 -1 2.1350 26 1 1 -1 -1 6.7916 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3633 atoms have been selected out of 3707 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 450 150 150 0.00 2 C002 has 762 254 254 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 453 151 151 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1677 559 559 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.02 Total of13110 atoms and 4361 groups and 4355 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3707 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1224 Number of atoms = 3707 Number of groups = 1229 Number of bonds = 3700 Number of angles = 1328 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1226 Number of HB donors = 2430 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1224 Number of atoms = 3707 Number of groups = 1229 Number of bonds = 3700 Number of angles = 1328 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1226 Number of HB donors = 2430 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.156" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1224" Evaluating: 1224-7 Parameter: NUMWAT <- "1217" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1217" Comparing "1081" and "1217". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.156" Parameter: BOX -> "33.156" Parameter: BOX -> "33.156" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.15600 B = 33.15600 C = 33.15600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1488 2 1 -1 0 -1 2.3681 3 1 -1 1 -1 5.4706 4 1 0 -1 -1 4.8408 5 1 0 0 -1 1.2798 6 1 0 1 -1 2.3086 7 1 -1 -1 0 5.1103 8 1 -1 0 0 1.4207 9 1 -1 1 0 5.1237 10 1 0 -1 0 1.1427 11 1 0 1 0 1.1427 12 1 -1 -1 1 6.0739 13 1 -1 0 1 2.1326 14 1 -1 1 1 6.7885 15 1 0 -1 1 2.3086 16 1 0 0 1 1.2798 17 1 0 1 1 4.8408 18 1 1 1 1 6.1488 19 1 1 0 1 2.3681 20 1 1 -1 1 5.4706 21 1 1 1 0 5.1103 22 1 1 0 0 1.4207 23 1 1 -1 0 5.1237 24 1 1 1 -1 6.0739 25 1 1 0 -1 2.1326 26 1 1 -1 -1 6.7885 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3633 atoms have been selected out of 3707 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 450 150 150 0.00 2 C002 has 762 254 254 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 453 151 151 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1677 559 559 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.02 Total of13110 atoms and 4361 groups and 4355 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3707 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1224 Number of atoms = 3707 Number of groups = 1229 Number of bonds = 3700 Number of angles = 1328 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1226 Number of HB donors = 2430 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1224 Number of atoms = 3707 Number of groups = 1229 Number of bonds = 3700 Number of angles = 1328 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1226 Number of HB donors = 2430 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.154" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1224" Evaluating: 1224-7 Parameter: NUMWAT <- "1217" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1217" Comparing "1081" and "1217". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.154" Parameter: BOX -> "33.154" Parameter: BOX -> "33.154" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.15400 B = 33.15400 C = 33.15400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1472 2 1 -1 0 -1 2.3654 3 1 -1 1 -1 5.4672 4 1 0 -1 -1 4.8410 5 1 0 0 -1 1.2780 6 1 0 1 -1 2.3059 7 1 -1 -1 0 5.1083 8 1 -1 0 0 1.4189 9 1 -1 1 0 5.1211 10 1 0 -1 0 1.1408 11 1 0 1 0 1.1408 12 1 -1 -1 1 6.0710 13 1 -1 0 1 2.1302 14 1 -1 1 1 6.7855 15 1 0 -1 1 2.3059 16 1 0 0 1 1.2780 17 1 0 1 1 4.8410 18 1 1 1 1 6.1472 19 1 1 0 1 2.3654 20 1 1 -1 1 5.4672 21 1 1 1 0 5.1083 22 1 1 0 0 1.4189 23 1 1 -1 0 5.1211 24 1 1 1 -1 6.0710 25 1 1 0 -1 2.1302 26 1 1 -1 -1 6.7855 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3633 atoms have been selected out of 3707 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 956 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 453 151 151 0.00 2 C002 has 765 255 255 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1596 532 532 0.00 6 C006 has 453 151 151 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1677 559 559 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.02 Total of13122 atoms and 4365 groups and 4359 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3707 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1223 Number of atoms = 3704 Number of groups = 1228 Number of bonds = 3697 Number of angles = 1327 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1225 Number of HB donors = 2428 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1223 Number of atoms = 3704 Number of groups = 1228 Number of bonds = 3697 Number of angles = 1327 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1225 Number of HB donors = 2428 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.152" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1223" Evaluating: 1223-7 Parameter: NUMWAT <- "1216" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1216" Comparing "1081" and "1216". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.152" Parameter: BOX -> "33.152" Parameter: BOX -> "33.152" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.15200 B = 33.15200 C = 33.15200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1455 2 1 -1 0 -1 2.3627 3 1 -1 1 -1 5.4637 4 1 0 -1 -1 4.8413 5 1 0 0 -1 1.2762 6 1 0 1 -1 2.3032 7 1 -1 -1 0 5.1063 8 1 -1 0 0 1.4171 9 1 -1 1 0 5.1186 10 1 0 -1 0 1.1389 11 1 0 1 0 1.1389 12 1 -1 -1 1 6.0681 13 1 -1 0 1 2.1278 14 1 -1 1 1 6.7824 15 1 0 -1 1 2.3032 16 1 0 0 1 1.2762 17 1 0 1 1 4.8413 18 1 1 1 1 6.1455 19 1 1 0 1 2.3627 20 1 1 -1 1 5.4637 21 1 1 1 0 5.1063 22 1 1 0 0 1.4171 23 1 1 -1 0 5.1186 24 1 1 1 -1 6.0681 25 1 1 0 -1 2.1278 26 1 1 -1 -1 6.7824 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3630 atoms have been selected out of 3704 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 450 150 150 0.00 2 C002 has 762 254 254 0.00 3 C003 has 111 37 37 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 453 151 151 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1674 558 558 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.01 Total of13098 atoms and 4357 groups and 4351 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3704 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1223 Number of atoms = 3704 Number of groups = 1228 Number of bonds = 3697 Number of angles = 1327 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1225 Number of HB donors = 2428 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1223 Number of atoms = 3704 Number of groups = 1228 Number of bonds = 3697 Number of angles = 1327 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1225 Number of HB donors = 2428 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.15" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1223" Evaluating: 1223-7 Parameter: NUMWAT <- "1216" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1216" Comparing "1081" and "1216". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.15" Parameter: BOX -> "33.15" Parameter: BOX -> "33.15" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.15000 B = 33.15000 C = 33.15000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1439 2 1 -1 0 -1 2.3601 3 1 -1 1 -1 5.4603 4 1 0 -1 -1 4.8416 5 1 0 0 -1 1.2743 6 1 0 1 -1 2.3005 7 1 -1 -1 0 5.1043 8 1 -1 0 0 1.4153 9 1 -1 1 0 5.1160 10 1 0 -1 0 1.1370 11 1 0 1 0 1.1370 12 1 -1 -1 1 6.0652 13 1 -1 0 1 2.1254 14 1 -1 1 1 6.7794 15 1 0 -1 1 2.3005 16 1 0 0 1 1.2743 17 1 0 1 1 4.8416 18 1 1 1 1 6.1439 19 1 1 0 1 2.3601 20 1 1 -1 1 5.4603 21 1 1 1 0 5.1043 22 1 1 0 0 1.4153 23 1 1 -1 0 5.1160 24 1 1 1 -1 6.0652 25 1 1 0 -1 2.1254 26 1 1 -1 -1 6.7794 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3630 atoms have been selected out of 3704 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 450 150 150 0.00 2 C002 has 762 254 254 0.00 3 C003 has 111 37 37 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 453 151 151 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1674 558 558 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.01 Total of13098 atoms and 4357 groups and 4351 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3704 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1223 Number of atoms = 3704 Number of groups = 1228 Number of bonds = 3697 Number of angles = 1327 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1225 Number of HB donors = 2428 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1223 Number of atoms = 3704 Number of groups = 1228 Number of bonds = 3697 Number of angles = 1327 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1225 Number of HB donors = 2428 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.148" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1223" Evaluating: 1223-7 Parameter: NUMWAT <- "1216" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1216" Comparing "1081" and "1216". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.148" Parameter: BOX -> "33.148" Parameter: BOX -> "33.148" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.14800 B = 33.14800 C = 33.14800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1423 2 1 -1 0 -1 2.3574 3 1 -1 1 -1 5.4569 4 1 0 -1 -1 4.8418 5 1 0 0 -1 1.2725 6 1 0 1 -1 2.2978 7 1 -1 -1 0 5.1023 8 1 -1 0 0 1.4135 9 1 -1 1 0 5.1135 10 1 0 -1 0 1.1351 11 1 0 1 0 1.1351 12 1 -1 -1 1 6.0623 13 1 -1 0 1 2.1230 14 1 -1 1 1 6.7763 15 1 0 -1 1 2.2978 16 1 0 0 1 1.2725 17 1 0 1 1 4.8418 18 1 1 1 1 6.1423 19 1 1 0 1 2.3574 20 1 1 -1 1 5.4569 21 1 1 1 0 5.1023 22 1 1 0 0 1.4135 23 1 1 -1 0 5.1135 24 1 1 1 -1 6.0623 25 1 1 0 -1 2.1230 26 1 1 -1 -1 6.7763 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3630 atoms have been selected out of 3704 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 450 150 150 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 453 151 151 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1674 558 558 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.01 Total of13101 atoms and 4358 groups and 4352 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3704 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1223 Number of atoms = 3704 Number of groups = 1228 Number of bonds = 3697 Number of angles = 1327 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1225 Number of HB donors = 2428 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1223 Number of atoms = 3704 Number of groups = 1228 Number of bonds = 3697 Number of angles = 1327 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1225 Number of HB donors = 2428 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.146" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1223" Evaluating: 1223-7 Parameter: NUMWAT <- "1216" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1216" Comparing "1081" and "1216". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.146" Parameter: BOX -> "33.146" Parameter: BOX -> "33.146" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.14600 B = 33.14600 C = 33.14600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1407 2 1 -1 0 -1 2.3547 3 1 -1 1 -1 5.4534 4 1 0 -1 -1 4.8421 5 1 0 0 -1 1.2707 6 1 0 1 -1 2.2952 7 1 -1 -1 0 5.1003 8 1 -1 0 0 1.4117 9 1 -1 1 0 5.1109 10 1 0 -1 0 1.1331 11 1 0 1 0 1.1331 12 1 -1 -1 1 6.0594 13 1 -1 0 1 2.1206 14 1 -1 1 1 6.7733 15 1 0 -1 1 2.2952 16 1 0 0 1 1.2707 17 1 0 1 1 4.8421 18 1 1 1 1 6.1407 19 1 1 0 1 2.3547 20 1 1 -1 1 5.4534 21 1 1 1 0 5.1003 22 1 1 0 0 1.4117 23 1 1 -1 0 5.1109 24 1 1 1 -1 6.0594 25 1 1 0 -1 2.1206 26 1 1 -1 -1 6.7733 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3630 atoms have been selected out of 3704 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 450 150 150 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 453 151 151 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1674 558 558 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.01 Total of13101 atoms and 4358 groups and 4352 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3704 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1223 Number of atoms = 3704 Number of groups = 1228 Number of bonds = 3697 Number of angles = 1327 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1225 Number of HB donors = 2428 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1223 Number of atoms = 3704 Number of groups = 1228 Number of bonds = 3697 Number of angles = 1327 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1225 Number of HB donors = 2428 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.144" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1223" Evaluating: 1223-7 Parameter: NUMWAT <- "1216" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1216" Comparing "1081" and "1216". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.144" Parameter: BOX -> "33.144" Parameter: BOX -> "33.144" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.14400 B = 33.14400 C = 33.14400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1390 2 1 -1 0 -1 2.3520 3 1 -1 1 -1 5.4500 4 1 0 -1 -1 4.8424 5 1 0 0 -1 1.2688 6 1 0 1 -1 2.2925 7 1 -1 -1 0 5.0984 8 1 -1 0 0 1.4099 9 1 -1 1 0 5.1084 10 1 0 -1 0 1.1312 11 1 0 1 0 1.1312 12 1 -1 -1 1 6.0565 13 1 -1 0 1 2.1182 14 1 -1 1 1 6.7702 15 1 0 -1 1 2.2925 16 1 0 0 1 1.2688 17 1 0 1 1 4.8424 18 1 1 1 1 6.1390 19 1 1 0 1 2.3520 20 1 1 -1 1 5.4500 21 1 1 1 0 5.0984 22 1 1 0 0 1.4099 23 1 1 -1 0 5.1084 24 1 1 1 -1 6.0565 25 1 1 0 -1 2.1182 26 1 1 -1 -1 6.7702 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3630 atoms have been selected out of 3704 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 450 150 150 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 453 151 151 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1674 558 558 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.01 Total of13101 atoms and 4358 groups and 4352 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3704 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1223 Number of atoms = 3704 Number of groups = 1228 Number of bonds = 3697 Number of angles = 1327 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1225 Number of HB donors = 2428 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1223 Number of atoms = 3704 Number of groups = 1228 Number of bonds = 3697 Number of angles = 1327 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1225 Number of HB donors = 2428 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.142" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1223" Evaluating: 1223-7 Parameter: NUMWAT <- "1216" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1216" Comparing "1081" and "1216". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.142" Parameter: BOX -> "33.142" Parameter: BOX -> "33.142" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.14200 B = 33.14200 C = 33.14200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1374 2 1 -1 0 -1 2.3494 3 1 -1 1 -1 5.4466 4 1 0 -1 -1 4.8427 5 1 0 0 -1 1.2670 6 1 0 1 -1 2.2898 7 1 -1 -1 0 5.0964 8 1 -1 0 0 1.4081 9 1 -1 1 0 5.1059 10 1 0 -1 0 1.1293 11 1 0 1 0 1.1293 12 1 -1 -1 1 6.0536 13 1 -1 0 1 2.1158 14 1 -1 1 1 6.7672 15 1 0 -1 1 2.2898 16 1 0 0 1 1.2670 17 1 0 1 1 4.8427 18 1 1 1 1 6.1374 19 1 1 0 1 2.3494 20 1 1 -1 1 5.4466 21 1 1 1 0 5.0964 22 1 1 0 0 1.4081 23 1 1 -1 0 5.1059 24 1 1 1 -1 6.0536 25 1 1 0 -1 2.1158 26 1 1 -1 -1 6.7672 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3630 atoms have been selected out of 3704 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 717 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1060 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 447 149 149 0.00 2 C002 has 768 256 256 0.00 3 C003 has 114 38 38 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1593 531 531 0.00 6 C006 has 459 153 153 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1774 589 588 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.00 Total of13110 atoms and 4361 groups and 4355 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3704 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1221 Number of atoms = 3698 Number of groups = 1226 Number of bonds = 3691 Number of angles = 1325 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1223 Number of HB donors = 2424 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1221 Number of atoms = 3698 Number of groups = 1226 Number of bonds = 3691 Number of angles = 1325 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1223 Number of HB donors = 2424 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.14" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1221" Evaluating: 1221-7 Parameter: NUMWAT <- "1214" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1214" Comparing "1081" and "1214". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.14" Parameter: BOX -> "33.14" Parameter: BOX -> "33.14" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.14000 B = 33.14000 C = 33.14000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1358 2 1 -1 0 -1 2.3467 3 1 -1 1 -1 5.4431 4 1 0 -1 -1 4.8430 5 1 0 0 -1 1.2652 6 1 0 1 -1 2.2871 7 1 -1 -1 0 5.0944 8 1 -1 0 0 1.4063 9 1 -1 1 0 5.1033 10 1 0 -1 0 1.1274 11 1 0 1 0 1.1274 12 1 -1 -1 1 6.0507 13 1 -1 0 1 2.1134 14 1 -1 1 1 6.7641 15 1 0 -1 1 2.2871 16 1 0 0 1 1.2652 17 1 0 1 1 4.8430 18 1 1 1 1 6.1358 19 1 1 0 1 2.3467 20 1 1 -1 1 5.4431 21 1 1 1 0 5.0944 22 1 1 0 0 1.4063 23 1 1 -1 0 5.1033 24 1 1 1 -1 6.0507 25 1 1 0 -1 2.1134 26 1 1 -1 -1 6.7641 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3624 atoms have been selected out of 3698 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 447 149 149 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 456 152 152 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1674 558 558 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 108 36 36 1.00 Total of13089 atoms and 4354 groups and 4348 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3698 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1221 Number of atoms = 3698 Number of groups = 1226 Number of bonds = 3691 Number of angles = 1325 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1223 Number of HB donors = 2424 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1221 Number of atoms = 3698 Number of groups = 1226 Number of bonds = 3691 Number of angles = 1325 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1223 Number of HB donors = 2424 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.138" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1221" Evaluating: 1221-7 Parameter: NUMWAT <- "1214" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1214" Comparing "1081" and "1214". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.138" Parameter: BOX -> "33.138" Parameter: BOX -> "33.138" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.13800 B = 33.13800 C = 33.13800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1342 2 1 -1 0 -1 2.3440 3 1 -1 1 -1 5.4397 4 1 0 -1 -1 4.8432 5 1 0 0 -1 1.2633 6 1 0 1 -1 2.2844 7 1 -1 -1 0 5.0924 8 1 -1 0 0 1.4046 9 1 -1 1 0 5.1008 10 1 0 -1 0 1.1255 11 1 0 1 0 1.1255 12 1 -1 -1 1 6.0478 13 1 -1 0 1 2.1111 14 1 -1 1 1 6.7611 15 1 0 -1 1 2.2844 16 1 0 0 1 1.2633 17 1 0 1 1 4.8432 18 1 1 1 1 6.1342 19 1 1 0 1 2.3440 20 1 1 -1 1 5.4397 21 1 1 1 0 5.0924 22 1 1 0 0 1.4046 23 1 1 -1 0 5.1008 24 1 1 1 -1 6.0478 25 1 1 0 -1 2.1111 26 1 1 -1 -1 6.7611 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3624 atoms have been selected out of 3698 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 447 149 149 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 456 152 152 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1774 589 588 0.00 9 C009 has 492 164 164 0.00 10 C010 has 1674 558 558 0.00 12 C012 has 90 30 30 0.00 13 C013 has 501 167 167 0.00 14 C014 has 108 36 36 1.00 Total of13098 atoms and 4357 groups and 4351 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3698 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1221 Number of atoms = 3698 Number of groups = 1226 Number of bonds = 3691 Number of angles = 1325 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1223 Number of HB donors = 2424 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1221 Number of atoms = 3698 Number of groups = 1226 Number of bonds = 3691 Number of angles = 1325 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1223 Number of HB donors = 2424 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.136" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1221" Evaluating: 1221-7 Parameter: NUMWAT <- "1214" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1214" Comparing "1081" and "1214". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.136" Parameter: BOX -> "33.136" Parameter: BOX -> "33.136" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.13600 B = 33.13600 C = 33.13600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1326 2 1 -1 0 -1 2.3413 3 1 -1 1 -1 5.4363 4 1 0 -1 -1 4.8435 5 1 0 0 -1 1.2615 6 1 0 1 -1 2.2817 7 1 -1 -1 0 5.0904 8 1 -1 0 0 1.4028 9 1 -1 1 0 5.0982 10 1 0 -1 0 1.1236 11 1 0 1 0 1.1236 12 1 -1 -1 1 6.0449 13 1 -1 0 1 2.1087 14 1 -1 1 1 6.7580 15 1 0 -1 1 2.2817 16 1 0 0 1 1.2615 17 1 0 1 1 4.8435 18 1 1 1 1 6.1326 19 1 1 0 1 2.3413 20 1 1 -1 1 5.4363 21 1 1 1 0 5.0904 22 1 1 0 0 1.4028 23 1 1 -1 0 5.0982 24 1 1 1 -1 6.0449 25 1 1 0 -1 2.1087 26 1 1 -1 -1 6.7580 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3624 atoms have been selected out of 3698 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 303 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 447 149 149 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 603 201 201 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 474 158 158 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1774 589 588 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 93 31 31 0.00 13 C013 has 501 167 167 0.00 14 C014 has 105 35 35 1.00 Total of13101 atoms and 4358 groups and 4352 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3698 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1220 Number of atoms = 3695 Number of groups = 1225 Number of bonds = 3688 Number of angles = 1324 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1222 Number of HB donors = 2422 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1220 Number of atoms = 3695 Number of groups = 1225 Number of bonds = 3688 Number of angles = 1324 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1222 Number of HB donors = 2422 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.134" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1220" Evaluating: 1220-7 Parameter: NUMWAT <- "1213" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1213" Comparing "1081" and "1213". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.134" Parameter: BOX -> "33.134" Parameter: BOX -> "33.134" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.13400 B = 33.13400 C = 33.13400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1310 2 1 -1 0 -1 2.3387 3 1 -1 1 -1 5.4328 4 1 0 -1 -1 4.8438 5 1 0 0 -1 1.2597 6 1 0 1 -1 2.2791 7 1 -1 -1 0 5.0884 8 1 -1 0 0 1.4010 9 1 -1 1 0 5.0957 10 1 0 -1 0 1.1217 11 1 0 1 0 1.1217 12 1 -1 -1 1 6.0420 13 1 -1 0 1 2.1063 14 1 -1 1 1 6.7550 15 1 0 -1 1 2.2791 16 1 0 0 1 1.2597 17 1 0 1 1 4.8438 18 1 1 1 1 6.1310 19 1 1 0 1 2.3387 20 1 1 -1 1 5.4328 21 1 1 1 0 5.0884 22 1 1 0 0 1.4010 23 1 1 -1 0 5.0957 24 1 1 1 -1 6.0420 25 1 1 0 -1 2.1063 26 1 1 -1 -1 6.7550 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3621 atoms have been selected out of 3695 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 447 149 149 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 603 201 201 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 456 152 152 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1668 556 556 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 105 35 35 1.00 Total of13065 atoms and 4346 groups and 4340 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3695 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1220 Number of atoms = 3695 Number of groups = 1225 Number of bonds = 3688 Number of angles = 1324 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1222 Number of HB donors = 2422 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1220 Number of atoms = 3695 Number of groups = 1225 Number of bonds = 3688 Number of angles = 1324 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1222 Number of HB donors = 2422 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.132" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1220" Evaluating: 1220-7 Parameter: NUMWAT <- "1213" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1213" Comparing "1081" and "1213". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.132" Parameter: BOX -> "33.132" Parameter: BOX -> "33.132" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.13200 B = 33.13200 C = 33.13200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1293 2 1 -1 0 -1 2.3360 3 1 -1 1 -1 5.4294 4 1 0 -1 -1 4.8441 5 1 0 0 -1 1.2578 6 1 0 1 -1 2.2764 7 1 -1 -1 0 5.0864 8 1 -1 0 0 1.3992 9 1 -1 1 0 5.0932 10 1 0 -1 0 1.1198 11 1 0 1 0 1.1198 12 1 -1 -1 1 6.0391 13 1 -1 0 1 2.1039 14 1 -1 1 1 6.7519 15 1 0 -1 1 2.2764 16 1 0 0 1 1.2578 17 1 0 1 1 4.8441 18 1 1 1 1 6.1293 19 1 1 0 1 2.3360 20 1 1 -1 1 5.4294 21 1 1 1 0 5.0864 22 1 1 0 0 1.3992 23 1 1 -1 0 5.0932 24 1 1 1 -1 6.0391 25 1 1 0 -1 2.1039 26 1 1 -1 -1 6.7519 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3621 atoms have been selected out of 3695 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 450 150 150 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 603 201 201 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 456 152 152 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1668 556 556 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 105 35 35 0.99 Total of13068 atoms and 4347 groups and 4341 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3695 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1220 Number of atoms = 3695 Number of groups = 1225 Number of bonds = 3688 Number of angles = 1324 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1222 Number of HB donors = 2422 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1220 Number of atoms = 3695 Number of groups = 1225 Number of bonds = 3688 Number of angles = 1324 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1222 Number of HB donors = 2422 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.13" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1220" Evaluating: 1220-7 Parameter: NUMWAT <- "1213" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1213" Comparing "1081" and "1213". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.13" Parameter: BOX -> "33.13" Parameter: BOX -> "33.13" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.13000 B = 33.13000 C = 33.13000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1277 2 1 -1 0 -1 2.3333 3 1 -1 1 -1 5.4260 4 1 0 -1 -1 4.8444 5 1 0 0 -1 1.2560 6 1 0 1 -1 2.2737 7 1 -1 -1 0 5.0844 8 1 -1 0 0 1.3974 9 1 -1 1 0 5.0906 10 1 0 -1 0 1.1179 11 1 0 1 0 1.1179 12 1 -1 -1 1 6.0363 13 1 -1 0 1 2.1015 14 1 -1 1 1 6.7489 15 1 0 -1 1 2.2737 16 1 0 0 1 1.2560 17 1 0 1 1 4.8444 18 1 1 1 1 6.1277 19 1 1 0 1 2.3333 20 1 1 -1 1 5.4260 21 1 1 1 0 5.0844 22 1 1 0 0 1.3974 23 1 1 -1 0 5.0906 24 1 1 1 -1 6.0363 25 1 1 0 -1 2.1015 26 1 1 -1 -1 6.7489 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3621 atoms have been selected out of 3695 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 451 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 450 150 150 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 606 202 202 0.00 5 C005 has 1590 530 530 0.00 6 C006 has 456 152 152 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1668 556 556 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 105 35 35 0.99 Total of13074 atoms and 4349 groups and 4343 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3695 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1219 Number of atoms = 3692 Number of groups = 1224 Number of bonds = 3685 Number of angles = 1323 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1221 Number of HB donors = 2420 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1219 Number of atoms = 3692 Number of groups = 1224 Number of bonds = 3685 Number of angles = 1323 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1221 Number of HB donors = 2420 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.128" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1219" Evaluating: 1219-7 Parameter: NUMWAT <- "1212" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1212" Comparing "1081" and "1212". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.128" Parameter: BOX -> "33.128" Parameter: BOX -> "33.128" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.12800 B = 33.12800 C = 33.12800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1261 2 1 -1 0 -1 2.3307 3 1 -1 1 -1 5.4225 4 1 0 -1 -1 4.8447 5 1 0 0 -1 1.2542 6 1 0 1 -1 2.2710 7 1 -1 -1 0 5.0824 8 1 -1 0 0 1.3956 9 1 -1 1 0 5.0881 10 1 0 -1 0 1.1160 11 1 0 1 0 1.1160 12 1 -1 -1 1 6.0334 13 1 -1 0 1 2.0991 14 1 -1 1 1 6.7458 15 1 0 -1 1 2.2710 16 1 0 0 1 1.2542 17 1 0 1 1 4.8447 18 1 1 1 1 6.1261 19 1 1 0 1 2.3307 20 1 1 -1 1 5.4225 21 1 1 1 0 5.0824 22 1 1 0 0 1.3956 23 1 1 -1 0 5.0881 24 1 1 1 -1 6.0334 25 1 1 0 -1 2.0991 26 1 1 -1 -1 6.7458 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3618 atoms have been selected out of 3692 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 450 150 150 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 603 201 201 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 456 152 152 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 105 35 35 0.99 Total of13062 atoms and 4345 groups and 4339 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3692 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1219 Number of atoms = 3692 Number of groups = 1224 Number of bonds = 3685 Number of angles = 1323 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1221 Number of HB donors = 2420 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1219 Number of atoms = 3692 Number of groups = 1224 Number of bonds = 3685 Number of angles = 1323 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1221 Number of HB donors = 2420 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.126" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1219" Evaluating: 1219-7 Parameter: NUMWAT <- "1212" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1212" Comparing "1081" and "1212". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.126" Parameter: BOX -> "33.126" Parameter: BOX -> "33.126" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.12600 B = 33.12600 C = 33.12600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1245 2 1 -1 0 -1 2.3280 3 1 -1 1 -1 5.4191 4 1 0 -1 -1 4.8449 5 1 0 0 -1 1.2523 6 1 0 1 -1 2.2683 7 1 -1 -1 0 5.0804 8 1 -1 0 0 1.3939 9 1 -1 1 0 5.0855 10 1 0 -1 0 1.1141 11 1 0 1 0 1.1141 12 1 -1 -1 1 6.0305 13 1 -1 0 1 2.0967 14 1 -1 1 1 6.7428 15 1 0 -1 1 2.2683 16 1 0 0 1 1.2523 17 1 0 1 1 4.8449 18 1 1 1 1 6.1245 19 1 1 0 1 2.3280 20 1 1 -1 1 5.4191 21 1 1 1 0 5.0804 22 1 1 0 0 1.3939 23 1 1 -1 0 5.0855 24 1 1 1 -1 6.0305 25 1 1 0 -1 2.0967 26 1 1 -1 -1 6.7428 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3618 atoms have been selected out of 3692 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 450 150 150 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 603 201 201 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 456 152 152 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1774 589 588 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 105 35 35 0.99 Total of13065 atoms and 4346 groups and 4340 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3692 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1219 Number of atoms = 3692 Number of groups = 1224 Number of bonds = 3685 Number of angles = 1323 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1221 Number of HB donors = 2420 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1219 Number of atoms = 3692 Number of groups = 1224 Number of bonds = 3685 Number of angles = 1323 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1221 Number of HB donors = 2420 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.124" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1219" Evaluating: 1219-7 Parameter: NUMWAT <- "1212" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1212" Comparing "1081" and "1212". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.124" Parameter: BOX -> "33.124" Parameter: BOX -> "33.124" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.12400 B = 33.12400 C = 33.12400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1229 2 1 -1 0 -1 2.3253 3 1 -1 1 -1 5.4157 4 1 0 -1 -1 4.8452 5 1 0 0 -1 1.2505 6 1 0 1 -1 2.2657 7 1 -1 -1 0 5.0784 8 1 -1 0 0 1.3921 9 1 -1 1 0 5.0830 10 1 0 -1 0 1.1121 11 1 0 1 0 1.1121 12 1 -1 -1 1 6.0276 13 1 -1 0 1 2.0944 14 1 -1 1 1 6.7397 15 1 0 -1 1 2.2657 16 1 0 0 1 1.2505 17 1 0 1 1 4.8452 18 1 1 1 1 6.1229 19 1 1 0 1 2.3253 20 1 1 -1 1 5.4157 21 1 1 1 0 5.0784 22 1 1 0 0 1.3921 23 1 1 -1 0 5.0830 24 1 1 1 -1 6.0276 25 1 1 0 -1 2.0944 26 1 1 -1 -1 6.7397 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3618 atoms have been selected out of 3692 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 887 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 450 150 150 0.00 2 C002 has 762 254 254 0.00 3 C003 has 111 37 37 0.00 4 C004 has 603 201 201 0.00 5 C005 has 1587 529 529 0.00 6 C006 has 456 152 152 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1774 589 588 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 105 35 35 0.99 Total of13059 atoms and 4344 groups and 4338 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3692 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1218 Number of atoms = 3689 Number of groups = 1223 Number of bonds = 3682 Number of angles = 1322 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1220 Number of HB donors = 2418 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1218 Number of atoms = 3689 Number of groups = 1223 Number of bonds = 3682 Number of angles = 1322 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1220 Number of HB donors = 2418 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.122" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1218" Evaluating: 1218-7 Parameter: NUMWAT <- "1211" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1211" Comparing "1081" and "1211". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.122" Parameter: BOX -> "33.122" Parameter: BOX -> "33.122" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.12200 B = 33.12200 C = 33.12200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1213 2 1 -1 0 -1 2.3226 3 1 -1 1 -1 5.4123 4 1 0 -1 -1 4.8455 5 1 0 0 -1 1.2487 6 1 0 1 -1 2.2630 7 1 -1 -1 0 5.0764 8 1 -1 0 0 1.3903 9 1 -1 1 0 5.0805 10 1 0 -1 0 1.1102 11 1 0 1 0 1.1102 12 1 -1 -1 1 6.0247 13 1 -1 0 1 2.0920 14 1 -1 1 1 6.7367 15 1 0 -1 1 2.2630 16 1 0 0 1 1.2487 17 1 0 1 1 4.8455 18 1 1 1 1 6.1213 19 1 1 0 1 2.3226 20 1 1 -1 1 5.4123 21 1 1 1 0 5.0764 22 1 1 0 0 1.3903 23 1 1 -1 0 5.0805 24 1 1 1 -1 6.0247 25 1 1 0 -1 2.0920 26 1 1 -1 -1 6.7367 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3615 atoms have been selected out of 3689 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 450 150 150 0.00 2 C002 has 762 254 254 0.00 3 C003 has 111 37 37 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 453 151 151 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 105 35 35 0.98 Total of13050 atoms and 4341 groups and 4335 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3689 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1218 Number of atoms = 3689 Number of groups = 1223 Number of bonds = 3682 Number of angles = 1322 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1220 Number of HB donors = 2418 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1218 Number of atoms = 3689 Number of groups = 1223 Number of bonds = 3682 Number of angles = 1322 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1220 Number of HB donors = 2418 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.12" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1218" Evaluating: 1218-7 Parameter: NUMWAT <- "1211" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1211" Comparing "1081" and "1211". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.12" Parameter: BOX -> "33.12" Parameter: BOX -> "33.12" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.12000 B = 33.12000 C = 33.12000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1197 2 1 -1 0 -1 2.3200 3 1 -1 1 -1 5.4088 4 1 0 -1 -1 4.8458 5 1 0 0 -1 1.2469 6 1 0 1 -1 2.2603 7 1 -1 -1 0 5.0745 8 1 -1 0 0 1.3885 9 1 -1 1 0 5.0779 10 1 0 -1 0 1.1083 11 1 0 1 0 1.1083 12 1 -1 -1 1 6.0218 13 1 -1 0 1 2.0896 14 1 -1 1 1 6.7336 15 1 0 -1 1 2.2603 16 1 0 0 1 1.2469 17 1 0 1 1 4.8458 18 1 1 1 1 6.1197 19 1 1 0 1 2.3200 20 1 1 -1 1 5.4088 21 1 1 1 0 5.0745 22 1 1 0 0 1.3885 23 1 1 -1 0 5.0779 24 1 1 1 -1 6.0218 25 1 1 0 -1 2.0896 26 1 1 -1 -1 6.7336 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3615 atoms have been selected out of 3689 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 450 150 150 0.00 2 C002 has 765 255 255 0.00 3 C003 has 111 37 37 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 453 151 151 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 105 35 35 0.98 Total of13053 atoms and 4342 groups and 4336 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3689 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1218 Number of atoms = 3689 Number of groups = 1223 Number of bonds = 3682 Number of angles = 1322 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1220 Number of HB donors = 2418 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1218 Number of atoms = 3689 Number of groups = 1223 Number of bonds = 3682 Number of angles = 1322 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1220 Number of HB donors = 2418 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.118" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1218" Evaluating: 1218-7 Parameter: NUMWAT <- "1211" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1211" Comparing "1081" and "1211". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.118" Parameter: BOX -> "33.118" Parameter: BOX -> "33.118" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.11800 B = 33.11800 C = 33.11800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1181 2 1 -1 0 -1 2.3173 3 1 -1 1 -1 5.4054 4 1 0 -1 -1 4.8461 5 1 0 0 -1 1.2450 6 1 0 1 -1 2.2576 7 1 -1 -1 0 5.0725 8 1 -1 0 0 1.3867 9 1 -1 1 0 5.0754 10 1 0 -1 0 1.1064 11 1 0 1 0 1.1064 12 1 -1 -1 1 6.0189 13 1 -1 0 1 2.0872 14 1 -1 1 1 6.7306 15 1 0 -1 1 2.2576 16 1 0 0 1 1.2450 17 1 0 1 1 4.8461 18 1 1 1 1 6.1181 19 1 1 0 1 2.3173 20 1 1 -1 1 5.4054 21 1 1 1 0 5.0725 22 1 1 0 0 1.3867 23 1 1 -1 0 5.0754 24 1 1 1 -1 6.0189 25 1 1 0 -1 2.0872 26 1 1 -1 -1 6.7306 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3615 atoms have been selected out of 3689 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 450 150 150 0.00 2 C002 has 765 255 255 0.00 3 C003 has 111 37 37 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 453 151 151 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 105 35 35 0.98 Total of13053 atoms and 4342 groups and 4336 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3689 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1218 Number of atoms = 3689 Number of groups = 1223 Number of bonds = 3682 Number of angles = 1322 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1220 Number of HB donors = 2418 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1218 Number of atoms = 3689 Number of groups = 1223 Number of bonds = 3682 Number of angles = 1322 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1220 Number of HB donors = 2418 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.116" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1218" Evaluating: 1218-7 Parameter: NUMWAT <- "1211" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1211" Comparing "1081" and "1211". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.116" Parameter: BOX -> "33.116" Parameter: BOX -> "33.116" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.11600 B = 33.11600 C = 33.11600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1165 2 1 -1 0 -1 2.3146 3 1 -1 1 -1 5.4020 4 1 0 -1 -1 4.8464 5 1 0 0 -1 1.2432 6 1 0 1 -1 2.2550 7 1 -1 -1 0 5.0705 8 1 -1 0 0 1.3850 9 1 -1 1 0 5.0728 10 1 0 -1 0 1.1045 11 1 0 1 0 1.1045 12 1 -1 -1 1 6.0160 13 1 -1 0 1 2.0848 14 1 -1 1 1 6.7276 15 1 0 -1 1 2.2550 16 1 0 0 1 1.2432 17 1 0 1 1 4.8464 18 1 1 1 1 6.1165 19 1 1 0 1 2.3146 20 1 1 -1 1 5.4020 21 1 1 1 0 5.0705 22 1 1 0 0 1.3850 23 1 1 -1 0 5.0728 24 1 1 1 -1 6.0160 25 1 1 0 -1 2.0848 26 1 1 -1 -1 6.7276 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3615 atoms have been selected out of 3689 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 677 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 453 151 151 0.00 2 C002 has 762 254 254 0.00 3 C003 has 111 37 37 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1584 528 528 0.00 6 C006 has 450 150 150 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1668 556 556 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 105 35 35 0.98 Total of13056 atoms and 4343 groups and 4337 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3689 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1217 Number of atoms = 3686 Number of groups = 1222 Number of bonds = 3679 Number of angles = 1321 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1219 Number of HB donors = 2416 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1217 Number of atoms = 3686 Number of groups = 1222 Number of bonds = 3679 Number of angles = 1321 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1219 Number of HB donors = 2416 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.114" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1217" Evaluating: 1217-7 Parameter: NUMWAT <- "1210" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1210" Comparing "1081" and "1210". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.114" Parameter: BOX -> "33.114" Parameter: BOX -> "33.114" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.11400 B = 33.11400 C = 33.11400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1149 2 1 -1 0 -1 2.3120 3 1 -1 1 -1 5.3985 4 1 0 -1 -1 4.8467 5 1 0 0 -1 1.2414 6 1 0 1 -1 2.2523 7 1 -1 -1 0 5.0685 8 1 -1 0 0 1.3832 9 1 -1 1 0 5.0703 10 1 0 -1 0 1.1026 11 1 0 1 0 1.1026 12 1 -1 -1 1 6.0131 13 1 -1 0 1 2.0825 14 1 -1 1 1 6.7245 15 1 0 -1 1 2.2523 16 1 0 0 1 1.2414 17 1 0 1 1 4.8467 18 1 1 1 1 6.1149 19 1 1 0 1 2.3120 20 1 1 -1 1 5.3985 21 1 1 1 0 5.0685 22 1 1 0 0 1.3832 23 1 1 -1 0 5.0703 24 1 1 1 -1 6.0131 25 1 1 0 -1 2.0825 26 1 1 -1 -1 6.7245 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3612 atoms have been selected out of 3686 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 450 150 150 0.00 2 C002 has 762 254 254 0.00 3 C003 has 111 37 37 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 450 150 150 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 105 35 35 0.98 Total of13041 atoms and 4338 groups and 4332 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3686 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1217 Number of atoms = 3686 Number of groups = 1222 Number of bonds = 3679 Number of angles = 1321 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1219 Number of HB donors = 2416 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1217 Number of atoms = 3686 Number of groups = 1222 Number of bonds = 3679 Number of angles = 1321 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1219 Number of HB donors = 2416 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.112" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1217" Evaluating: 1217-7 Parameter: NUMWAT <- "1210" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1210" Comparing "1081" and "1210". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.112" Parameter: BOX -> "33.112" Parameter: BOX -> "33.112" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.11200 B = 33.11200 C = 33.11200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1133 2 1 -1 0 -1 2.3093 3 1 -1 1 -1 5.3951 4 1 0 -1 -1 4.8470 5 1 0 0 -1 1.2395 6 1 0 1 -1 2.2496 7 1 -1 -1 0 5.0665 8 1 -1 0 0 1.3814 9 1 -1 1 0 5.0678 10 1 0 -1 0 1.1007 11 1 0 1 0 1.1007 12 1 -1 -1 1 6.0102 13 1 -1 0 1 2.0801 14 1 -1 1 1 6.7215 15 1 0 -1 1 2.2496 16 1 0 0 1 1.2395 17 1 0 1 1 4.8470 18 1 1 1 1 6.1133 19 1 1 0 1 2.3093 20 1 1 -1 1 5.3951 21 1 1 1 0 5.0665 22 1 1 0 0 1.3814 23 1 1 -1 0 5.0678 24 1 1 1 -1 6.0102 25 1 1 0 -1 2.0801 26 1 1 -1 -1 6.7215 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3612 atoms have been selected out of 3686 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 450 150 150 0.00 2 C002 has 765 255 255 0.00 3 C003 has 111 37 37 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 450 150 150 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 105 35 35 0.97 Total of13044 atoms and 4339 groups and 4333 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3686 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1217 Number of atoms = 3686 Number of groups = 1222 Number of bonds = 3679 Number of angles = 1321 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1219 Number of HB donors = 2416 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1217 Number of atoms = 3686 Number of groups = 1222 Number of bonds = 3679 Number of angles = 1321 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1219 Number of HB donors = 2416 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.11" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1217" Evaluating: 1217-7 Parameter: NUMWAT <- "1210" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1210" Comparing "1081" and "1210". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.11" Parameter: BOX -> "33.11" Parameter: BOX -> "33.11" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.11000 B = 33.11000 C = 33.11000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1117 2 1 -1 0 -1 2.3066 3 1 -1 1 -1 5.3917 4 1 0 -1 -1 4.8473 5 1 0 0 -1 1.2377 6 1 0 1 -1 2.2469 7 1 -1 -1 0 5.0645 8 1 -1 0 0 1.3796 9 1 -1 1 0 5.0652 10 1 0 -1 0 1.0988 11 1 0 1 0 1.0988 12 1 -1 -1 1 6.0073 13 1 -1 0 1 2.0777 14 1 -1 1 1 6.7184 15 1 0 -1 1 2.2469 16 1 0 0 1 1.2377 17 1 0 1 1 4.8473 18 1 1 1 1 6.1117 19 1 1 0 1 2.3066 20 1 1 -1 1 5.3917 21 1 1 1 0 5.0645 22 1 1 0 0 1.3796 23 1 1 -1 0 5.0652 24 1 1 1 -1 6.0073 25 1 1 0 -1 2.0777 26 1 1 -1 -1 6.7184 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3612 atoms have been selected out of 3686 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 450 150 150 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 450 150 150 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1668 556 556 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 105 35 35 0.97 Total of13050 atoms and 4341 groups and 4335 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3686 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1217 Number of atoms = 3686 Number of groups = 1222 Number of bonds = 3679 Number of angles = 1321 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1219 Number of HB donors = 2416 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1217 Number of atoms = 3686 Number of groups = 1222 Number of bonds = 3679 Number of angles = 1321 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1219 Number of HB donors = 2416 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.108" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1217" Evaluating: 1217-7 Parameter: NUMWAT <- "1210" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1210" Comparing "1081" and "1210". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.108" Parameter: BOX -> "33.108" Parameter: BOX -> "33.108" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.10800 B = 33.10800 C = 33.10800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1101 2 1 -1 0 -1 2.3040 3 1 -1 1 -1 5.3882 4 1 0 -1 -1 4.8476 5 1 0 0 -1 1.2359 6 1 0 1 -1 2.2442 7 1 -1 -1 0 5.0626 8 1 -1 0 0 1.3778 9 1 -1 1 0 5.0627 10 1 0 -1 0 1.0969 11 1 0 1 0 1.0969 12 1 -1 -1 1 6.0044 13 1 -1 0 1 2.0754 14 1 -1 1 1 6.7154 15 1 0 -1 1 2.2442 16 1 0 0 1 1.2359 17 1 0 1 1 4.8476 18 1 1 1 1 6.1101 19 1 1 0 1 2.3040 20 1 1 -1 1 5.3882 21 1 1 1 0 5.0626 22 1 1 0 0 1.3778 23 1 1 -1 0 5.0627 24 1 1 1 -1 6.0044 25 1 1 0 -1 2.0754 26 1 1 -1 -1 6.7154 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3612 atoms have been selected out of 3686 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 450 150 150 0.00 2 C002 has 768 256 256 0.00 3 C003 has 114 38 38 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 450 150 150 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1668 556 556 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 105 35 35 0.97 Total of13053 atoms and 4342 groups and 4336 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3686 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1217 Number of atoms = 3686 Number of groups = 1222 Number of bonds = 3679 Number of angles = 1321 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1219 Number of HB donors = 2416 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1217 Number of atoms = 3686 Number of groups = 1222 Number of bonds = 3679 Number of angles = 1321 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1219 Number of HB donors = 2416 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.106" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1217" Evaluating: 1217-7 Parameter: NUMWAT <- "1210" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1210" Comparing "1081" and "1210". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.106" Parameter: BOX -> "33.106" Parameter: BOX -> "33.106" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.10600 B = 33.10600 C = 33.10600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1085 2 1 -1 0 -1 2.3013 3 1 -1 1 -1 5.3848 4 1 0 -1 -1 4.8479 5 1 0 0 -1 1.2341 6 1 0 1 -1 2.2416 7 1 -1 -1 0 5.0606 8 1 -1 0 0 1.3761 9 1 -1 1 0 5.0602 10 1 0 -1 0 1.0950 11 1 0 1 0 1.0950 12 1 -1 -1 1 6.0016 13 1 -1 0 1 2.0730 14 1 -1 1 1 6.7123 15 1 0 -1 1 2.2416 16 1 0 0 1 1.2341 17 1 0 1 1 4.8479 18 1 1 1 1 6.1085 19 1 1 0 1 2.3013 20 1 1 -1 1 5.3848 21 1 1 1 0 5.0606 22 1 1 0 0 1.3761 23 1 1 -1 0 5.0602 24 1 1 1 -1 6.0016 25 1 1 0 -1 2.0730 26 1 1 -1 -1 6.7123 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3612 atoms have been selected out of 3686 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 450 150 150 0.00 2 C002 has 768 256 256 0.00 3 C003 has 114 38 38 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 450 150 150 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1668 556 556 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 105 35 35 0.97 Total of13053 atoms and 4342 groups and 4336 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3686 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1217 Number of atoms = 3686 Number of groups = 1222 Number of bonds = 3679 Number of angles = 1321 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1219 Number of HB donors = 2416 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1217 Number of atoms = 3686 Number of groups = 1222 Number of bonds = 3679 Number of angles = 1321 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1219 Number of HB donors = 2416 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.104" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1217" Evaluating: 1217-7 Parameter: NUMWAT <- "1210" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1210" Comparing "1081" and "1210". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.104" Parameter: BOX -> "33.104" Parameter: BOX -> "33.104" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.10400 B = 33.10400 C = 33.10400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1069 2 1 -1 0 -1 2.2986 3 1 -1 1 -1 5.3814 4 1 0 -1 -1 4.8482 5 1 0 0 -1 1.2322 6 1 0 1 -1 2.2389 7 1 -1 -1 0 5.0586 8 1 -1 0 0 1.3743 9 1 -1 1 0 5.0576 10 1 0 -1 0 1.0931 11 1 0 1 0 1.0931 12 1 -1 -1 1 5.9987 13 1 -1 0 1 2.0706 14 1 -1 1 1 6.7093 15 1 0 -1 1 2.2389 16 1 0 0 1 1.2322 17 1 0 1 1 4.8482 18 1 1 1 1 6.1069 19 1 1 0 1 2.2986 20 1 1 -1 1 5.3814 21 1 1 1 0 5.0586 22 1 1 0 0 1.3743 23 1 1 -1 0 5.0576 24 1 1 1 -1 5.9987 25 1 1 0 -1 2.0706 26 1 1 -1 -1 6.7093 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3612 atoms have been selected out of 3686 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 106 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 450 150 150 0.00 2 C002 has 771 257 257 0.00 3 C003 has 114 38 38 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 453 151 151 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1774 589 588 0.00 9 C009 has 489 163 163 0.00 10 C010 has 1668 556 556 0.00 12 C012 has 90 30 30 0.00 13 C013 has 501 167 167 0.00 14 C014 has 105 35 35 0.97 Total of13068 atoms and 4347 groups and 4341 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3686 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1216 Number of atoms = 3683 Number of groups = 1221 Number of bonds = 3676 Number of angles = 1320 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1218 Number of HB donors = 2414 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1216 Number of atoms = 3683 Number of groups = 1221 Number of bonds = 3676 Number of angles = 1320 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1218 Number of HB donors = 2414 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.102" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1216" Evaluating: 1216-7 Parameter: NUMWAT <- "1209" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1209" Comparing "1081" and "1209". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.102" Parameter: BOX -> "33.102" Parameter: BOX -> "33.102" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.10200 B = 33.10200 C = 33.10200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1053 2 1 -1 0 -1 2.2960 3 1 -1 1 -1 5.3779 4 1 0 -1 -1 4.8486 5 1 0 0 -1 1.2304 6 1 0 1 -1 2.2362 7 1 -1 -1 0 5.0566 8 1 -1 0 0 1.3725 9 1 -1 1 0 5.0551 10 1 0 -1 0 1.0912 11 1 0 1 0 1.0912 12 1 -1 -1 1 5.9958 13 1 -1 0 1 2.0682 14 1 -1 1 1 6.7063 15 1 0 -1 1 2.2362 16 1 0 0 1 1.2304 17 1 0 1 1 4.8486 18 1 1 1 1 6.1053 19 1 1 0 1 2.2960 20 1 1 -1 1 5.3779 21 1 1 1 0 5.0566 22 1 1 0 0 1.3725 23 1 1 -1 0 5.0551 24 1 1 1 -1 5.9958 25 1 1 0 -1 2.0682 26 1 1 -1 -1 6.7063 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3609 atoms have been selected out of 3683 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 450 150 150 0.00 2 C002 has 771 257 257 0.00 3 C003 has 114 38 38 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 453 151 151 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1668 556 556 0.00 12 C012 has 90 30 30 0.00 13 C013 has 498 166 166 0.00 14 C014 has 105 35 35 0.96 Total of13056 atoms and 4343 groups and 4337 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3683 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1216 Number of atoms = 3683 Number of groups = 1221 Number of bonds = 3676 Number of angles = 1320 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1218 Number of HB donors = 2414 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1216 Number of atoms = 3683 Number of groups = 1221 Number of bonds = 3676 Number of angles = 1320 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1218 Number of HB donors = 2414 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.1" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1216" Evaluating: 1216-7 Parameter: NUMWAT <- "1209" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1209" Comparing "1081" and "1209". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.1" Parameter: BOX -> "33.1" Parameter: BOX -> "33.1" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.10000 B = 33.10000 C = 33.10000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1038 2 1 -1 0 -1 2.2933 3 1 -1 1 -1 5.3745 4 1 0 -1 -1 4.8489 5 1 0 0 -1 1.2286 6 1 0 1 -1 2.2335 7 1 -1 -1 0 5.0546 8 1 -1 0 0 1.3707 9 1 -1 1 0 5.0525 10 1 0 -1 0 1.0893 11 1 0 1 0 1.0893 12 1 -1 -1 1 5.9929 13 1 -1 0 1 2.0659 14 1 -1 1 1 6.7032 15 1 0 -1 1 2.2335 16 1 0 0 1 1.2286 17 1 0 1 1 4.8489 18 1 1 1 1 6.1038 19 1 1 0 1 2.2933 20 1 1 -1 1 5.3745 21 1 1 1 0 5.0546 22 1 1 0 0 1.3707 23 1 1 -1 0 5.0525 24 1 1 1 -1 5.9929 25 1 1 0 -1 2.0659 26 1 1 -1 -1 6.7032 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3609 atoms have been selected out of 3683 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 163 OPERATED ON BY TRANSFORMATION C008 RESIDUE 716 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 450 150 150 0.00 2 C002 has 771 257 257 0.00 3 C003 has 114 38 38 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1581 527 527 0.00 6 C006 has 453 151 151 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1668 556 556 0.00 12 C012 has 90 30 30 0.00 13 C013 has 495 165 165 0.00 14 C014 has 102 34 34 0.96 Total of13047 atoms and 4340 groups and 4334 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3683 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1214 Number of atoms = 3677 Number of groups = 1219 Number of bonds = 3670 Number of angles = 1318 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1216 Number of HB donors = 2410 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1214 Number of atoms = 3677 Number of groups = 1219 Number of bonds = 3670 Number of angles = 1318 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1216 Number of HB donors = 2410 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.098" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1214" Evaluating: 1214-7 Parameter: NUMWAT <- "1207" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1207" Comparing "1081" and "1207". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.098" Parameter: BOX -> "33.098" Parameter: BOX -> "33.098" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.09800 B = 33.09800 C = 33.09800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1022 2 1 -1 0 -1 2.2906 3 1 -1 1 -1 5.3711 4 1 0 -1 -1 4.8492 5 1 0 0 -1 1.2268 6 1 0 1 -1 2.2309 7 1 -1 -1 0 5.0527 8 1 -1 0 0 1.3690 9 1 -1 1 0 5.0500 10 1 0 -1 0 1.0874 11 1 0 1 0 1.0874 12 1 -1 -1 1 5.9900 13 1 -1 0 1 2.0635 14 1 -1 1 1 6.7002 15 1 0 -1 1 2.2309 16 1 0 0 1 1.2268 17 1 0 1 1 4.8492 18 1 1 1 1 6.1022 19 1 1 0 1 2.2906 20 1 1 -1 1 5.3711 21 1 1 1 0 5.0527 22 1 1 0 0 1.3690 23 1 1 -1 0 5.0500 24 1 1 1 -1 5.9900 25 1 1 0 -1 2.0635 26 1 1 -1 -1 6.7002 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3603 atoms have been selected out of 3677 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 450 150 150 0.00 2 C002 has 771 257 257 0.00 3 C003 has 114 38 38 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1578 526 526 0.00 6 C006 has 453 151 151 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1668 556 556 0.00 12 C012 has 90 30 30 0.00 13 C013 has 495 165 165 0.00 14 C014 has 102 34 34 0.96 Total of13035 atoms and 4336 groups and 4330 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3677 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1214 Number of atoms = 3677 Number of groups = 1219 Number of bonds = 3670 Number of angles = 1318 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1216 Number of HB donors = 2410 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1214 Number of atoms = 3677 Number of groups = 1219 Number of bonds = 3670 Number of angles = 1318 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1216 Number of HB donors = 2410 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.096" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1214" Evaluating: 1214-7 Parameter: NUMWAT <- "1207" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1207" Comparing "1081" and "1207". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.096" Parameter: BOX -> "33.096" Parameter: BOX -> "33.096" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.09600 B = 33.09600 C = 33.09600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.1006 2 1 -1 0 -1 2.2880 3 1 -1 1 -1 5.3676 4 1 0 -1 -1 4.8495 5 1 0 0 -1 1.2250 6 1 0 1 -1 2.2282 7 1 -1 -1 0 5.0507 8 1 -1 0 0 1.3672 9 1 -1 1 0 5.0475 10 1 0 -1 0 1.0855 11 1 0 1 0 1.0855 12 1 -1 -1 1 5.9871 13 1 -1 0 1 2.0611 14 1 -1 1 1 6.6971 15 1 0 -1 1 2.2282 16 1 0 0 1 1.2250 17 1 0 1 1 4.8495 18 1 1 1 1 6.1006 19 1 1 0 1 2.2880 20 1 1 -1 1 5.3676 21 1 1 1 0 5.0507 22 1 1 0 0 1.3672 23 1 1 -1 0 5.0475 24 1 1 1 -1 5.9871 25 1 1 0 -1 2.0611 26 1 1 -1 -1 6.6971 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3603 atoms have been selected out of 3677 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 453 151 151 0.00 2 C002 has 771 257 257 0.00 3 C003 has 114 38 38 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1578 526 526 0.00 6 C006 has 453 151 151 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1668 556 556 0.00 12 C012 has 90 30 30 0.00 13 C013 has 495 165 165 0.00 14 C014 has 102 34 34 0.96 Total of13038 atoms and 4337 groups and 4331 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3677 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1214 Number of atoms = 3677 Number of groups = 1219 Number of bonds = 3670 Number of angles = 1318 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1216 Number of HB donors = 2410 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1214 Number of atoms = 3677 Number of groups = 1219 Number of bonds = 3670 Number of angles = 1318 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1216 Number of HB donors = 2410 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.094" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1214" Evaluating: 1214-7 Parameter: NUMWAT <- "1207" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1207" Comparing "1081" and "1207". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.094" Parameter: BOX -> "33.094" Parameter: BOX -> "33.094" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.09400 B = 33.09400 C = 33.09400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0990 2 1 -1 0 -1 2.2853 3 1 -1 1 -1 5.3642 4 1 0 -1 -1 4.8498 5 1 0 0 -1 1.2231 6 1 0 1 -1 2.2255 7 1 -1 -1 0 5.0487 8 1 -1 0 0 1.3654 9 1 -1 1 0 5.0449 10 1 0 -1 0 1.0836 11 1 0 1 0 1.0836 12 1 -1 -1 1 5.9842 13 1 -1 0 1 2.0588 14 1 -1 1 1 6.6941 15 1 0 -1 1 2.2255 16 1 0 0 1 1.2231 17 1 0 1 1 4.8498 18 1 1 1 1 6.0990 19 1 1 0 1 2.2853 20 1 1 -1 1 5.3642 21 1 1 1 0 5.0487 22 1 1 0 0 1.3654 23 1 1 -1 0 5.0449 24 1 1 1 -1 5.9842 25 1 1 0 -1 2.0588 26 1 1 -1 -1 6.6941 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3603 atoms have been selected out of 3677 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 453 151 151 0.00 2 C002 has 771 257 257 0.00 3 C003 has 114 38 38 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1578 526 526 0.00 6 C006 has 453 151 151 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1668 556 556 0.00 12 C012 has 90 30 30 0.00 13 C013 has 495 165 165 0.00 14 C014 has 102 34 34 0.96 Total of13038 atoms and 4337 groups and 4331 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3677 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1214 Number of atoms = 3677 Number of groups = 1219 Number of bonds = 3670 Number of angles = 1318 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1216 Number of HB donors = 2410 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1214 Number of atoms = 3677 Number of groups = 1219 Number of bonds = 3670 Number of angles = 1318 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1216 Number of HB donors = 2410 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.092" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1214" Evaluating: 1214-7 Parameter: NUMWAT <- "1207" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1207" Comparing "1081" and "1207". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.092" Parameter: BOX -> "33.092" Parameter: BOX -> "33.092" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.09200 B = 33.09200 C = 33.09200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0974 2 1 -1 0 -1 2.2826 3 1 -1 1 -1 5.3608 4 1 0 -1 -1 4.8501 5 1 0 0 -1 1.2213 6 1 0 1 -1 2.2229 7 1 -1 -1 0 5.0467 8 1 -1 0 0 1.3636 9 1 -1 1 0 5.0424 10 1 0 -1 0 1.0817 11 1 0 1 0 1.0817 12 1 -1 -1 1 5.9814 13 1 -1 0 1 2.0564 14 1 -1 1 1 6.6911 15 1 0 -1 1 2.2229 16 1 0 0 1 1.2213 17 1 0 1 1 4.8501 18 1 1 1 1 6.0974 19 1 1 0 1 2.2826 20 1 1 -1 1 5.3608 21 1 1 1 0 5.0467 22 1 1 0 0 1.3636 23 1 1 -1 0 5.0424 24 1 1 1 -1 5.9814 25 1 1 0 -1 2.0564 26 1 1 -1 -1 6.6911 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3603 atoms have been selected out of 3677 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 453 151 151 0.00 2 C002 has 771 257 257 0.00 3 C003 has 114 38 38 0.00 4 C004 has 609 203 203 0.00 5 C005 has 1578 526 526 0.00 6 C006 has 453 151 151 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1668 556 556 0.00 12 C012 has 90 30 30 0.00 13 C013 has 495 165 165 0.00 14 C014 has 102 34 34 0.95 Total of13038 atoms and 4337 groups and 4331 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3677 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1214 Number of atoms = 3677 Number of groups = 1219 Number of bonds = 3670 Number of angles = 1318 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1216 Number of HB donors = 2410 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1214 Number of atoms = 3677 Number of groups = 1219 Number of bonds = 3670 Number of angles = 1318 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1216 Number of HB donors = 2410 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.09" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1214" Evaluating: 1214-7 Parameter: NUMWAT <- "1207" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1207" Comparing "1081" and "1207". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.09" Parameter: BOX -> "33.09" Parameter: BOX -> "33.09" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.09000 B = 33.09000 C = 33.09000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0958 2 1 -1 0 -1 2.2800 3 1 -1 1 -1 5.3574 4 1 0 -1 -1 4.8505 5 1 0 0 -1 1.2195 6 1 0 1 -1 2.2202 7 1 -1 -1 0 5.0448 8 1 -1 0 0 1.3619 9 1 -1 1 0 5.0399 10 1 0 -1 0 1.0798 11 1 0 1 0 1.0798 12 1 -1 -1 1 5.9785 13 1 -1 0 1 2.0541 14 1 -1 1 1 6.6880 15 1 0 -1 1 2.2202 16 1 0 0 1 1.2195 17 1 0 1 1 4.8505 18 1 1 1 1 6.0958 19 1 1 0 1 2.2800 20 1 1 -1 1 5.3574 21 1 1 1 0 5.0448 22 1 1 0 0 1.3619 23 1 1 -1 0 5.0399 24 1 1 1 -1 5.9785 25 1 1 0 -1 2.0541 26 1 1 -1 -1 6.6880 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3603 atoms have been selected out of 3677 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 378 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 456 152 152 0.00 2 C002 has 771 257 257 0.00 3 C003 has 114 38 38 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1575 525 525 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1668 556 556 0.00 12 C012 has 90 30 30 0.00 13 C013 has 495 165 165 0.00 14 C014 has 102 34 34 0.95 Total of13041 atoms and 4338 groups and 4332 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3677 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1213 Number of atoms = 3674 Number of groups = 1218 Number of bonds = 3667 Number of angles = 1317 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1215 Number of HB donors = 2408 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1213 Number of atoms = 3674 Number of groups = 1218 Number of bonds = 3667 Number of angles = 1317 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1215 Number of HB donors = 2408 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.088" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1213" Evaluating: 1213-7 Parameter: NUMWAT <- "1206" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1206" Comparing "1081" and "1206". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.088" Parameter: BOX -> "33.088" Parameter: BOX -> "33.088" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.08800 B = 33.08800 C = 33.08800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0943 2 1 -1 0 -1 2.2773 3 1 -1 1 -1 5.3539 4 1 0 -1 -1 4.8508 5 1 0 0 -1 1.2177 6 1 0 1 -1 2.2175 7 1 -1 -1 0 5.0428 8 1 -1 0 0 1.3601 9 1 -1 1 0 5.0373 10 1 0 -1 0 1.0779 11 1 0 1 0 1.0779 12 1 -1 -1 1 5.9756 13 1 -1 0 1 2.0517 14 1 -1 1 1 6.6850 15 1 0 -1 1 2.2175 16 1 0 0 1 1.2177 17 1 0 1 1 4.8508 18 1 1 1 1 6.0943 19 1 1 0 1 2.2773 20 1 1 -1 1 5.3539 21 1 1 1 0 5.0428 22 1 1 0 0 1.3601 23 1 1 -1 0 5.0373 24 1 1 1 -1 5.9756 25 1 1 0 -1 2.0517 26 1 1 -1 -1 6.6850 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3600 atoms have been selected out of 3674 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 453 151 151 0.00 2 C002 has 771 257 257 0.00 3 C003 has 114 38 38 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1572 524 524 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 90 30 30 0.00 13 C013 has 495 165 165 0.00 14 C014 has 102 34 34 0.95 Total of13026 atoms and 4333 groups and 4327 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3674 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1213 Number of atoms = 3674 Number of groups = 1218 Number of bonds = 3667 Number of angles = 1317 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1215 Number of HB donors = 2408 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1213 Number of atoms = 3674 Number of groups = 1218 Number of bonds = 3667 Number of angles = 1317 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1215 Number of HB donors = 2408 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.086" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1213" Evaluating: 1213-7 Parameter: NUMWAT <- "1206" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1206" Comparing "1081" and "1206". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.086" Parameter: BOX -> "33.086" Parameter: BOX -> "33.086" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.08600 B = 33.08600 C = 33.08600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0927 2 1 -1 0 -1 2.2746 3 1 -1 1 -1 5.3505 4 1 0 -1 -1 4.8511 5 1 0 0 -1 1.2158 6 1 0 1 -1 2.2148 7 1 -1 -1 0 5.0408 8 1 -1 0 0 1.3583 9 1 -1 1 0 5.0348 10 1 0 -1 0 1.0760 11 1 0 1 0 1.0760 12 1 -1 -1 1 5.9727 13 1 -1 0 1 2.0493 14 1 -1 1 1 6.6819 15 1 0 -1 1 2.2148 16 1 0 0 1 1.2158 17 1 0 1 1 4.8511 18 1 1 1 1 6.0927 19 1 1 0 1 2.2746 20 1 1 -1 1 5.3505 21 1 1 1 0 5.0408 22 1 1 0 0 1.3583 23 1 1 -1 0 5.0348 24 1 1 1 -1 5.9727 25 1 1 0 -1 2.0493 26 1 1 -1 -1 6.6819 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3600 atoms have been selected out of 3674 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 453 151 151 0.00 2 C002 has 771 257 257 0.00 3 C003 has 114 38 38 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1572 524 524 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 90 30 30 0.00 13 C013 has 495 165 165 0.00 14 C014 has 102 34 34 0.95 Total of13026 atoms and 4333 groups and 4327 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3674 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1213 Number of atoms = 3674 Number of groups = 1218 Number of bonds = 3667 Number of angles = 1317 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1215 Number of HB donors = 2408 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1213 Number of atoms = 3674 Number of groups = 1218 Number of bonds = 3667 Number of angles = 1317 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1215 Number of HB donors = 2408 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.084" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1213" Evaluating: 1213-7 Parameter: NUMWAT <- "1206" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1206" Comparing "1081" and "1206". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.084" Parameter: BOX -> "33.084" Parameter: BOX -> "33.084" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.08400 B = 33.08400 C = 33.08400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0911 2 1 -1 0 -1 2.2720 3 1 -1 1 -1 5.3471 4 1 0 -1 -1 4.8514 5 1 0 0 -1 1.2140 6 1 0 1 -1 2.2122 7 1 -1 -1 0 5.0388 8 1 -1 0 0 1.3566 9 1 -1 1 0 5.0323 10 1 0 -1 0 1.0741 11 1 0 1 0 1.0741 12 1 -1 -1 1 5.9698 13 1 -1 0 1 2.0470 14 1 -1 1 1 6.6789 15 1 0 -1 1 2.2122 16 1 0 0 1 1.2140 17 1 0 1 1 4.8514 18 1 1 1 1 6.0911 19 1 1 0 1 2.2720 20 1 1 -1 1 5.3471 21 1 1 1 0 5.0388 22 1 1 0 0 1.3566 23 1 1 -1 0 5.0323 24 1 1 1 -1 5.9698 25 1 1 0 -1 2.0470 26 1 1 -1 -1 6.6789 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3600 atoms have been selected out of 3674 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 453 151 151 0.00 2 C002 has 771 257 257 0.00 3 C003 has 114 38 38 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1572 524 524 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1668 556 556 0.00 12 C012 has 90 30 30 0.00 13 C013 has 495 165 165 0.00 14 C014 has 102 34 34 0.95 Total of13029 atoms and 4334 groups and 4328 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3674 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1213 Number of atoms = 3674 Number of groups = 1218 Number of bonds = 3667 Number of angles = 1317 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1215 Number of HB donors = 2408 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1213 Number of atoms = 3674 Number of groups = 1218 Number of bonds = 3667 Number of angles = 1317 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1215 Number of HB donors = 2408 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.082" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1213" Evaluating: 1213-7 Parameter: NUMWAT <- "1206" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1206" Comparing "1081" and "1206". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.082" Parameter: BOX -> "33.082" Parameter: BOX -> "33.082" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.08200 B = 33.08200 C = 33.08200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0895 2 1 -1 0 -1 2.2693 3 1 -1 1 -1 5.3436 4 1 0 -1 -1 4.8517 5 1 0 0 -1 1.2122 6 1 0 1 -1 2.2095 7 1 -1 -1 0 5.0369 8 1 -1 0 0 1.3548 9 1 -1 1 0 5.0297 10 1 0 -1 0 1.0722 11 1 0 1 0 1.0722 12 1 -1 -1 1 5.9670 13 1 -1 0 1 2.0446 14 1 -1 1 1 6.6759 15 1 0 -1 1 2.2095 16 1 0 0 1 1.2122 17 1 0 1 1 4.8517 18 1 1 1 1 6.0895 19 1 1 0 1 2.2693 20 1 1 -1 1 5.3436 21 1 1 1 0 5.0369 22 1 1 0 0 1.3548 23 1 1 -1 0 5.0297 24 1 1 1 -1 5.9670 25 1 1 0 -1 2.0446 26 1 1 -1 -1 6.6759 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3600 atoms have been selected out of 3674 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 453 151 151 0.00 2 C002 has 774 258 258 0.00 3 C003 has 114 38 38 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1572 524 524 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1768 587 586 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1677 559 559 0.00 12 C012 has 90 30 30 0.00 13 C013 has 495 165 165 0.00 14 C014 has 102 34 34 0.94 Total of13044 atoms and 4339 groups and 4333 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3674 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1213 Number of atoms = 3674 Number of groups = 1218 Number of bonds = 3667 Number of angles = 1317 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1215 Number of HB donors = 2408 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1213 Number of atoms = 3674 Number of groups = 1218 Number of bonds = 3667 Number of angles = 1317 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1215 Number of HB donors = 2408 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.08" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1213" Evaluating: 1213-7 Parameter: NUMWAT <- "1206" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1206" Comparing "1081" and "1206". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.08" Parameter: BOX -> "33.08" Parameter: BOX -> "33.08" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.08000 B = 33.08000 C = 33.08000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0880 2 1 -1 0 -1 2.2667 3 1 -1 1 -1 5.3402 4 1 0 -1 -1 4.8521 5 1 0 0 -1 1.2104 6 1 0 1 -1 2.2068 7 1 -1 -1 0 5.0349 8 1 -1 0 0 1.3530 9 1 -1 1 0 5.0272 10 1 0 -1 0 1.0703 11 1 0 1 0 1.0703 12 1 -1 -1 1 5.9641 13 1 -1 0 1 2.0423 14 1 -1 1 1 6.6728 15 1 0 -1 1 2.2068 16 1 0 0 1 1.2104 17 1 0 1 1 4.8521 18 1 1 1 1 6.0880 19 1 1 0 1 2.2667 20 1 1 -1 1 5.3402 21 1 1 1 0 5.0349 22 1 1 0 0 1.3530 23 1 1 -1 0 5.0272 24 1 1 1 -1 5.9641 25 1 1 0 -1 2.0423 26 1 1 -1 -1 6.6728 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3600 atoms have been selected out of 3674 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 842 OPERATED ON BY TRANSFORMATION C008 RESIDUE 866 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 456 152 152 0.00 2 C002 has 768 256 256 0.00 3 C003 has 114 38 38 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1572 524 524 0.00 6 C006 has 450 150 150 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1771 588 587 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1677 559 559 0.00 12 C012 has 90 30 30 0.00 13 C013 has 495 165 165 0.00 14 C014 has 102 34 34 0.94 Total of13041 atoms and 4338 groups and 4332 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3674 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1211 Number of atoms = 3668 Number of groups = 1216 Number of bonds = 3661 Number of angles = 1315 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1213 Number of HB donors = 2404 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1211 Number of atoms = 3668 Number of groups = 1216 Number of bonds = 3661 Number of angles = 1315 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1213 Number of HB donors = 2404 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.078" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1211" Evaluating: 1211-7 Parameter: NUMWAT <- "1204" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1204" Comparing "1081" and "1204". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.078" Parameter: BOX -> "33.078" Parameter: BOX -> "33.078" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.07800 B = 33.07800 C = 33.07800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0864 2 1 -1 0 -1 2.2640 3 1 -1 1 -1 5.3368 4 1 0 -1 -1 4.8524 5 1 0 0 -1 1.2086 6 1 0 1 -1 2.2042 7 1 -1 -1 0 5.0329 8 1 -1 0 0 1.3513 9 1 -1 1 0 5.0247 10 1 0 -1 0 1.0684 11 1 0 1 0 1.0684 12 1 -1 -1 1 5.9612 13 1 -1 0 1 2.0399 14 1 -1 1 1 6.6698 15 1 0 -1 1 2.2042 16 1 0 0 1 1.2086 17 1 0 1 1 4.8524 18 1 1 1 1 6.0864 19 1 1 0 1 2.2640 20 1 1 -1 1 5.3368 21 1 1 1 0 5.0329 22 1 1 0 0 1.3513 23 1 1 -1 0 5.0247 24 1 1 1 -1 5.9612 25 1 1 0 -1 2.0399 26 1 1 -1 -1 6.6698 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3594 atoms have been selected out of 3668 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 453 151 151 0.00 2 C002 has 768 256 256 0.00 3 C003 has 114 38 38 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1566 522 522 0.00 6 C006 has 450 150 150 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1674 558 558 0.00 12 C012 has 90 30 30 0.00 13 C013 has 495 165 165 0.00 14 C014 has 102 34 34 0.94 Total of13011 atoms and 4328 groups and 4322 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3668 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1211 Number of atoms = 3668 Number of groups = 1216 Number of bonds = 3661 Number of angles = 1315 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1213 Number of HB donors = 2404 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1211 Number of atoms = 3668 Number of groups = 1216 Number of bonds = 3661 Number of angles = 1315 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1213 Number of HB donors = 2404 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.076" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1211" Evaluating: 1211-7 Parameter: NUMWAT <- "1204" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1204" Comparing "1081" and "1204". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.076" Parameter: BOX -> "33.076" Parameter: BOX -> "33.076" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.07600 B = 33.07600 C = 33.07600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0848 2 1 -1 0 -1 2.2613 3 1 -1 1 -1 5.3333 4 1 0 -1 -1 4.8527 5 1 0 0 -1 1.2068 6 1 0 1 -1 2.2015 7 1 -1 -1 0 5.0310 8 1 -1 0 0 1.3495 9 1 -1 1 0 5.0221 10 1 0 -1 0 1.0665 11 1 0 1 0 1.0665 12 1 -1 -1 1 5.9583 13 1 -1 0 1 2.0376 14 1 -1 1 1 6.6668 15 1 0 -1 1 2.2015 16 1 0 0 1 1.2068 17 1 0 1 1 4.8527 18 1 1 1 1 6.0848 19 1 1 0 1 2.2613 20 1 1 -1 1 5.3333 21 1 1 1 0 5.0310 22 1 1 0 0 1.3495 23 1 1 -1 0 5.0221 24 1 1 1 -1 5.9583 25 1 1 0 -1 2.0376 26 1 1 -1 -1 6.6668 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3594 atoms have been selected out of 3668 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 453 151 151 0.00 2 C002 has 768 256 256 0.00 3 C003 has 114 38 38 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1566 522 522 0.00 6 C006 has 450 150 150 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1674 558 558 0.00 12 C012 has 90 30 30 0.00 13 C013 has 495 165 165 0.00 14 C014 has 102 34 34 0.94 Total of13011 atoms and 4328 groups and 4322 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3668 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1211 Number of atoms = 3668 Number of groups = 1216 Number of bonds = 3661 Number of angles = 1315 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1213 Number of HB donors = 2404 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1211 Number of atoms = 3668 Number of groups = 1216 Number of bonds = 3661 Number of angles = 1315 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1213 Number of HB donors = 2404 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.074" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1211" Evaluating: 1211-7 Parameter: NUMWAT <- "1204" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1204" Comparing "1081" and "1204". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.074" Parameter: BOX -> "33.074" Parameter: BOX -> "33.074" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.07400 B = 33.07400 C = 33.07400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0833 2 1 -1 0 -1 2.2587 3 1 -1 1 -1 5.3299 4 1 0 -1 -1 4.8531 5 1 0 0 -1 1.2049 6 1 0 1 -1 2.1988 7 1 -1 -1 0 5.0290 8 1 -1 0 0 1.3477 9 1 -1 1 0 5.0196 10 1 0 -1 0 1.0646 11 1 0 1 0 1.0646 12 1 -1 -1 1 5.9554 13 1 -1 0 1 2.0352 14 1 -1 1 1 6.6637 15 1 0 -1 1 2.1988 16 1 0 0 1 1.2049 17 1 0 1 1 4.8531 18 1 1 1 1 6.0833 19 1 1 0 1 2.2587 20 1 1 -1 1 5.3299 21 1 1 1 0 5.0290 22 1 1 0 0 1.3477 23 1 1 -1 0 5.0196 24 1 1 1 -1 5.9554 25 1 1 0 -1 2.0352 26 1 1 -1 -1 6.6637 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3594 atoms have been selected out of 3668 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 456 152 152 0.00 2 C002 has 768 256 256 0.00 3 C003 has 114 38 38 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1566 522 522 0.00 6 C006 has 450 150 150 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1674 558 558 0.00 12 C012 has 90 30 30 0.00 13 C013 has 495 165 165 0.00 14 C014 has 105 35 35 0.94 Total of13020 atoms and 4331 groups and 4325 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3668 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1211 Number of atoms = 3668 Number of groups = 1216 Number of bonds = 3661 Number of angles = 1315 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1213 Number of HB donors = 2404 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1211 Number of atoms = 3668 Number of groups = 1216 Number of bonds = 3661 Number of angles = 1315 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1213 Number of HB donors = 2404 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.072" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1211" Evaluating: 1211-7 Parameter: NUMWAT <- "1204" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1204" Comparing "1081" and "1204". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.072" Parameter: BOX -> "33.072" Parameter: BOX -> "33.072" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.07200 B = 33.07200 C = 33.07200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0817 2 1 -1 0 -1 2.2560 3 1 -1 1 -1 5.3265 4 1 0 -1 -1 4.8534 5 1 0 0 -1 1.2031 6 1 0 1 -1 2.1961 7 1 -1 -1 0 5.0270 8 1 -1 0 0 1.3460 9 1 -1 1 0 5.0171 10 1 0 -1 0 1.0627 11 1 0 1 0 1.0627 12 1 -1 -1 1 5.9526 13 1 -1 0 1 2.0329 14 1 -1 1 1 6.6607 15 1 0 -1 1 2.1961 16 1 0 0 1 1.2031 17 1 0 1 1 4.8534 18 1 1 1 1 6.0817 19 1 1 0 1 2.2560 20 1 1 -1 1 5.3265 21 1 1 1 0 5.0270 22 1 1 0 0 1.3460 23 1 1 -1 0 5.0171 24 1 1 1 -1 5.9526 25 1 1 0 -1 2.0329 26 1 1 -1 -1 6.6607 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3594 atoms have been selected out of 3668 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 456 152 152 0.00 2 C002 has 771 257 257 0.00 3 C003 has 114 38 38 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1566 522 522 0.00 6 C006 has 450 150 150 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1674 558 558 0.00 12 C012 has 90 30 30 0.00 13 C013 has 495 165 165 0.00 14 C014 has 105 35 35 0.93 Total of13026 atoms and 4333 groups and 4327 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3668 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1211 Number of atoms = 3668 Number of groups = 1216 Number of bonds = 3661 Number of angles = 1315 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1213 Number of HB donors = 2404 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1211 Number of atoms = 3668 Number of groups = 1216 Number of bonds = 3661 Number of angles = 1315 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1213 Number of HB donors = 2404 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.07" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1211" Evaluating: 1211-7 Parameter: NUMWAT <- "1204" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1204" Comparing "1081" and "1204". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.07" Parameter: BOX -> "33.07" Parameter: BOX -> "33.07" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.07000 B = 33.07000 C = 33.07000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0801 2 1 -1 0 -1 2.2533 3 1 -1 1 -1 5.3231 4 1 0 -1 -1 4.8537 5 1 0 0 -1 1.2013 6 1 0 1 -1 2.1935 7 1 -1 -1 0 5.0251 8 1 -1 0 0 1.3442 9 1 -1 1 0 5.0145 10 1 0 -1 0 1.0608 11 1 0 1 0 1.0608 12 1 -1 -1 1 5.9497 13 1 -1 0 1 2.0305 14 1 -1 1 1 6.6577 15 1 0 -1 1 2.1935 16 1 0 0 1 1.2013 17 1 0 1 1 4.8537 18 1 1 1 1 6.0801 19 1 1 0 1 2.2533 20 1 1 -1 1 5.3231 21 1 1 1 0 5.0251 22 1 1 0 0 1.3442 23 1 1 -1 0 5.0145 24 1 1 1 -1 5.9497 25 1 1 0 -1 2.0305 26 1 1 -1 -1 6.6577 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3594 atoms have been selected out of 3668 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 456 152 152 0.00 2 C002 has 771 257 257 0.00 3 C003 has 114 38 38 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1566 522 522 0.00 6 C006 has 450 150 150 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1674 558 558 0.00 12 C012 has 90 30 30 0.00 13 C013 has 495 165 165 0.00 14 C014 has 105 35 35 0.93 Total of13026 atoms and 4333 groups and 4327 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3668 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1211 Number of atoms = 3668 Number of groups = 1216 Number of bonds = 3661 Number of angles = 1315 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1213 Number of HB donors = 2404 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1211 Number of atoms = 3668 Number of groups = 1216 Number of bonds = 3661 Number of angles = 1315 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1213 Number of HB donors = 2404 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.068" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1211" Evaluating: 1211-7 Parameter: NUMWAT <- "1204" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1204" Comparing "1081" and "1204". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.068" Parameter: BOX -> "33.068" Parameter: BOX -> "33.068" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.06800 B = 33.06800 C = 33.06800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0786 2 1 -1 0 -1 2.2507 3 1 -1 1 -1 5.3196 4 1 0 -1 -1 4.8541 5 1 0 0 -1 1.1995 6 1 0 1 -1 2.1908 7 1 -1 -1 0 5.0231 8 1 -1 0 0 1.3424 9 1 -1 1 0 5.0120 10 1 0 -1 0 1.0589 11 1 0 1 0 1.0589 12 1 -1 -1 1 5.9468 13 1 -1 0 1 2.0282 14 1 -1 1 1 6.6546 15 1 0 -1 1 2.1908 16 1 0 0 1 1.1995 17 1 0 1 1 4.8541 18 1 1 1 1 6.0786 19 1 1 0 1 2.2507 20 1 1 -1 1 5.3196 21 1 1 1 0 5.0231 22 1 1 0 0 1.3424 23 1 1 -1 0 5.0120 24 1 1 1 -1 5.9468 25 1 1 0 -1 2.0282 26 1 1 -1 -1 6.6546 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3594 atoms have been selected out of 3668 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 939 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 453 151 151 0.00 2 C002 has 774 258 258 0.00 3 C003 has 114 38 38 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1566 522 522 0.00 6 C006 has 453 151 151 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 90 30 30 0.00 13 C013 has 495 165 165 0.00 14 C014 has 105 35 35 0.93 Total of13023 atoms and 4332 groups and 4326 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3668 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1210 Number of atoms = 3665 Number of groups = 1215 Number of bonds = 3658 Number of angles = 1314 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1212 Number of HB donors = 2402 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1210 Number of atoms = 3665 Number of groups = 1215 Number of bonds = 3658 Number of angles = 1314 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1212 Number of HB donors = 2402 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.066" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1210" Evaluating: 1210-7 Parameter: NUMWAT <- "1203" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1203" Comparing "1081" and "1203". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.066" Parameter: BOX -> "33.066" Parameter: BOX -> "33.066" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.06600 B = 33.06600 C = 33.06600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0770 2 1 -1 0 -1 2.2480 3 1 -1 1 -1 5.3162 4 1 0 -1 -1 4.8544 5 1 0 0 -1 1.1977 6 1 0 1 -1 2.1881 7 1 -1 -1 0 5.0211 8 1 -1 0 0 1.3407 9 1 -1 1 0 5.0095 10 1 0 -1 0 1.0570 11 1 0 1 0 1.0570 12 1 -1 -1 1 5.9439 13 1 -1 0 1 2.0258 14 1 -1 1 1 6.6516 15 1 0 -1 1 2.1881 16 1 0 0 1 1.1977 17 1 0 1 1 4.8544 18 1 1 1 1 6.0770 19 1 1 0 1 2.2480 20 1 1 -1 1 5.3162 21 1 1 1 0 5.0211 22 1 1 0 0 1.3407 23 1 1 -1 0 5.0095 24 1 1 1 -1 5.9439 25 1 1 0 -1 2.0258 26 1 1 -1 -1 6.6516 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3591 atoms have been selected out of 3665 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 453 151 151 0.00 2 C002 has 771 257 257 0.00 3 C003 has 114 38 38 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1563 521 521 0.00 6 C006 has 450 150 150 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1762 585 584 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 90 30 30 0.00 13 C013 has 495 165 165 0.00 14 C014 has 105 35 35 0.93 Total of13011 atoms and 4328 groups and 4322 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3665 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1210 Number of atoms = 3665 Number of groups = 1215 Number of bonds = 3658 Number of angles = 1314 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1212 Number of HB donors = 2402 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1210 Number of atoms = 3665 Number of groups = 1215 Number of bonds = 3658 Number of angles = 1314 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1212 Number of HB donors = 2402 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.064" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1210" Evaluating: 1210-7 Parameter: NUMWAT <- "1203" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1203" Comparing "1081" and "1203". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.064" Parameter: BOX -> "33.064" Parameter: BOX -> "33.064" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.06400 B = 33.06400 C = 33.06400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0755 2 1 -1 0 -1 2.2454 3 1 -1 1 -1 5.3128 4 1 0 -1 -1 4.8548 5 1 0 0 -1 1.1959 6 1 0 1 -1 2.1855 7 1 -1 -1 0 5.0192 8 1 -1 0 0 1.3389 9 1 -1 1 0 5.0070 10 1 0 -1 0 1.0551 11 1 0 1 0 1.0551 12 1 -1 -1 1 5.9411 13 1 -1 0 1 2.0235 14 1 -1 1 1 6.6486 15 1 0 -1 1 2.1855 16 1 0 0 1 1.1959 17 1 0 1 1 4.8548 18 1 1 1 1 6.0755 19 1 1 0 1 2.2454 20 1 1 -1 1 5.3128 21 1 1 1 0 5.0192 22 1 1 0 0 1.3389 23 1 1 -1 0 5.0070 24 1 1 1 -1 5.9411 25 1 1 0 -1 2.0235 26 1 1 -1 -1 6.6486 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3591 atoms have been selected out of 3665 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 905 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1122 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 453 151 151 0.00 2 C002 has 771 257 257 0.00 3 C003 has 114 38 38 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1566 522 522 0.00 6 C006 has 450 150 150 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1674 558 558 0.00 12 C012 has 90 30 30 0.00 13 C013 has 495 165 165 0.00 14 C014 has 105 35 35 0.93 Total of13008 atoms and 4327 groups and 4321 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3665 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1208 Number of atoms = 3659 Number of groups = 1213 Number of bonds = 3652 Number of angles = 1312 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1210 Number of HB donors = 2398 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1208 Number of atoms = 3659 Number of groups = 1213 Number of bonds = 3652 Number of angles = 1312 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1210 Number of HB donors = 2398 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.062" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1208" Evaluating: 1208-7 Parameter: NUMWAT <- "1201" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1201" Comparing "1081" and "1201". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.062" Parameter: BOX -> "33.062" Parameter: BOX -> "33.062" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.06200 B = 33.06200 C = 33.06200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0739 2 1 -1 0 -1 2.2427 3 1 -1 1 -1 5.3093 4 1 0 -1 -1 4.8551 5 1 0 0 -1 1.1941 6 1 0 1 -1 2.1828 7 1 -1 -1 0 5.0172 8 1 -1 0 0 1.3371 9 1 -1 1 0 5.0044 10 1 0 -1 0 1.0532 11 1 0 1 0 1.0532 12 1 -1 -1 1 5.9382 13 1 -1 0 1 2.0211 14 1 -1 1 1 6.6455 15 1 0 -1 1 2.1828 16 1 0 0 1 1.1941 17 1 0 1 1 4.8551 18 1 1 1 1 6.0739 19 1 1 0 1 2.2427 20 1 1 -1 1 5.3093 21 1 1 1 0 5.0172 22 1 1 0 0 1.3371 23 1 1 -1 0 5.0044 24 1 1 1 -1 5.9382 25 1 1 0 -1 2.0211 26 1 1 -1 -1 6.6455 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3585 atoms have been selected out of 3659 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 453 151 151 0.00 2 C002 has 771 257 257 0.00 3 C003 has 114 38 38 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1560 520 520 0.00 6 C006 has 450 150 150 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1671 557 557 0.00 12 C012 has 90 30 30 0.00 13 C013 has 495 165 165 0.00 14 C014 has 105 35 35 0.92 Total of12993 atoms and 4322 groups and 4316 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3659 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1208 Number of atoms = 3659 Number of groups = 1213 Number of bonds = 3652 Number of angles = 1312 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1210 Number of HB donors = 2398 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1208 Number of atoms = 3659 Number of groups = 1213 Number of bonds = 3652 Number of angles = 1312 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1210 Number of HB donors = 2398 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.06" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1208" Evaluating: 1208-7 Parameter: NUMWAT <- "1201" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1201" Comparing "1081" and "1201". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.06" Parameter: BOX -> "33.06" Parameter: BOX -> "33.06" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.06000 B = 33.06000 C = 33.06000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0723 2 1 -1 0 -1 2.2401 3 1 -1 1 -1 5.3059 4 1 0 -1 -1 4.8554 5 1 0 0 -1 1.1922 6 1 0 1 -1 2.1801 7 1 -1 -1 0 5.0152 8 1 -1 0 0 1.3354 9 1 -1 1 0 5.0019 10 1 0 -1 0 1.0513 11 1 0 1 0 1.0513 12 1 -1 -1 1 5.9353 13 1 -1 0 1 2.0188 14 1 -1 1 1 6.6425 15 1 0 -1 1 2.1801 16 1 0 0 1 1.1922 17 1 0 1 1 4.8554 18 1 1 1 1 6.0723 19 1 1 0 1 2.2401 20 1 1 -1 1 5.3059 21 1 1 1 0 5.0152 22 1 1 0 0 1.3354 23 1 1 -1 0 5.0019 24 1 1 1 -1 5.9353 25 1 1 0 -1 2.0188 26 1 1 -1 -1 6.6425 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3585 atoms have been selected out of 3659 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 46 OPERATED ON BY TRANSFORMATION C016 RESIDUE 185 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 456 152 152 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1560 520 520 0.00 6 C006 has 450 150 150 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1668 556 556 0.00 12 C012 has 90 30 30 0.00 13 C013 has 507 169 169 0.00 14 C014 has 105 35 35 0.92 Total of12996 atoms and 4323 groups and 4317 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3659 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1206 Number of atoms = 3653 Number of groups = 1211 Number of bonds = 3646 Number of angles = 1310 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1208 Number of HB donors = 2394 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1206 Number of atoms = 3653 Number of groups = 1211 Number of bonds = 3646 Number of angles = 1310 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1208 Number of HB donors = 2394 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.058" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1206" Evaluating: 1206-7 Parameter: NUMWAT <- "1199" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1199" Comparing "1081" and "1199". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.058" Parameter: BOX -> "33.058" Parameter: BOX -> "33.058" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.05800 B = 33.05800 C = 33.05800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0708 2 1 -1 0 -1 2.2374 3 1 -1 1 -1 5.3025 4 1 0 -1 -1 4.8558 5 1 0 0 -1 1.1904 6 1 0 1 -1 2.1775 7 1 -1 -1 0 5.0133 8 1 -1 0 0 1.3336 9 1 -1 1 0 4.9994 10 1 0 -1 0 1.0494 11 1 0 1 0 1.0494 12 1 -1 -1 1 5.9324 13 1 -1 0 1 2.0164 14 1 -1 1 1 6.6395 15 1 0 -1 1 2.1775 16 1 0 0 1 1.1904 17 1 0 1 1 4.8558 18 1 1 1 1 6.0708 19 1 1 0 1 2.2374 20 1 1 -1 1 5.3025 21 1 1 1 0 5.0133 22 1 1 0 0 1.3336 23 1 1 -1 0 4.9994 24 1 1 1 -1 5.9324 25 1 1 0 -1 2.0164 26 1 1 -1 -1 6.6395 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3579 atoms have been selected out of 3653 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 453 151 151 0.00 2 C002 has 759 253 253 0.00 3 C003 has 114 38 38 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1554 518 518 0.00 6 C006 has 450 150 150 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1756 583 582 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1668 556 556 0.00 12 C012 has 90 30 30 0.00 13 C013 has 492 164 164 0.00 14 C014 has 105 35 35 0.92 Total of12957 atoms and 4310 groups and 4304 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3653 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1206 Number of atoms = 3653 Number of groups = 1211 Number of bonds = 3646 Number of angles = 1310 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1208 Number of HB donors = 2394 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1206 Number of atoms = 3653 Number of groups = 1211 Number of bonds = 3646 Number of angles = 1310 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1208 Number of HB donors = 2394 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.056" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1206" Evaluating: 1206-7 Parameter: NUMWAT <- "1199" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1199" Comparing "1081" and "1199". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.056" Parameter: BOX -> "33.056" Parameter: BOX -> "33.056" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.05600 B = 33.05600 C = 33.05600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0692 2 1 -1 0 -1 2.2347 3 1 -1 1 -1 5.2990 4 1 0 -1 -1 4.8561 5 1 0 0 -1 1.1886 6 1 0 1 -1 2.1748 7 1 -1 -1 0 5.0113 8 1 -1 0 0 1.3319 9 1 -1 1 0 4.9968 10 1 0 -1 0 1.0475 11 1 0 1 0 1.0475 12 1 -1 -1 1 5.9296 13 1 -1 0 1 2.0141 14 1 -1 1 1 6.6364 15 1 0 -1 1 2.1748 16 1 0 0 1 1.1886 17 1 0 1 1 4.8561 18 1 1 1 1 6.0692 19 1 1 0 1 2.2347 20 1 1 -1 1 5.2990 21 1 1 1 0 5.0113 22 1 1 0 0 1.3319 23 1 1 -1 0 4.9968 24 1 1 1 -1 5.9296 25 1 1 0 -1 2.0141 26 1 1 -1 -1 6.6364 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3579 atoms have been selected out of 3653 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 453 151 151 0.00 2 C002 has 759 253 253 0.00 3 C003 has 114 38 38 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1557 519 519 0.00 6 C006 has 450 150 150 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1756 583 582 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1668 556 556 0.00 12 C012 has 90 30 30 0.00 13 C013 has 492 164 164 0.00 14 C014 has 105 35 35 0.92 Total of12960 atoms and 4311 groups and 4305 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3653 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1206 Number of atoms = 3653 Number of groups = 1211 Number of bonds = 3646 Number of angles = 1310 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1208 Number of HB donors = 2394 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1206 Number of atoms = 3653 Number of groups = 1211 Number of bonds = 3646 Number of angles = 1310 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1208 Number of HB donors = 2394 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.054" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1206" Evaluating: 1206-7 Parameter: NUMWAT <- "1199" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1199" Comparing "1081" and "1199". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.054" Parameter: BOX -> "33.054" Parameter: BOX -> "33.054" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.05400 B = 33.05400 C = 33.05400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0677 2 1 -1 0 -1 2.2321 3 1 -1 1 -1 5.2956 4 1 0 -1 -1 4.8565 5 1 0 0 -1 1.1868 6 1 0 1 -1 2.1721 7 1 -1 -1 0 5.0094 8 1 -1 0 0 1.3301 9 1 -1 1 0 4.9943 10 1 0 -1 0 1.0456 11 1 0 1 0 1.0456 12 1 -1 -1 1 5.9267 13 1 -1 0 1 2.0118 14 1 -1 1 1 6.6334 15 1 0 -1 1 2.1721 16 1 0 0 1 1.1868 17 1 0 1 1 4.8565 18 1 1 1 1 6.0677 19 1 1 0 1 2.2321 20 1 1 -1 1 5.2956 21 1 1 1 0 5.0094 22 1 1 0 0 1.3301 23 1 1 -1 0 4.9943 24 1 1 1 -1 5.9267 25 1 1 0 -1 2.0118 26 1 1 -1 -1 6.6334 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3579 atoms have been selected out of 3653 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 640 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 453 151 151 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1557 519 519 0.00 6 C006 has 447 149 149 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1756 583 582 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1668 556 556 0.00 12 C012 has 90 30 30 0.00 13 C013 has 492 164 164 0.00 14 C014 has 105 35 35 0.92 Total of12963 atoms and 4312 groups and 4306 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3653 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1205 Number of atoms = 3650 Number of groups = 1210 Number of bonds = 3643 Number of angles = 1309 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1207 Number of HB donors = 2392 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1205 Number of atoms = 3650 Number of groups = 1210 Number of bonds = 3643 Number of angles = 1309 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1207 Number of HB donors = 2392 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.052" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1205" Evaluating: 1205-7 Parameter: NUMWAT <- "1198" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1198" Comparing "1081" and "1198". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.052" Parameter: BOX -> "33.052" Parameter: BOX -> "33.052" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.05200 B = 33.05200 C = 33.05200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0661 2 1 -1 0 -1 2.2294 3 1 -1 1 -1 5.2922 4 1 0 -1 -1 4.8568 5 1 0 0 -1 1.1850 6 1 0 1 -1 2.1695 7 1 -1 -1 0 5.0074 8 1 -1 0 0 1.3283 9 1 -1 1 0 4.9918 10 1 0 -1 0 1.0437 11 1 0 1 0 1.0437 12 1 -1 -1 1 5.9238 13 1 -1 0 1 2.0094 14 1 -1 1 1 6.6304 15 1 0 -1 1 2.1695 16 1 0 0 1 1.1850 17 1 0 1 1 4.8568 18 1 1 1 1 6.0661 19 1 1 0 1 2.2294 20 1 1 -1 1 5.2922 21 1 1 1 0 5.0074 22 1 1 0 0 1.3283 23 1 1 -1 0 4.9918 24 1 1 1 -1 5.9238 25 1 1 0 -1 2.0094 26 1 1 -1 -1 6.6304 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3576 atoms have been selected out of 3650 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 453 151 151 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1554 518 518 0.00 6 C006 has 447 149 149 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 90 30 30 0.00 13 C013 has 492 164 164 0.00 14 C014 has 105 35 35 0.91 Total of12954 atoms and 4309 groups and 4303 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3650 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1205 Number of atoms = 3650 Number of groups = 1210 Number of bonds = 3643 Number of angles = 1309 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1207 Number of HB donors = 2392 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1205 Number of atoms = 3650 Number of groups = 1210 Number of bonds = 3643 Number of angles = 1309 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1207 Number of HB donors = 2392 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.05" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1205" Evaluating: 1205-7 Parameter: NUMWAT <- "1198" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1198" Comparing "1081" and "1198". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.05" Parameter: BOX -> "33.05" Parameter: BOX -> "33.05" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.05000 B = 33.05000 C = 33.05000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0646 2 1 -1 0 -1 2.2268 3 1 -1 1 -1 5.2888 4 1 0 -1 -1 4.8572 5 1 0 0 -1 1.1832 6 1 0 1 -1 2.1668 7 1 -1 -1 0 5.0054 8 1 -1 0 0 1.3266 9 1 -1 1 0 4.9893 10 1 0 -1 0 1.0418 11 1 0 1 0 1.0418 12 1 -1 -1 1 5.9210 13 1 -1 0 1 2.0071 14 1 -1 1 1 6.6273 15 1 0 -1 1 2.1668 16 1 0 0 1 1.1832 17 1 0 1 1 4.8572 18 1 1 1 1 6.0646 19 1 1 0 1 2.2268 20 1 1 -1 1 5.2888 21 1 1 1 0 5.0054 22 1 1 0 0 1.3266 23 1 1 -1 0 4.9893 24 1 1 1 -1 5.9210 25 1 1 0 -1 2.0071 26 1 1 -1 -1 6.6273 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3576 atoms have been selected out of 3650 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 453 151 151 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1557 519 519 0.00 6 C006 has 447 149 149 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 90 30 30 0.00 13 C013 has 492 164 164 0.00 14 C014 has 105 35 35 0.91 Total of12957 atoms and 4310 groups and 4304 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3650 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1205 Number of atoms = 3650 Number of groups = 1210 Number of bonds = 3643 Number of angles = 1309 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1207 Number of HB donors = 2392 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1205 Number of atoms = 3650 Number of groups = 1210 Number of bonds = 3643 Number of angles = 1309 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1207 Number of HB donors = 2392 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.048" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1205" Evaluating: 1205-7 Parameter: NUMWAT <- "1198" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1198" Comparing "1081" and "1198". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.048" Parameter: BOX -> "33.048" Parameter: BOX -> "33.048" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.04800 B = 33.04800 C = 33.04800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0630 2 1 -1 0 -1 2.2241 3 1 -1 1 -1 5.2853 4 1 0 -1 -1 4.8575 5 1 0 0 -1 1.1814 6 1 0 1 -1 2.1641 7 1 -1 -1 0 5.0035 8 1 -1 0 0 1.3248 9 1 -1 1 0 4.9867 10 1 0 -1 0 1.0399 11 1 0 1 0 1.0399 12 1 -1 -1 1 5.9181 13 1 -1 0 1 2.0047 14 1 -1 1 1 6.6243 15 1 0 -1 1 2.1641 16 1 0 0 1 1.1814 17 1 0 1 1 4.8575 18 1 1 1 1 6.0630 19 1 1 0 1 2.2241 20 1 1 -1 1 5.2853 21 1 1 1 0 5.0035 22 1 1 0 0 1.3248 23 1 1 -1 0 4.9867 24 1 1 1 -1 5.9181 25 1 1 0 -1 2.0047 26 1 1 -1 -1 6.6243 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3576 atoms have been selected out of 3650 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 453 151 151 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1557 519 519 0.00 6 C006 has 447 149 149 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 90 30 30 0.00 13 C013 has 492 164 164 0.00 14 C014 has 105 35 35 0.91 Total of12957 atoms and 4310 groups and 4304 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3650 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1205 Number of atoms = 3650 Number of groups = 1210 Number of bonds = 3643 Number of angles = 1309 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1207 Number of HB donors = 2392 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1205 Number of atoms = 3650 Number of groups = 1210 Number of bonds = 3643 Number of angles = 1309 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1207 Number of HB donors = 2392 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.046" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1205" Evaluating: 1205-7 Parameter: NUMWAT <- "1198" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1198" Comparing "1081" and "1198". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.046" Parameter: BOX -> "33.046" Parameter: BOX -> "33.046" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.04600 B = 33.04600 C = 33.04600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0615 2 1 -1 0 -1 2.2215 3 1 -1 1 -1 5.2819 4 1 0 -1 -1 4.8579 5 1 0 0 -1 1.1796 6 1 0 1 -1 2.1615 7 1 -1 -1 0 5.0015 8 1 -1 0 0 1.3231 9 1 -1 1 0 4.9842 10 1 0 -1 0 1.0380 11 1 0 1 0 1.0380 12 1 -1 -1 1 5.9152 13 1 -1 0 1 2.0024 14 1 -1 1 1 6.6213 15 1 0 -1 1 2.1615 16 1 0 0 1 1.1796 17 1 0 1 1 4.8579 18 1 1 1 1 6.0615 19 1 1 0 1 2.2215 20 1 1 -1 1 5.2819 21 1 1 1 0 5.0015 22 1 1 0 0 1.3231 23 1 1 -1 0 4.9842 24 1 1 1 -1 5.9152 25 1 1 0 -1 2.0024 26 1 1 -1 -1 6.6213 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3576 atoms have been selected out of 3650 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 453 151 151 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1560 520 520 0.00 6 C006 has 450 150 150 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1759 584 583 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 90 30 30 0.00 13 C013 has 492 164 164 0.00 14 C014 has 105 35 35 0.91 Total of12963 atoms and 4312 groups and 4306 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3650 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1205 Number of atoms = 3650 Number of groups = 1210 Number of bonds = 3643 Number of angles = 1309 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1207 Number of HB donors = 2392 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1205 Number of atoms = 3650 Number of groups = 1210 Number of bonds = 3643 Number of angles = 1309 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1207 Number of HB donors = 2392 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.044" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1205" Evaluating: 1205-7 Parameter: NUMWAT <- "1198" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1198" Comparing "1081" and "1198". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.044" Parameter: BOX -> "33.044" Parameter: BOX -> "33.044" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.04400 B = 33.04400 C = 33.04400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0599 2 1 -1 0 -1 2.2188 3 1 -1 1 -1 5.2785 4 1 0 -1 -1 4.8582 5 1 0 0 -1 1.1778 6 1 0 1 -1 2.1588 7 1 -1 -1 0 4.9996 8 1 -1 0 0 1.3213 9 1 -1 1 0 4.9817 10 1 0 -1 0 1.0361 11 1 0 1 0 1.0361 12 1 -1 -1 1 5.9123 13 1 -1 0 1 2.0001 14 1 -1 1 1 6.6182 15 1 0 -1 1 2.1588 16 1 0 0 1 1.1778 17 1 0 1 1 4.8582 18 1 1 1 1 6.0599 19 1 1 0 1 2.2188 20 1 1 -1 1 5.2785 21 1 1 1 0 4.9996 22 1 1 0 0 1.3213 23 1 1 -1 0 4.9817 24 1 1 1 -1 5.9123 25 1 1 0 -1 2.0001 26 1 1 -1 -1 6.6182 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3576 atoms have been selected out of 3650 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 753 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 459 153 153 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1557 519 519 0.00 6 C006 has 450 150 150 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1753 582 581 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 90 30 30 0.00 13 C013 has 492 164 164 0.00 14 C014 has 105 35 35 0.91 Total of12969 atoms and 4314 groups and 4308 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3650 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1204 Number of atoms = 3647 Number of groups = 1209 Number of bonds = 3640 Number of angles = 1308 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1206 Number of HB donors = 2390 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1204 Number of atoms = 3647 Number of groups = 1209 Number of bonds = 3640 Number of angles = 1308 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1206 Number of HB donors = 2390 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.042" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1204" Evaluating: 1204-7 Parameter: NUMWAT <- "1197" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1197" Comparing "1081" and "1197". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.042" Parameter: BOX -> "33.042" Parameter: BOX -> "33.042" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.04200 B = 33.04200 C = 33.04200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0584 2 1 -1 0 -1 2.2162 3 1 -1 1 -1 5.2750 4 1 0 -1 -1 4.8586 5 1 0 0 -1 1.1760 6 1 0 1 -1 2.1562 7 1 -1 -1 0 4.9976 8 1 -1 0 0 1.3196 9 1 -1 1 0 4.9791 10 1 0 -1 0 1.0342 11 1 0 1 0 1.0342 12 1 -1 -1 1 5.9095 13 1 -1 0 1 1.9977 14 1 -1 1 1 6.6152 15 1 0 -1 1 2.1562 16 1 0 0 1 1.1760 17 1 0 1 1 4.8586 18 1 1 1 1 6.0584 19 1 1 0 1 2.2162 20 1 1 -1 1 5.2750 21 1 1 1 0 4.9976 22 1 1 0 0 1.3196 23 1 1 -1 0 4.9791 24 1 1 1 -1 5.9095 25 1 1 0 -1 1.9977 26 1 1 -1 -1 6.6152 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3573 atoms have been selected out of 3647 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 462 154 154 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1557 519 519 0.00 6 C006 has 450 150 150 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1750 581 580 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 90 30 30 0.00 13 C013 has 492 164 164 0.00 14 C014 has 105 35 35 0.90 Total of12960 atoms and 4311 groups and 4305 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3647 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1204 Number of atoms = 3647 Number of groups = 1209 Number of bonds = 3640 Number of angles = 1308 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1206 Number of HB donors = 2390 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1204 Number of atoms = 3647 Number of groups = 1209 Number of bonds = 3640 Number of angles = 1308 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1206 Number of HB donors = 2390 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.04" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1204" Evaluating: 1204-7 Parameter: NUMWAT <- "1197" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1197" Comparing "1081" and "1197". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.04" Parameter: BOX -> "33.04" Parameter: BOX -> "33.04" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.04000 B = 33.04000 C = 33.04000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0569 2 1 -1 0 -1 2.2135 3 1 -1 1 -1 5.2716 4 1 0 -1 -1 4.8590 5 1 0 0 -1 1.1742 6 1 0 1 -1 2.1535 7 1 -1 -1 0 4.9957 8 1 -1 0 0 1.3178 9 1 -1 1 0 4.9766 10 1 0 -1 0 1.0323 11 1 0 1 0 1.0323 12 1 -1 -1 1 5.9066 13 1 -1 0 1 1.9954 14 1 -1 1 1 6.6122 15 1 0 -1 1 2.1535 16 1 0 0 1 1.1742 17 1 0 1 1 4.8590 18 1 1 1 1 6.0569 19 1 1 0 1 2.2135 20 1 1 -1 1 5.2716 21 1 1 1 0 4.9957 22 1 1 0 0 1.3178 23 1 1 -1 0 4.9766 24 1 1 1 -1 5.9066 25 1 1 0 -1 1.9954 26 1 1 -1 -1 6.6122 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3573 atoms have been selected out of 3647 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 462 154 154 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1557 519 519 0.00 6 C006 has 450 150 150 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1750 581 580 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 90 30 30 0.00 13 C013 has 492 164 164 0.00 14 C014 has 105 35 35 0.90 Total of12960 atoms and 4311 groups and 4305 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3647 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1204 Number of atoms = 3647 Number of groups = 1209 Number of bonds = 3640 Number of angles = 1308 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1206 Number of HB donors = 2390 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1204 Number of atoms = 3647 Number of groups = 1209 Number of bonds = 3640 Number of angles = 1308 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1206 Number of HB donors = 2390 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.038" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1204" Evaluating: 1204-7 Parameter: NUMWAT <- "1197" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1197" Comparing "1081" and "1197". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.038" Parameter: BOX -> "33.038" Parameter: BOX -> "33.038" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.03800 B = 33.03800 C = 33.03800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0553 2 1 -1 0 -1 2.2108 3 1 -1 1 -1 5.2682 4 1 0 -1 -1 4.8593 5 1 0 0 -1 1.1724 6 1 0 1 -1 2.1508 7 1 -1 -1 0 4.9937 8 1 -1 0 0 1.3161 9 1 -1 1 0 4.9741 10 1 0 -1 0 1.0304 11 1 0 1 0 1.0304 12 1 -1 -1 1 5.9037 13 1 -1 0 1 1.9931 14 1 -1 1 1 6.6092 15 1 0 -1 1 2.1508 16 1 0 0 1 1.1724 17 1 0 1 1 4.8593 18 1 1 1 1 6.0553 19 1 1 0 1 2.2108 20 1 1 -1 1 5.2682 21 1 1 1 0 4.9937 22 1 1 0 0 1.3161 23 1 1 -1 0 4.9741 24 1 1 1 -1 5.9037 25 1 1 0 -1 1.9931 26 1 1 -1 -1 6.6092 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3573 atoms have been selected out of 3647 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 462 154 154 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1557 519 519 0.00 6 C006 has 450 150 150 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1750 581 580 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 90 30 30 0.00 13 C013 has 492 164 164 0.00 14 C014 has 105 35 35 0.90 Total of12960 atoms and 4311 groups and 4305 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3647 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1204 Number of atoms = 3647 Number of groups = 1209 Number of bonds = 3640 Number of angles = 1308 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1206 Number of HB donors = 2390 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1204 Number of atoms = 3647 Number of groups = 1209 Number of bonds = 3640 Number of angles = 1308 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1206 Number of HB donors = 2390 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.036" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1204" Evaluating: 1204-7 Parameter: NUMWAT <- "1197" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1197" Comparing "1081" and "1197". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.036" Parameter: BOX -> "33.036" Parameter: BOX -> "33.036" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.03600 B = 33.03600 C = 33.03600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0538 2 1 -1 0 -1 2.2082 3 1 -1 1 -1 5.2647 4 1 0 -1 -1 4.8597 5 1 0 0 -1 1.1706 6 1 0 1 -1 2.1482 7 1 -1 -1 0 4.9917 8 1 -1 0 0 1.3143 9 1 -1 1 0 4.9716 10 1 0 -1 0 1.0285 11 1 0 1 0 1.0285 12 1 -1 -1 1 5.9009 13 1 -1 0 1 1.9908 14 1 -1 1 1 6.6061 15 1 0 -1 1 2.1482 16 1 0 0 1 1.1706 17 1 0 1 1 4.8597 18 1 1 1 1 6.0538 19 1 1 0 1 2.2082 20 1 1 -1 1 5.2647 21 1 1 1 0 4.9917 22 1 1 0 0 1.3143 23 1 1 -1 0 4.9716 24 1 1 1 -1 5.9009 25 1 1 0 -1 1.9908 26 1 1 -1 -1 6.6061 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3573 atoms have been selected out of 3647 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 462 154 154 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1557 519 519 0.00 6 C006 has 450 150 150 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1750 581 580 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 90 30 30 0.00 13 C013 has 492 164 164 0.00 14 C014 has 105 35 35 0.90 Total of12963 atoms and 4312 groups and 4306 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3647 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1204 Number of atoms = 3647 Number of groups = 1209 Number of bonds = 3640 Number of angles = 1308 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1206 Number of HB donors = 2390 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1204 Number of atoms = 3647 Number of groups = 1209 Number of bonds = 3640 Number of angles = 1308 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1206 Number of HB donors = 2390 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.034" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1204" Evaluating: 1204-7 Parameter: NUMWAT <- "1197" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1197" Comparing "1081" and "1197". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.034" Parameter: BOX -> "33.034" Parameter: BOX -> "33.034" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.03400 B = 33.03400 C = 33.03400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0523 2 1 -1 0 -1 2.2055 3 1 -1 1 -1 5.2613 4 1 0 -1 -1 4.8601 5 1 0 0 -1 1.1688 6 1 0 1 -1 2.1455 7 1 -1 -1 0 4.9898 8 1 -1 0 0 1.3126 9 1 -1 1 0 4.9690 10 1 0 -1 0 1.0266 11 1 0 1 0 1.0266 12 1 -1 -1 1 5.8980 13 1 -1 0 1 1.9884 14 1 -1 1 1 6.6031 15 1 0 -1 1 2.1455 16 1 0 0 1 1.1688 17 1 0 1 1 4.8601 18 1 1 1 1 6.0523 19 1 1 0 1 2.2055 20 1 1 -1 1 5.2613 21 1 1 1 0 4.9898 22 1 1 0 0 1.3126 23 1 1 -1 0 4.9690 24 1 1 1 -1 5.8980 25 1 1 0 -1 1.9884 26 1 1 -1 -1 6.6031 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3573 atoms have been selected out of 3647 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 449 OPERATED ON BY TRANSFORMATION C022 RESIDUE 1034 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 747 249 249 0.00 3 C003 has 114 38 38 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1557 519 519 0.00 6 C006 has 450 150 150 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1747 580 579 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1665 555 555 0.00 12 C012 has 93 31 31 0.00 13 C013 has 486 162 162 0.00 14 C014 has 105 35 35 0.90 Total of12951 atoms and 4308 groups and 4302 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3647 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1202 Number of atoms = 3641 Number of groups = 1207 Number of bonds = 3634 Number of angles = 1306 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1204 Number of HB donors = 2386 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1202 Number of atoms = 3641 Number of groups = 1207 Number of bonds = 3634 Number of angles = 1306 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1204 Number of HB donors = 2386 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.032" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1202" Evaluating: 1202-7 Parameter: NUMWAT <- "1195" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1195" Comparing "1081" and "1195". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.032" Parameter: BOX -> "33.032" Parameter: BOX -> "33.032" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.03200 B = 33.03200 C = 33.03200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0507 2 1 -1 0 -1 2.2029 3 1 -1 1 -1 5.2579 4 1 0 -1 -1 4.8604 5 1 0 0 -1 1.1669 6 1 0 1 -1 2.1428 7 1 -1 -1 0 4.9878 8 1 -1 0 0 1.3108 9 1 -1 1 0 4.9665 10 1 0 -1 0 1.0248 11 1 0 1 0 1.0248 12 1 -1 -1 1 5.8951 13 1 -1 0 1 1.9861 14 1 -1 1 1 6.6001 15 1 0 -1 1 2.1428 16 1 0 0 1 1.1669 17 1 0 1 1 4.8604 18 1 1 1 1 6.0507 19 1 1 0 1 2.2029 20 1 1 -1 1 5.2579 21 1 1 1 0 4.9878 22 1 1 0 0 1.3108 23 1 1 -1 0 4.9665 24 1 1 1 -1 5.8951 25 1 1 0 -1 1.9861 26 1 1 -1 -1 6.6001 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3567 atoms have been selected out of 3641 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 462 154 154 0.00 2 C002 has 744 248 248 0.00 3 C003 has 114 38 38 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1554 518 518 0.00 6 C006 has 450 150 150 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1741 578 577 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 90 30 30 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 0.89 Total of12915 atoms and 4296 groups and 4290 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3641 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1202 Number of atoms = 3641 Number of groups = 1207 Number of bonds = 3634 Number of angles = 1306 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1204 Number of HB donors = 2386 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1202 Number of atoms = 3641 Number of groups = 1207 Number of bonds = 3634 Number of angles = 1306 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1204 Number of HB donors = 2386 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.03" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1202" Evaluating: 1202-7 Parameter: NUMWAT <- "1195" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1195" Comparing "1081" and "1195". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.03" Parameter: BOX -> "33.03" Parameter: BOX -> "33.03" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.03000 B = 33.03000 C = 33.03000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0492 2 1 -1 0 -1 2.2002 3 1 -1 1 -1 5.2545 4 1 0 -1 -1 4.8608 5 1 0 0 -1 1.1651 6 1 0 1 -1 2.1402 7 1 -1 -1 0 4.9859 8 1 -1 0 0 1.3090 9 1 -1 1 0 4.9640 10 1 0 -1 0 1.0229 11 1 0 1 0 1.0229 12 1 -1 -1 1 5.8923 13 1 -1 0 1 1.9838 14 1 -1 1 1 6.5971 15 1 0 -1 1 2.1402 16 1 0 0 1 1.1651 17 1 0 1 1 4.8608 18 1 1 1 1 6.0492 19 1 1 0 1 2.2002 20 1 1 -1 1 5.2545 21 1 1 1 0 4.9859 22 1 1 0 0 1.3090 23 1 1 -1 0 4.9640 24 1 1 1 -1 5.8923 25 1 1 0 -1 1.9838 26 1 1 -1 -1 6.5971 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3567 atoms have been selected out of 3641 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 744 248 248 0.00 3 C003 has 114 38 38 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1554 518 518 0.00 6 C006 has 450 150 150 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1744 579 578 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 90 30 30 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 0.89 Total of12921 atoms and 4298 groups and 4292 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3641 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1202 Number of atoms = 3641 Number of groups = 1207 Number of bonds = 3634 Number of angles = 1306 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1204 Number of HB donors = 2386 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1202 Number of atoms = 3641 Number of groups = 1207 Number of bonds = 3634 Number of angles = 1306 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1204 Number of HB donors = 2386 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.028" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1202" Evaluating: 1202-7 Parameter: NUMWAT <- "1195" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1195" Comparing "1081" and "1195". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.028" Parameter: BOX -> "33.028" Parameter: BOX -> "33.028" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.02800 B = 33.02800 C = 33.02800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0477 2 1 -1 0 -1 2.1976 3 1 -1 1 -1 5.2510 4 1 0 -1 -1 4.8612 5 1 0 0 -1 1.1633 6 1 0 1 -1 2.1375 7 1 -1 -1 0 4.9839 8 1 -1 0 0 1.3073 9 1 -1 1 0 4.9615 10 1 0 -1 0 1.0210 11 1 0 1 0 1.0210 12 1 -1 -1 1 5.8894 13 1 -1 0 1 1.9815 14 1 -1 1 1 6.5940 15 1 0 -1 1 2.1375 16 1 0 0 1 1.1633 17 1 0 1 1 4.8612 18 1 1 1 1 6.0477 19 1 1 0 1 2.1976 20 1 1 -1 1 5.2510 21 1 1 1 0 4.9839 22 1 1 0 0 1.3073 23 1 1 -1 0 4.9615 24 1 1 1 -1 5.8894 25 1 1 0 -1 1.9815 26 1 1 -1 -1 6.5940 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3567 atoms have been selected out of 3641 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 858 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 741 247 247 0.00 3 C003 has 111 37 37 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1554 518 518 0.00 6 C006 has 450 150 150 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1747 580 579 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1662 554 554 0.00 12 C012 has 90 30 30 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 0.89 Total of12918 atoms and 4297 groups and 4291 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3641 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1201 Number of atoms = 3638 Number of groups = 1206 Number of bonds = 3631 Number of angles = 1305 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1203 Number of HB donors = 2384 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1201 Number of atoms = 3638 Number of groups = 1206 Number of bonds = 3631 Number of angles = 1305 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1203 Number of HB donors = 2384 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.026" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1201" Evaluating: 1201-7 Parameter: NUMWAT <- "1194" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1194" Comparing "1081" and "1194". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.026" Parameter: BOX -> "33.026" Parameter: BOX -> "33.026" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.02600 B = 33.02600 C = 33.02600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0461 2 1 -1 0 -1 2.1949 3 1 -1 1 -1 5.2476 4 1 0 -1 -1 4.8615 5 1 0 0 -1 1.1615 6 1 0 1 -1 2.1349 7 1 -1 -1 0 4.9820 8 1 -1 0 0 1.3055 9 1 -1 1 0 4.9589 10 1 0 -1 0 1.0191 11 1 0 1 0 1.0191 12 1 -1 -1 1 5.8866 13 1 -1 0 1 1.9791 14 1 -1 1 1 6.5910 15 1 0 -1 1 2.1349 16 1 0 0 1 1.1615 17 1 0 1 1 4.8615 18 1 1 1 1 6.0461 19 1 1 0 1 2.1949 20 1 1 -1 1 5.2476 21 1 1 1 0 4.9820 22 1 1 0 0 1.3055 23 1 1 -1 0 4.9589 24 1 1 1 -1 5.8866 25 1 1 0 -1 1.9791 26 1 1 -1 -1 6.5910 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3564 atoms have been selected out of 3638 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 741 247 247 0.00 3 C003 has 111 37 37 0.00 4 C004 has 612 204 204 0.00 5 C005 has 1551 517 517 0.00 6 C006 has 447 149 149 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1741 578 577 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1662 554 554 0.00 12 C012 has 90 30 30 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 0.89 Total of12903 atoms and 4292 groups and 4286 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3638 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1201 Number of atoms = 3638 Number of groups = 1206 Number of bonds = 3631 Number of angles = 1305 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1203 Number of HB donors = 2384 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1201 Number of atoms = 3638 Number of groups = 1206 Number of bonds = 3631 Number of angles = 1305 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1203 Number of HB donors = 2384 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.024" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1201" Evaluating: 1201-7 Parameter: NUMWAT <- "1194" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1194" Comparing "1081" and "1194". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.024" Parameter: BOX -> "33.024" Parameter: BOX -> "33.024" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.02400 B = 33.02400 C = 33.02400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0446 2 1 -1 0 -1 2.1923 3 1 -1 1 -1 5.2442 4 1 0 -1 -1 4.8619 5 1 0 0 -1 1.1597 6 1 0 1 -1 2.1322 7 1 -1 -1 0 4.9801 8 1 -1 0 0 1.3038 9 1 -1 1 0 4.9564 10 1 0 -1 0 1.0172 11 1 0 1 0 1.0172 12 1 -1 -1 1 5.8837 13 1 -1 0 1 1.9768 14 1 -1 1 1 6.5880 15 1 0 -1 1 2.1322 16 1 0 0 1 1.1597 17 1 0 1 1 4.8619 18 1 1 1 1 6.0446 19 1 1 0 1 2.1923 20 1 1 -1 1 5.2442 21 1 1 1 0 4.9801 22 1 1 0 0 1.3038 23 1 1 -1 0 4.9564 24 1 1 1 -1 5.8837 25 1 1 0 -1 1.9768 26 1 1 -1 -1 6.5880 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3564 atoms have been selected out of 3638 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 741 247 247 0.00 3 C003 has 111 37 37 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1551 517 517 0.00 6 C006 has 447 149 149 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1741 578 577 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1662 554 554 0.00 12 C012 has 90 30 30 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 0.89 Total of12906 atoms and 4293 groups and 4287 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3638 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1201 Number of atoms = 3638 Number of groups = 1206 Number of bonds = 3631 Number of angles = 1305 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1203 Number of HB donors = 2384 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1201 Number of atoms = 3638 Number of groups = 1206 Number of bonds = 3631 Number of angles = 1305 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1203 Number of HB donors = 2384 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.022" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1201" Evaluating: 1201-7 Parameter: NUMWAT <- "1194" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1194" Comparing "1081" and "1194". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.022" Parameter: BOX -> "33.022" Parameter: BOX -> "33.022" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.02200 B = 33.02200 C = 33.02200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0431 2 1 -1 0 -1 2.1896 3 1 -1 1 -1 5.2407 4 1 0 -1 -1 4.8623 5 1 0 0 -1 1.1579 6 1 0 1 -1 2.1295 7 1 -1 -1 0 4.9781 8 1 -1 0 0 1.3021 9 1 -1 1 0 4.9539 10 1 0 -1 0 1.0153 11 1 0 1 0 1.0153 12 1 -1 -1 1 5.8808 13 1 -1 0 1 1.9745 14 1 -1 1 1 6.5850 15 1 0 -1 1 2.1295 16 1 0 0 1 1.1579 17 1 0 1 1 4.8623 18 1 1 1 1 6.0431 19 1 1 0 1 2.1896 20 1 1 -1 1 5.2407 21 1 1 1 0 4.9781 22 1 1 0 0 1.3021 23 1 1 -1 0 4.9539 24 1 1 1 -1 5.8808 25 1 1 0 -1 1.9745 26 1 1 -1 -1 6.5850 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3564 atoms have been selected out of 3638 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 741 247 247 0.00 3 C003 has 111 37 37 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1551 517 517 0.00 6 C006 has 447 149 149 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1741 578 577 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1662 554 554 0.00 12 C012 has 90 30 30 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 0.88 Total of12909 atoms and 4294 groups and 4288 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3638 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1201 Number of atoms = 3638 Number of groups = 1206 Number of bonds = 3631 Number of angles = 1305 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1203 Number of HB donors = 2384 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1201 Number of atoms = 3638 Number of groups = 1206 Number of bonds = 3631 Number of angles = 1305 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1203 Number of HB donors = 2384 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.02" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1201" Evaluating: 1201-7 Parameter: NUMWAT <- "1194" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1194" Comparing "1081" and "1194". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.02" Parameter: BOX -> "33.02" Parameter: BOX -> "33.02" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.02000 B = 33.02000 C = 33.02000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0415 2 1 -1 0 -1 2.1870 3 1 -1 1 -1 5.2373 4 1 0 -1 -1 4.8627 5 1 0 0 -1 1.1561 6 1 0 1 -1 2.1269 7 1 -1 -1 0 4.9762 8 1 -1 0 0 1.3003 9 1 -1 1 0 4.9514 10 1 0 -1 0 1.0134 11 1 0 1 0 1.0134 12 1 -1 -1 1 5.8780 13 1 -1 0 1 1.9722 14 1 -1 1 1 6.5819 15 1 0 -1 1 2.1269 16 1 0 0 1 1.1561 17 1 0 1 1 4.8627 18 1 1 1 1 6.0415 19 1 1 0 1 2.1870 20 1 1 -1 1 5.2373 21 1 1 1 0 4.9762 22 1 1 0 0 1.3003 23 1 1 -1 0 4.9514 24 1 1 1 -1 5.8780 25 1 1 0 -1 1.9722 26 1 1 -1 -1 6.5819 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3564 atoms have been selected out of 3638 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 447 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 741 247 247 0.00 3 C003 has 111 37 37 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1551 517 517 0.00 6 C006 has 447 149 149 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1744 579 578 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 90 30 30 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 1.18 Total of12906 atoms and 4293 groups and 4287 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3638 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1200 Number of atoms = 3635 Number of groups = 1205 Number of bonds = 3628 Number of angles = 1304 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1202 Number of HB donors = 2382 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1200 Number of atoms = 3635 Number of groups = 1205 Number of bonds = 3628 Number of angles = 1304 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1202 Number of HB donors = 2382 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.018" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1200" Evaluating: 1200-7 Parameter: NUMWAT <- "1193" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1193" Comparing "1081" and "1193". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.018" Parameter: BOX -> "33.018" Parameter: BOX -> "33.018" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.01800 B = 33.01800 C = 33.01800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0400 2 1 -1 0 -1 2.1843 3 1 -1 1 -1 5.2339 4 1 0 -1 -1 4.8630 5 1 0 0 -1 1.1543 6 1 0 1 -1 2.1242 7 1 -1 -1 0 4.9742 8 1 -1 0 0 1.2986 9 1 -1 1 0 4.9488 10 1 0 -1 0 1.0115 11 1 0 1 0 1.0115 12 1 -1 -1 1 5.8751 13 1 -1 0 1 1.9699 14 1 -1 1 1 6.5789 15 1 0 -1 1 2.1242 16 1 0 0 1 1.1543 17 1 0 1 1 4.8630 18 1 1 1 1 6.0400 19 1 1 0 1 2.1843 20 1 1 -1 1 5.2339 21 1 1 1 0 4.9742 22 1 1 0 0 1.2986 23 1 1 -1 0 4.9488 24 1 1 1 -1 5.8751 25 1 1 0 -1 1.9699 26 1 1 -1 -1 6.5789 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3561 atoms have been selected out of 3635 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 354 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1551 517 517 0.00 6 C006 has 447 149 149 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1741 578 577 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 90 30 30 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 1.18 Total of12888 atoms and 4287 groups and 4281 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3635 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1199 Number of atoms = 3632 Number of groups = 1204 Number of bonds = 3625 Number of angles = 1303 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1201 Number of HB donors = 2380 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1199 Number of atoms = 3632 Number of groups = 1204 Number of bonds = 3625 Number of angles = 1303 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1201 Number of HB donors = 2380 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.016" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1199" Evaluating: 1199-7 Parameter: NUMWAT <- "1192" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1192" Comparing "1081" and "1192". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.016" Parameter: BOX -> "33.016" Parameter: BOX -> "33.016" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.01600 B = 33.01600 C = 33.01600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0385 2 1 -1 0 -1 2.1817 3 1 -1 1 -1 5.2304 4 1 0 -1 -1 4.8634 5 1 0 0 -1 1.1525 6 1 0 1 -1 2.1216 7 1 -1 -1 0 4.9723 8 1 -1 0 0 1.2968 9 1 -1 1 0 4.9463 10 1 0 -1 0 1.0096 11 1 0 1 0 1.0096 12 1 -1 -1 1 5.8723 13 1 -1 0 1 1.9675 14 1 -1 1 1 6.5759 15 1 0 -1 1 2.1216 16 1 0 0 1 1.1525 17 1 0 1 1 4.8634 18 1 1 1 1 6.0385 19 1 1 0 1 2.1817 20 1 1 -1 1 5.2304 21 1 1 1 0 4.9723 22 1 1 0 0 1.2968 23 1 1 -1 0 4.9463 24 1 1 1 -1 5.8723 25 1 1 0 -1 1.9675 26 1 1 -1 -1 6.5759 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3558 atoms have been selected out of 3632 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1551 517 517 0.00 6 C006 has 447 149 149 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1744 579 578 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 90 30 30 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 1.18 Total of12888 atoms and 4287 groups and 4281 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3632 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1199 Number of atoms = 3632 Number of groups = 1204 Number of bonds = 3625 Number of angles = 1303 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1201 Number of HB donors = 2380 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1199 Number of atoms = 3632 Number of groups = 1204 Number of bonds = 3625 Number of angles = 1303 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1201 Number of HB donors = 2380 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.014" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1199" Evaluating: 1199-7 Parameter: NUMWAT <- "1192" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1192" Comparing "1081" and "1192". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.014" Parameter: BOX -> "33.014" Parameter: BOX -> "33.014" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.01400 B = 33.01400 C = 33.01400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0370 2 1 -1 0 -1 2.1790 3 1 -1 1 -1 5.2270 4 1 0 -1 -1 4.8638 5 1 0 0 -1 1.1507 6 1 0 1 -1 2.1189 7 1 -1 -1 0 4.9703 8 1 -1 0 0 1.2951 9 1 -1 1 0 4.9438 10 1 0 -1 0 1.0078 11 1 0 1 0 1.0078 12 1 -1 -1 1 5.8694 13 1 -1 0 1 1.9652 14 1 -1 1 1 6.5729 15 1 0 -1 1 2.1189 16 1 0 0 1 1.1507 17 1 0 1 1 4.8638 18 1 1 1 1 6.0370 19 1 1 0 1 2.1790 20 1 1 -1 1 5.2270 21 1 1 1 0 4.9703 22 1 1 0 0 1.2951 23 1 1 -1 0 4.9438 24 1 1 1 -1 5.8694 25 1 1 0 -1 1.9652 26 1 1 -1 -1 6.5729 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3558 atoms have been selected out of 3632 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1551 517 517 0.00 6 C006 has 447 149 149 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1744 579 578 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 90 30 30 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 1.17 Total of12888 atoms and 4287 groups and 4281 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3632 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1199 Number of atoms = 3632 Number of groups = 1204 Number of bonds = 3625 Number of angles = 1303 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1201 Number of HB donors = 2380 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1199 Number of atoms = 3632 Number of groups = 1204 Number of bonds = 3625 Number of angles = 1303 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1201 Number of HB donors = 2380 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.012" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1199" Evaluating: 1199-7 Parameter: NUMWAT <- "1192" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1192" Comparing "1081" and "1192". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.012" Parameter: BOX -> "33.012" Parameter: BOX -> "33.012" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.01200 B = 33.01200 C = 33.01200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0355 2 1 -1 0 -1 2.1764 3 1 -1 1 -1 5.2236 4 1 0 -1 -1 4.8642 5 1 0 0 -1 1.1490 6 1 0 1 -1 2.1163 7 1 -1 -1 0 4.9684 8 1 -1 0 0 1.2933 9 1 -1 1 0 4.9413 10 1 0 -1 0 1.0059 11 1 0 1 0 1.0059 12 1 -1 -1 1 5.8665 13 1 -1 0 1 1.9629 14 1 -1 1 1 6.5698 15 1 0 -1 1 2.1163 16 1 0 0 1 1.1490 17 1 0 1 1 4.8642 18 1 1 1 1 6.0355 19 1 1 0 1 2.1764 20 1 1 -1 1 5.2236 21 1 1 1 0 4.9684 22 1 1 0 0 1.2933 23 1 1 -1 0 4.9413 24 1 1 1 -1 5.8665 25 1 1 0 -1 1.9629 26 1 1 -1 -1 6.5698 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3558 atoms have been selected out of 3632 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 471 157 157 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1551 517 517 0.00 6 C006 has 447 149 149 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1744 579 578 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 90 30 30 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 1.17 Total of12891 atoms and 4288 groups and 4282 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3632 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1199 Number of atoms = 3632 Number of groups = 1204 Number of bonds = 3625 Number of angles = 1303 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1201 Number of HB donors = 2380 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1199 Number of atoms = 3632 Number of groups = 1204 Number of bonds = 3625 Number of angles = 1303 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1201 Number of HB donors = 2380 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.01" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1199" Evaluating: 1199-7 Parameter: NUMWAT <- "1192" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1192" Comparing "1081" and "1192". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.01" Parameter: BOX -> "33.01" Parameter: BOX -> "33.01" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.01000 B = 33.01000 C = 33.01000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0339 2 1 -1 0 -1 2.1737 3 1 -1 1 -1 5.2202 4 1 0 -1 -1 4.8646 5 1 0 0 -1 1.1472 6 1 0 1 -1 2.1136 7 1 -1 -1 0 4.9664 8 1 -1 0 0 1.2916 9 1 -1 1 0 4.9388 10 1 0 -1 0 1.0040 11 1 0 1 0 1.0040 12 1 -1 -1 1 5.8637 13 1 -1 0 1 1.9606 14 1 -1 1 1 6.5668 15 1 0 -1 1 2.1136 16 1 0 0 1 1.1472 17 1 0 1 1 4.8646 18 1 1 1 1 6.0339 19 1 1 0 1 2.1737 20 1 1 -1 1 5.2202 21 1 1 1 0 4.9664 22 1 1 0 0 1.2916 23 1 1 -1 0 4.9388 24 1 1 1 -1 5.8637 25 1 1 0 -1 1.9606 26 1 1 -1 -1 6.5668 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3558 atoms have been selected out of 3632 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 471 157 157 0.00 2 C002 has 741 247 247 0.00 3 C003 has 102 34 34 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1551 517 517 0.00 6 C006 has 447 149 149 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1744 579 578 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 90 30 30 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 1.17 Total of12894 atoms and 4289 groups and 4283 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3632 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1199 Number of atoms = 3632 Number of groups = 1204 Number of bonds = 3625 Number of angles = 1303 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1201 Number of HB donors = 2380 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1199 Number of atoms = 3632 Number of groups = 1204 Number of bonds = 3625 Number of angles = 1303 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1201 Number of HB donors = 2380 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.008" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1199" Evaluating: 1199-7 Parameter: NUMWAT <- "1192" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1192" Comparing "1081" and "1192". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.008" Parameter: BOX -> "33.008" Parameter: BOX -> "33.008" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.00800 B = 33.00800 C = 33.00800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0324 2 1 -1 0 -1 2.1711 3 1 -1 1 -1 5.2167 4 1 0 -1 -1 4.8650 5 1 0 0 -1 1.1454 6 1 0 1 -1 2.1109 7 1 -1 -1 0 4.9645 8 1 -1 0 0 1.2898 9 1 -1 1 0 4.9362 10 1 0 -1 0 1.0021 11 1 0 1 0 1.0021 12 1 -1 -1 1 5.8608 13 1 -1 0 1 1.9583 14 1 -1 1 1 6.5638 15 1 0 -1 1 2.1109 16 1 0 0 1 1.1454 17 1 0 1 1 4.8650 18 1 1 1 1 6.0324 19 1 1 0 1 2.1711 20 1 1 -1 1 5.2167 21 1 1 1 0 4.9645 22 1 1 0 0 1.2898 23 1 1 -1 0 4.9362 24 1 1 1 -1 5.8608 25 1 1 0 -1 1.9583 26 1 1 -1 -1 6.5638 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3558 atoms have been selected out of 3632 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 697 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 471 157 157 0.00 2 C002 has 747 249 249 0.00 3 C003 has 102 34 34 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1548 516 516 0.00 6 C006 has 447 149 149 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1744 579 578 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 90 30 30 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 1.17 Total of12900 atoms and 4291 groups and 4285 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3632 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1198 Number of atoms = 3629 Number of groups = 1203 Number of bonds = 3622 Number of angles = 1302 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1200 Number of HB donors = 2378 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1198 Number of atoms = 3629 Number of groups = 1203 Number of bonds = 3622 Number of angles = 1302 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1200 Number of HB donors = 2378 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.006" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1198" Evaluating: 1198-7 Parameter: NUMWAT <- "1191" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1191" Comparing "1081" and "1191". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.006" Parameter: BOX -> "33.006" Parameter: BOX -> "33.006" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.00600 B = 33.00600 C = 33.00600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0309 2 1 -1 0 -1 2.1685 3 1 -1 1 -1 5.2133 4 1 0 -1 -1 4.8653 5 1 0 0 -1 1.1436 6 1 0 1 -1 2.1083 7 1 -1 -1 0 4.9626 8 1 -1 0 0 1.2881 9 1 -1 1 0 4.9337 10 1 0 -1 0 1.0002 11 1 0 1 0 1.0002 12 1 -1 -1 1 5.8580 13 1 -1 0 1 1.9560 14 1 -1 1 1 6.5608 15 1 0 -1 1 2.1083 16 1 0 0 1 1.1436 17 1 0 1 1 4.8653 18 1 1 1 1 6.0309 19 1 1 0 1 2.1685 20 1 1 -1 1 5.2133 21 1 1 1 0 4.9626 22 1 1 0 0 1.2881 23 1 1 -1 0 4.9337 24 1 1 1 -1 5.8580 25 1 1 0 -1 1.9560 26 1 1 -1 -1 6.5608 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3555 atoms have been selected out of 3629 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 471 157 157 0.00 2 C002 has 747 249 249 0.00 3 C003 has 102 34 34 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1548 516 516 0.00 6 C006 has 447 149 149 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1741 578 577 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 90 30 30 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 1.17 Total of12891 atoms and 4288 groups and 4282 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3629 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1198 Number of atoms = 3629 Number of groups = 1203 Number of bonds = 3622 Number of angles = 1302 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1200 Number of HB donors = 2378 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1198 Number of atoms = 3629 Number of groups = 1203 Number of bonds = 3622 Number of angles = 1302 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1200 Number of HB donors = 2378 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.004" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1198" Evaluating: 1198-7 Parameter: NUMWAT <- "1191" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1191" Comparing "1081" and "1191". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.004" Parameter: BOX -> "33.004" Parameter: BOX -> "33.004" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.00400 B = 33.00400 C = 33.00400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0294 2 1 -1 0 -1 2.1658 3 1 -1 1 -1 5.2099 4 1 0 -1 -1 4.8657 5 1 0 0 -1 1.1418 6 1 0 1 -1 2.1056 7 1 -1 -1 0 4.9606 8 1 -1 0 0 1.2863 9 1 -1 1 0 4.9312 10 1 0 -1 0 0.9983 11 1 0 1 0 0.9983 12 1 -1 -1 1 5.8551 13 1 -1 0 1 1.9537 14 1 -1 1 1 6.5578 15 1 0 -1 1 2.1056 16 1 0 0 1 1.1418 17 1 0 1 1 4.8657 18 1 1 1 1 6.0294 19 1 1 0 1 2.1658 20 1 1 -1 1 5.2099 21 1 1 1 0 4.9606 22 1 1 0 0 1.2863 23 1 1 -1 0 4.9312 24 1 1 1 -1 5.8551 25 1 1 0 -1 1.9537 26 1 1 -1 -1 6.5578 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3555 atoms have been selected out of 3629 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 747 249 249 0.00 3 C003 has 102 34 34 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1548 516 516 0.00 6 C006 has 447 149 149 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1741 578 577 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 90 30 30 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 1.16 Total of12894 atoms and 4289 groups and 4283 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3629 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1198 Number of atoms = 3629 Number of groups = 1203 Number of bonds = 3622 Number of angles = 1302 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1200 Number of HB donors = 2378 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1198 Number of atoms = 3629 Number of groups = 1203 Number of bonds = 3622 Number of angles = 1302 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1200 Number of HB donors = 2378 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33.002" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1198" Evaluating: 1198-7 Parameter: NUMWAT <- "1191" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1191" Comparing "1081" and "1191". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33.002" Parameter: BOX -> "33.002" Parameter: BOX -> "33.002" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.00200 B = 33.00200 C = 33.00200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0279 2 1 -1 0 -1 2.1632 3 1 -1 1 -1 5.2064 4 1 0 -1 -1 4.8661 5 1 0 0 -1 1.1400 6 1 0 1 -1 2.1030 7 1 -1 -1 0 4.9587 8 1 -1 0 0 1.2846 9 1 -1 1 0 4.9287 10 1 0 -1 0 0.9964 11 1 0 1 0 0.9964 12 1 -1 -1 1 5.8523 13 1 -1 0 1 1.9514 14 1 -1 1 1 6.5547 15 1 0 -1 1 2.1030 16 1 0 0 1 1.1400 17 1 0 1 1 4.8661 18 1 1 1 1 6.0279 19 1 1 0 1 2.1632 20 1 1 -1 1 5.2064 21 1 1 1 0 4.9587 22 1 1 0 0 1.2846 23 1 1 -1 0 4.9287 24 1 1 1 -1 5.8523 25 1 1 0 -1 1.9514 26 1 1 -1 -1 6.5547 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3555 atoms have been selected out of 3629 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 747 249 249 0.00 3 C003 has 102 34 34 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1548 516 516 0.00 6 C006 has 447 149 149 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1741 578 577 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 90 30 30 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 1.16 Total of12897 atoms and 4290 groups and 4284 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3629 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1198 Number of atoms = 3629 Number of groups = 1203 Number of bonds = 3622 Number of angles = 1302 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1200 Number of HB donors = 2378 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1198 Number of atoms = 3629 Number of groups = 1203 Number of bonds = 3622 Number of angles = 1302 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1200 Number of HB donors = 2378 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "33" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1198" Evaluating: 1198-7 Parameter: NUMWAT <- "1191" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1191" Comparing "1081" and "1191". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "33" Parameter: BOX -> "33" Parameter: BOX -> "33" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 33.00000 B = 33.00000 C = 33.00000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0264 2 1 -1 0 -1 2.1605 3 1 -1 1 -1 5.2030 4 1 0 -1 -1 4.8665 5 1 0 0 -1 1.1382 6 1 0 1 -1 2.1003 7 1 -1 -1 0 4.9568 8 1 -1 0 0 1.2829 9 1 -1 1 0 4.9262 10 1 0 -1 0 0.9946 11 1 0 1 0 0.9946 12 1 -1 -1 1 5.8494 13 1 -1 0 1 1.9491 14 1 -1 1 1 6.5517 15 1 0 -1 1 2.1003 16 1 0 0 1 1.1382 17 1 0 1 1 4.8665 18 1 1 1 1 6.0264 19 1 1 0 1 2.1605 20 1 1 -1 1 5.2030 21 1 1 1 0 4.9568 22 1 1 0 0 1.2829 23 1 1 -1 0 4.9262 24 1 1 1 -1 5.8494 25 1 1 0 -1 1.9491 26 1 1 -1 -1 6.5517 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3555 atoms have been selected out of 3629 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 428 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 747 249 249 0.00 3 C003 has 102 34 34 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1548 516 516 0.00 6 C006 has 447 149 149 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1741 578 577 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1659 553 553 0.00 12 C012 has 90 30 30 0.00 13 C013 has 486 162 162 0.00 14 C014 has 105 35 35 1.16 Total of12903 atoms and 4292 groups and 4286 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3629 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1197 Number of atoms = 3626 Number of groups = 1202 Number of bonds = 3619 Number of angles = 1301 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2376 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1197 Number of atoms = 3626 Number of groups = 1202 Number of bonds = 3619 Number of angles = 1301 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2376 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.998" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1197" Evaluating: 1197-7 Parameter: NUMWAT <- "1190" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1190" Comparing "1081" and "1190". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.998" Parameter: BOX -> "32.998" Parameter: BOX -> "32.998" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.99800 B = 32.99800 C = 32.99800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0249 2 1 -1 0 -1 2.1579 3 1 -1 1 -1 5.1996 4 1 0 -1 -1 4.8669 5 1 0 0 -1 1.1364 6 1 0 1 -1 2.0977 7 1 -1 -1 0 4.9548 8 1 -1 0 0 1.2811 9 1 -1 1 0 4.9236 10 1 0 -1 0 0.9927 11 1 0 1 0 0.9927 12 1 -1 -1 1 5.8465 13 1 -1 0 1 1.9468 14 1 -1 1 1 6.5487 15 1 0 -1 1 2.0977 16 1 0 0 1 1.1364 17 1 0 1 1 4.8669 18 1 1 1 1 6.0249 19 1 1 0 1 2.1579 20 1 1 -1 1 5.1996 21 1 1 1 0 4.9548 22 1 1 0 0 1.2811 23 1 1 -1 0 4.9236 24 1 1 1 -1 5.8465 25 1 1 0 -1 1.9468 26 1 1 -1 -1 6.5487 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3552 atoms have been selected out of 3626 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 747 249 249 0.00 3 C003 has 102 34 34 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1548 516 516 0.00 6 C006 has 447 149 149 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1738 577 576 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 90 30 30 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 1.16 Total of12891 atoms and 4288 groups and 4282 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3626 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1197 Number of atoms = 3626 Number of groups = 1202 Number of bonds = 3619 Number of angles = 1301 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2376 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1197 Number of atoms = 3626 Number of groups = 1202 Number of bonds = 3619 Number of angles = 1301 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2376 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.996" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1197" Evaluating: 1197-7 Parameter: NUMWAT <- "1190" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1190" Comparing "1081" and "1190". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.996" Parameter: BOX -> "32.996" Parameter: BOX -> "32.996" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.99600 B = 32.99600 C = 32.99600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0234 2 1 -1 0 -1 2.1552 3 1 -1 1 -1 5.1962 4 1 0 -1 -1 4.8673 5 1 0 0 -1 1.1346 6 1 0 1 -1 2.0950 7 1 -1 -1 0 4.9529 8 1 -1 0 0 1.2794 9 1 -1 1 0 4.9211 10 1 0 -1 0 0.9908 11 1 0 1 0 0.9908 12 1 -1 -1 1 5.8437 13 1 -1 0 1 1.9445 14 1 -1 1 1 6.5457 15 1 0 -1 1 2.0950 16 1 0 0 1 1.1346 17 1 0 1 1 4.8673 18 1 1 1 1 6.0234 19 1 1 0 1 2.1552 20 1 1 -1 1 5.1962 21 1 1 1 0 4.9529 22 1 1 0 0 1.2794 23 1 1 -1 0 4.9211 24 1 1 1 -1 5.8437 25 1 1 0 -1 1.9445 26 1 1 -1 -1 6.5457 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3552 atoms have been selected out of 3626 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 747 249 249 0.00 3 C003 has 102 34 34 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1548 516 516 0.00 6 C006 has 447 149 149 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1738 577 576 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 90 30 30 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 1.16 Total of12894 atoms and 4289 groups and 4283 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3626 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1197 Number of atoms = 3626 Number of groups = 1202 Number of bonds = 3619 Number of angles = 1301 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2376 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1197 Number of atoms = 3626 Number of groups = 1202 Number of bonds = 3619 Number of angles = 1301 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2376 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.994" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1197" Evaluating: 1197-7 Parameter: NUMWAT <- "1190" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1190" Comparing "1081" and "1190". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.994" Parameter: BOX -> "32.994" Parameter: BOX -> "32.994" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.99400 B = 32.99400 C = 32.99400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0219 2 1 -1 0 -1 2.1526 3 1 -1 1 -1 5.1927 4 1 0 -1 -1 4.8677 5 1 0 0 -1 1.1328 6 1 0 1 -1 2.0924 7 1 -1 -1 0 4.9509 8 1 -1 0 0 1.2777 9 1 -1 1 0 4.9186 10 1 0 -1 0 0.9889 11 1 0 1 0 0.9889 12 1 -1 -1 1 5.8408 13 1 -1 0 1 1.9422 14 1 -1 1 1 6.5427 15 1 0 -1 1 2.0924 16 1 0 0 1 1.1328 17 1 0 1 1 4.8677 18 1 1 1 1 6.0219 19 1 1 0 1 2.1526 20 1 1 -1 1 5.1927 21 1 1 1 0 4.9509 22 1 1 0 0 1.2777 23 1 1 -1 0 4.9186 24 1 1 1 -1 5.8408 25 1 1 0 -1 1.9422 26 1 1 -1 -1 6.5427 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3552 atoms have been selected out of 3626 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 747 249 249 0.00 3 C003 has 102 34 34 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1548 516 516 0.00 6 C006 has 447 149 149 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1738 577 576 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 90 30 30 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 1.15 Total of12894 atoms and 4289 groups and 4283 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3626 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1197 Number of atoms = 3626 Number of groups = 1202 Number of bonds = 3619 Number of angles = 1301 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2376 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1197 Number of atoms = 3626 Number of groups = 1202 Number of bonds = 3619 Number of angles = 1301 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2376 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.992" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1197" Evaluating: 1197-7 Parameter: NUMWAT <- "1190" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1190" Comparing "1081" and "1190". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.992" Parameter: BOX -> "32.992" Parameter: BOX -> "32.992" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.99200 B = 32.99200 C = 32.99200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0204 2 1 -1 0 -1 2.1499 3 1 -1 1 -1 5.1893 4 1 0 -1 -1 4.8681 5 1 0 0 -1 1.1310 6 1 0 1 -1 2.0897 7 1 -1 -1 0 4.9490 8 1 -1 0 0 1.2759 9 1 -1 1 0 4.9161 10 1 0 -1 0 0.9870 11 1 0 1 0 0.9870 12 1 -1 -1 1 5.8380 13 1 -1 0 1 1.9399 14 1 -1 1 1 6.5396 15 1 0 -1 1 2.0897 16 1 0 0 1 1.1310 17 1 0 1 1 4.8681 18 1 1 1 1 6.0204 19 1 1 0 1 2.1499 20 1 1 -1 1 5.1893 21 1 1 1 0 4.9490 22 1 1 0 0 1.2759 23 1 1 -1 0 4.9161 24 1 1 1 -1 5.8380 25 1 1 0 -1 1.9399 26 1 1 -1 -1 6.5396 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3552 atoms have been selected out of 3626 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 747 249 249 0.00 3 C003 has 105 35 35 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1551 517 517 0.00 6 C006 has 447 149 149 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1738 577 576 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1656 552 552 0.00 12 C012 has 90 30 30 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 1.15 Total of12903 atoms and 4292 groups and 4286 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3626 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1197 Number of atoms = 3626 Number of groups = 1202 Number of bonds = 3619 Number of angles = 1301 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2376 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1197 Number of atoms = 3626 Number of groups = 1202 Number of bonds = 3619 Number of angles = 1301 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2376 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.99" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1197" Evaluating: 1197-7 Parameter: NUMWAT <- "1190" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1190" Comparing "1081" and "1190". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.99" Parameter: BOX -> "32.99" Parameter: BOX -> "32.99" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.99000 B = 32.99000 C = 32.99000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0189 2 1 -1 0 -1 2.1473 3 1 -1 1 -1 5.1859 4 1 0 -1 -1 4.8685 5 1 0 0 -1 1.1292 6 1 0 1 -1 2.0871 7 1 -1 -1 0 4.9471 8 1 -1 0 0 1.2742 9 1 -1 1 0 4.9136 10 1 0 -1 0 0.9851 11 1 0 1 0 0.9851 12 1 -1 -1 1 5.8351 13 1 -1 0 1 1.9376 14 1 -1 1 1 6.5366 15 1 0 -1 1 2.0871 16 1 0 0 1 1.1292 17 1 0 1 1 4.8685 18 1 1 1 1 6.0189 19 1 1 0 1 2.1473 20 1 1 -1 1 5.1859 21 1 1 1 0 4.9471 22 1 1 0 0 1.2742 23 1 1 -1 0 4.9136 24 1 1 1 -1 5.8351 25 1 1 0 -1 1.9376 26 1 1 -1 -1 6.5366 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3552 atoms have been selected out of 3626 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 735 OPERATED ON BY TRANSFORMATION C011 RESIDUE 804 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1551 517 517 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1738 577 576 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1653 551 551 0.00 12 C012 has 90 30 30 0.00 13 C013 has 483 161 161 0.00 14 C014 has 105 35 35 0.83 Total of12900 atoms and 4291 groups and 4285 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3626 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1195 Number of atoms = 3620 Number of groups = 1200 Number of bonds = 3613 Number of angles = 1299 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1197 Number of HB donors = 2372 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1195 Number of atoms = 3620 Number of groups = 1200 Number of bonds = 3613 Number of angles = 1299 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1197 Number of HB donors = 2372 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.988" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1195" Evaluating: 1195-7 Parameter: NUMWAT <- "1188" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1188" Comparing "1081" and "1188". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.988" Parameter: BOX -> "32.988" Parameter: BOX -> "32.988" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.98800 B = 32.98800 C = 32.98800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0174 2 1 -1 0 -1 2.1447 3 1 -1 1 -1 5.1824 4 1 0 -1 -1 4.8689 5 1 0 0 -1 1.1274 6 1 0 1 -1 2.0844 7 1 -1 -1 0 4.9451 8 1 -1 0 0 1.2724 9 1 -1 1 0 4.9110 10 1 0 -1 0 0.9833 11 1 0 1 0 0.9833 12 1 -1 -1 1 5.8323 13 1 -1 0 1 1.9353 14 1 -1 1 1 6.5336 15 1 0 -1 1 2.0844 16 1 0 0 1 1.1274 17 1 0 1 1 4.8689 18 1 1 1 1 6.0174 19 1 1 0 1 2.1447 20 1 1 -1 1 5.1824 21 1 1 1 0 4.9451 22 1 1 0 0 1.2724 23 1 1 -1 0 4.9110 24 1 1 1 -1 5.8323 25 1 1 0 -1 1.9353 26 1 1 -1 -1 6.5336 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3546 atoms have been selected out of 3620 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1741 578 577 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 90 30 30 0.00 13 C013 has 483 161 161 0.00 14 C014 has 108 36 36 1.15 Total of12876 atoms and 4283 groups and 4277 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3620 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1195 Number of atoms = 3620 Number of groups = 1200 Number of bonds = 3613 Number of angles = 1299 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1197 Number of HB donors = 2372 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1195 Number of atoms = 3620 Number of groups = 1200 Number of bonds = 3613 Number of angles = 1299 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1197 Number of HB donors = 2372 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.986" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1195" Evaluating: 1195-7 Parameter: NUMWAT <- "1188" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1188" Comparing "1081" and "1188". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.986" Parameter: BOX -> "32.986" Parameter: BOX -> "32.986" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.98600 B = 32.98600 C = 32.98600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0159 2 1 -1 0 -1 2.1420 3 1 -1 1 -1 5.1790 4 1 0 -1 -1 4.8693 5 1 0 0 -1 1.1257 6 1 0 1 -1 2.0818 7 1 -1 -1 0 4.9432 8 1 -1 0 0 1.2707 9 1 -1 1 0 4.9085 10 1 0 -1 0 0.9814 11 1 0 1 0 0.9814 12 1 -1 -1 1 5.8294 13 1 -1 0 1 1.9330 14 1 -1 1 1 6.5306 15 1 0 -1 1 2.0818 16 1 0 0 1 1.1257 17 1 0 1 1 4.8693 18 1 1 1 1 6.0159 19 1 1 0 1 2.1420 20 1 1 -1 1 5.1790 21 1 1 1 0 4.9432 22 1 1 0 0 1.2707 23 1 1 -1 0 4.9085 24 1 1 1 -1 5.8294 25 1 1 0 -1 1.9330 26 1 1 -1 -1 6.5306 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3546 atoms have been selected out of 3620 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1741 578 577 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 90 30 30 0.00 13 C013 has 483 161 161 0.00 14 C014 has 108 36 36 1.15 Total of12876 atoms and 4283 groups and 4277 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3620 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1195 Number of atoms = 3620 Number of groups = 1200 Number of bonds = 3613 Number of angles = 1299 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1197 Number of HB donors = 2372 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1195 Number of atoms = 3620 Number of groups = 1200 Number of bonds = 3613 Number of angles = 1299 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1197 Number of HB donors = 2372 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.984" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1195" Evaluating: 1195-7 Parameter: NUMWAT <- "1188" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1188" Comparing "1081" and "1188". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.984" Parameter: BOX -> "32.984" Parameter: BOX -> "32.984" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.98400 B = 32.98400 C = 32.98400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0144 2 1 -1 0 -1 2.1394 3 1 -1 1 -1 5.1756 4 1 0 -1 -1 4.8697 5 1 0 0 -1 1.1239 6 1 0 1 -1 2.0791 7 1 -1 -1 0 4.9413 8 1 -1 0 0 1.2690 9 1 -1 1 0 4.9060 10 1 0 -1 0 0.9795 11 1 0 1 0 0.9795 12 1 -1 -1 1 5.8266 13 1 -1 0 1 1.9307 14 1 -1 1 1 6.5276 15 1 0 -1 1 2.0791 16 1 0 0 1 1.1239 17 1 0 1 1 4.8697 18 1 1 1 1 6.0144 19 1 1 0 1 2.1394 20 1 1 -1 1 5.1756 21 1 1 1 0 4.9413 22 1 1 0 0 1.2690 23 1 1 -1 0 4.9060 24 1 1 1 -1 5.8266 25 1 1 0 -1 1.9307 26 1 1 -1 -1 6.5276 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3546 atoms have been selected out of 3620 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1741 578 577 0.00 9 C009 has 480 160 160 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 90 30 30 0.00 13 C013 has 483 161 161 0.00 14 C014 has 108 36 36 1.14 Total of12876 atoms and 4283 groups and 4277 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3620 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1195 Number of atoms = 3620 Number of groups = 1200 Number of bonds = 3613 Number of angles = 1299 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1197 Number of HB donors = 2372 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1195 Number of atoms = 3620 Number of groups = 1200 Number of bonds = 3613 Number of angles = 1299 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1197 Number of HB donors = 2372 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.982" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1195" Evaluating: 1195-7 Parameter: NUMWAT <- "1188" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1188" Comparing "1081" and "1188". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.982" Parameter: BOX -> "32.982" Parameter: BOX -> "32.982" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.98200 B = 32.98200 C = 32.98200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0129 2 1 -1 0 -1 2.1367 3 1 -1 1 -1 5.1722 4 1 0 -1 -1 4.8701 5 1 0 0 -1 1.1221 6 1 0 1 -1 2.0765 7 1 -1 -1 0 4.9394 8 1 -1 0 0 1.2672 9 1 -1 1 0 4.9035 10 1 0 -1 0 0.9776 11 1 0 1 0 0.9776 12 1 -1 -1 1 5.8237 13 1 -1 0 1 1.9284 14 1 -1 1 1 6.5246 15 1 0 -1 1 2.0765 16 1 0 0 1 1.1221 17 1 0 1 1 4.8701 18 1 1 1 1 6.0129 19 1 1 0 1 2.1367 20 1 1 -1 1 5.1722 21 1 1 1 0 4.9394 22 1 1 0 0 1.2672 23 1 1 -1 0 4.9035 24 1 1 1 -1 5.8237 25 1 1 0 -1 1.9284 26 1 1 -1 -1 6.5246 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3546 atoms have been selected out of 3620 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1741 578 577 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 90 30 30 0.00 13 C013 has 483 161 161 0.00 14 C014 has 108 36 36 1.14 Total of12879 atoms and 4284 groups and 4278 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3620 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1195 Number of atoms = 3620 Number of groups = 1200 Number of bonds = 3613 Number of angles = 1299 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1197 Number of HB donors = 2372 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1195 Number of atoms = 3620 Number of groups = 1200 Number of bonds = 3613 Number of angles = 1299 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1197 Number of HB donors = 2372 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.98" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1195" Evaluating: 1195-7 Parameter: NUMWAT <- "1188" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1188" Comparing "1081" and "1188". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.98" Parameter: BOX -> "32.98" Parameter: BOX -> "32.98" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.98000 B = 32.98000 C = 32.98000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0114 2 1 -1 0 -1 2.1341 3 1 -1 1 -1 5.1687 4 1 0 -1 -1 4.8705 5 1 0 0 -1 1.1203 6 1 0 1 -1 2.0738 7 1 -1 -1 0 4.9374 8 1 -1 0 0 1.2655 9 1 -1 1 0 4.9010 10 1 0 -1 0 0.9757 11 1 0 1 0 0.9757 12 1 -1 -1 1 5.8209 13 1 -1 0 1 1.9261 14 1 -1 1 1 6.5215 15 1 0 -1 1 2.0738 16 1 0 0 1 1.1203 17 1 0 1 1 4.8705 18 1 1 1 1 6.0114 19 1 1 0 1 2.1341 20 1 1 -1 1 5.1687 21 1 1 1 0 4.9374 22 1 1 0 0 1.2655 23 1 1 -1 0 4.9010 24 1 1 1 -1 5.8209 25 1 1 0 -1 1.9261 26 1 1 -1 -1 6.5215 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3546 atoms have been selected out of 3620 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1548 516 516 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1741 578 577 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 108 36 36 1.14 Total of12885 atoms and 4286 groups and 4280 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3620 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1195 Number of atoms = 3620 Number of groups = 1200 Number of bonds = 3613 Number of angles = 1299 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1197 Number of HB donors = 2372 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1195 Number of atoms = 3620 Number of groups = 1200 Number of bonds = 3613 Number of angles = 1299 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1197 Number of HB donors = 2372 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.978" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1195" Evaluating: 1195-7 Parameter: NUMWAT <- "1188" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1188" Comparing "1081" and "1188". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.978" Parameter: BOX -> "32.978" Parameter: BOX -> "32.978" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.97800 B = 32.97800 C = 32.97800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0099 2 1 -1 0 -1 2.1315 3 1 -1 1 -1 5.1653 4 1 0 -1 -1 4.8709 5 1 0 0 -1 1.1185 6 1 0 1 -1 2.0712 7 1 -1 -1 0 4.9355 8 1 -1 0 0 1.2638 9 1 -1 1 0 4.8985 10 1 0 -1 0 0.9739 11 1 0 1 0 0.9739 12 1 -1 -1 1 5.8180 13 1 -1 0 1 1.9238 14 1 -1 1 1 6.5185 15 1 0 -1 1 2.0712 16 1 0 0 1 1.1185 17 1 0 1 1 4.8709 18 1 1 1 1 6.0099 19 1 1 0 1 2.1315 20 1 1 -1 1 5.1653 21 1 1 1 0 4.9355 22 1 1 0 0 1.2638 23 1 1 -1 0 4.8985 24 1 1 1 -1 5.8180 25 1 1 0 -1 1.9238 26 1 1 -1 -1 6.5185 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3546 atoms have been selected out of 3620 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1548 516 516 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1741 578 577 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 108 36 36 1.14 Total of12885 atoms and 4286 groups and 4280 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3620 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1195 Number of atoms = 3620 Number of groups = 1200 Number of bonds = 3613 Number of angles = 1299 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1197 Number of HB donors = 2372 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1195 Number of atoms = 3620 Number of groups = 1200 Number of bonds = 3613 Number of angles = 1299 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1197 Number of HB donors = 2372 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.976" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1195" Evaluating: 1195-7 Parameter: NUMWAT <- "1188" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1188" Comparing "1081" and "1188". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.976" Parameter: BOX -> "32.976" Parameter: BOX -> "32.976" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.97600 B = 32.97600 C = 32.97600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0084 2 1 -1 0 -1 2.1288 3 1 -1 1 -1 5.1619 4 1 0 -1 -1 4.8713 5 1 0 0 -1 1.1167 6 1 0 1 -1 2.0685 7 1 -1 -1 0 4.9336 8 1 -1 0 0 1.2620 9 1 -1 1 0 4.8959 10 1 0 -1 0 0.9720 11 1 0 1 0 0.9720 12 1 -1 -1 1 5.8152 13 1 -1 0 1 1.9215 14 1 -1 1 1 6.5155 15 1 0 -1 1 2.0685 16 1 0 0 1 1.1167 17 1 0 1 1 4.8713 18 1 1 1 1 6.0084 19 1 1 0 1 2.1288 20 1 1 -1 1 5.1619 21 1 1 1 0 4.9336 22 1 1 0 0 1.2620 23 1 1 -1 0 4.8959 24 1 1 1 -1 5.8152 25 1 1 0 -1 1.9215 26 1 1 -1 -1 6.5155 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3546 atoms have been selected out of 3620 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1548 516 516 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1741 578 577 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 93 31 31 0.00 13 C013 has 483 161 161 0.00 14 C014 has 108 36 36 1.14 Total of12888 atoms and 4287 groups and 4281 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3620 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1195 Number of atoms = 3620 Number of groups = 1200 Number of bonds = 3613 Number of angles = 1299 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1197 Number of HB donors = 2372 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1195 Number of atoms = 3620 Number of groups = 1200 Number of bonds = 3613 Number of angles = 1299 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1197 Number of HB donors = 2372 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.974" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1195" Evaluating: 1195-7 Parameter: NUMWAT <- "1188" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1188" Comparing "1081" and "1188". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.974" Parameter: BOX -> "32.974" Parameter: BOX -> "32.974" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.97400 B = 32.97400 C = 32.97400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0069 2 1 -1 0 -1 2.1262 3 1 -1 1 -1 5.1585 4 1 0 -1 -1 4.8718 5 1 0 0 -1 1.1149 6 1 0 1 -1 2.0659 7 1 -1 -1 0 4.9316 8 1 -1 0 0 1.2603 9 1 -1 1 0 4.8934 10 1 0 -1 0 0.9701 11 1 0 1 0 0.9701 12 1 -1 -1 1 5.8124 13 1 -1 0 1 1.9192 14 1 -1 1 1 6.5125 15 1 0 -1 1 2.0659 16 1 0 0 1 1.1149 17 1 0 1 1 4.8718 18 1 1 1 1 6.0069 19 1 1 0 1 2.1262 20 1 1 -1 1 5.1585 21 1 1 1 0 4.9316 22 1 1 0 0 1.2603 23 1 1 -1 0 4.8934 24 1 1 1 -1 5.8124 25 1 1 0 -1 1.9192 26 1 1 -1 -1 6.5125 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3546 atoms have been selected out of 3620 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1009 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 744 248 248 0.00 3 C003 has 105 35 35 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1548 516 516 0.00 6 C006 has 441 147 147 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1738 577 576 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1653 551 551 0.00 12 C012 has 93 31 31 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 1.13 Total of12897 atoms and 4290 groups and 4284 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3620 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1194 Number of atoms = 3617 Number of groups = 1199 Number of bonds = 3610 Number of angles = 1298 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1196 Number of HB donors = 2370 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1194 Number of atoms = 3617 Number of groups = 1199 Number of bonds = 3610 Number of angles = 1298 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1196 Number of HB donors = 2370 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.972" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1194" Evaluating: 1194-7 Parameter: NUMWAT <- "1187" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1187" Comparing "1081" and "1187". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.972" Parameter: BOX -> "32.972" Parameter: BOX -> "32.972" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.97200 B = 32.97200 C = 32.97200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0054 2 1 -1 0 -1 2.1235 3 1 -1 1 -1 5.1550 4 1 0 -1 -1 4.8722 5 1 0 0 -1 1.1132 6 1 0 1 -1 2.0632 7 1 -1 -1 0 4.9297 8 1 -1 0 0 1.2586 9 1 -1 1 0 4.8909 10 1 0 -1 0 0.9682 11 1 0 1 0 0.9682 12 1 -1 -1 1 5.8095 13 1 -1 0 1 1.9170 14 1 -1 1 1 6.5095 15 1 0 -1 1 2.0632 16 1 0 0 1 1.1132 17 1 0 1 1 4.8722 18 1 1 1 1 6.0054 19 1 1 0 1 2.1235 20 1 1 -1 1 5.1550 21 1 1 1 0 4.9297 22 1 1 0 0 1.2586 23 1 1 -1 0 4.8909 24 1 1 1 -1 5.8095 25 1 1 0 -1 1.9170 26 1 1 -1 -1 6.5095 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3543 atoms have been selected out of 3617 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1735 576 575 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 93 31 31 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 1.13 Total of12876 atoms and 4283 groups and 4277 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3617 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1194 Number of atoms = 3617 Number of groups = 1199 Number of bonds = 3610 Number of angles = 1298 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1196 Number of HB donors = 2370 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1194 Number of atoms = 3617 Number of groups = 1199 Number of bonds = 3610 Number of angles = 1298 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1196 Number of HB donors = 2370 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.97" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1194" Evaluating: 1194-7 Parameter: NUMWAT <- "1187" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1187" Comparing "1081" and "1187". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.97" Parameter: BOX -> "32.97" Parameter: BOX -> "32.97" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.97000 B = 32.97000 C = 32.97000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0040 2 1 -1 0 -1 2.1209 3 1 -1 1 -1 5.1516 4 1 0 -1 -1 4.8726 5 1 0 0 -1 1.1114 6 1 0 1 -1 2.0606 7 1 -1 -1 0 4.9278 8 1 -1 0 0 1.2569 9 1 -1 1 0 4.8884 10 1 0 -1 0 0.9663 11 1 0 1 0 0.9663 12 1 -1 -1 1 5.8067 13 1 -1 0 1 1.9147 14 1 -1 1 1 6.5065 15 1 0 -1 1 2.0606 16 1 0 0 1 1.1114 17 1 0 1 1 4.8726 18 1 1 1 1 6.0040 19 1 1 0 1 2.1209 20 1 1 -1 1 5.1516 21 1 1 1 0 4.9278 22 1 1 0 0 1.2569 23 1 1 -1 0 4.8884 24 1 1 1 -1 5.8067 25 1 1 0 -1 1.9147 26 1 1 -1 -1 6.5065 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3543 atoms have been selected out of 3617 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1735 576 575 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 93 31 31 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 1.13 Total of12876 atoms and 4283 groups and 4277 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3617 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1194 Number of atoms = 3617 Number of groups = 1199 Number of bonds = 3610 Number of angles = 1298 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1196 Number of HB donors = 2370 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1194 Number of atoms = 3617 Number of groups = 1199 Number of bonds = 3610 Number of angles = 1298 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1196 Number of HB donors = 2370 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.968" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1194" Evaluating: 1194-7 Parameter: NUMWAT <- "1187" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1187" Comparing "1081" and "1187". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.968" Parameter: BOX -> "32.968" Parameter: BOX -> "32.968" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.96800 B = 32.96800 C = 32.96800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0025 2 1 -1 0 -1 2.1183 3 1 -1 1 -1 5.1482 4 1 0 -1 -1 4.8730 5 1 0 0 -1 1.1096 6 1 0 1 -1 2.0579 7 1 -1 -1 0 4.9259 8 1 -1 0 0 1.2551 9 1 -1 1 0 4.8859 10 1 0 -1 0 0.9645 11 1 0 1 0 0.9645 12 1 -1 -1 1 5.8038 13 1 -1 0 1 1.9124 14 1 -1 1 1 6.5035 15 1 0 -1 1 2.0579 16 1 0 0 1 1.1096 17 1 0 1 1 4.8730 18 1 1 1 1 6.0025 19 1 1 0 1 2.1183 20 1 1 -1 1 5.1482 21 1 1 1 0 4.9259 22 1 1 0 0 1.2551 23 1 1 -1 0 4.8859 24 1 1 1 -1 5.8038 25 1 1 0 -1 1.9124 26 1 1 -1 -1 6.5035 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3543 atoms have been selected out of 3617 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1735 576 575 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 93 31 31 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 1.13 Total of12876 atoms and 4283 groups and 4277 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3617 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1194 Number of atoms = 3617 Number of groups = 1199 Number of bonds = 3610 Number of angles = 1298 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1196 Number of HB donors = 2370 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1194 Number of atoms = 3617 Number of groups = 1199 Number of bonds = 3610 Number of angles = 1298 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1196 Number of HB donors = 2370 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.966" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1194" Evaluating: 1194-7 Parameter: NUMWAT <- "1187" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1187" Comparing "1081" and "1187". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.966" Parameter: BOX -> "32.966" Parameter: BOX -> "32.966" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.96600 B = 32.96600 C = 32.96600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.0010 2 1 -1 0 -1 2.1156 3 1 -1 1 -1 5.1447 4 1 0 -1 -1 4.8734 5 1 0 0 -1 1.1078 6 1 0 1 -1 2.0553 7 1 -1 -1 0 4.9240 8 1 -1 0 0 1.2534 9 1 -1 1 0 4.8834 10 1 0 -1 0 0.9626 11 1 0 1 0 0.9626 12 1 -1 -1 1 5.8010 13 1 -1 0 1 1.9101 14 1 -1 1 1 6.5005 15 1 0 -1 1 2.0553 16 1 0 0 1 1.1078 17 1 0 1 1 4.8734 18 1 1 1 1 6.0010 19 1 1 0 1 2.1156 20 1 1 -1 1 5.1447 21 1 1 1 0 4.9240 22 1 1 0 0 1.2534 23 1 1 -1 0 4.8834 24 1 1 1 -1 5.8010 25 1 1 0 -1 1.9101 26 1 1 -1 -1 6.5005 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3543 atoms have been selected out of 3617 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1735 576 575 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 93 31 31 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 1.13 Total of12876 atoms and 4283 groups and 4277 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3617 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1194 Number of atoms = 3617 Number of groups = 1199 Number of bonds = 3610 Number of angles = 1298 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1196 Number of HB donors = 2370 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1194 Number of atoms = 3617 Number of groups = 1199 Number of bonds = 3610 Number of angles = 1298 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1196 Number of HB donors = 2370 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.964" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1194" Evaluating: 1194-7 Parameter: NUMWAT <- "1187" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1187" Comparing "1081" and "1187". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.964" Parameter: BOX -> "32.964" Parameter: BOX -> "32.964" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.96400 B = 32.96400 C = 32.96400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9995 2 1 -1 0 -1 2.1130 3 1 -1 1 -1 5.1413 4 1 0 -1 -1 4.8739 5 1 0 0 -1 1.1060 6 1 0 1 -1 2.0526 7 1 -1 -1 0 4.9220 8 1 -1 0 0 1.2517 9 1 -1 1 0 4.8809 10 1 0 -1 0 0.9607 11 1 0 1 0 0.9607 12 1 -1 -1 1 5.7981 13 1 -1 0 1 1.9078 14 1 -1 1 1 6.4974 15 1 0 -1 1 2.0526 16 1 0 0 1 1.1060 17 1 0 1 1 4.8739 18 1 1 1 1 5.9995 19 1 1 0 1 2.1130 20 1 1 -1 1 5.1413 21 1 1 1 0 4.9220 22 1 1 0 0 1.2517 23 1 1 -1 0 4.8809 24 1 1 1 -1 5.7981 25 1 1 0 -1 1.9078 26 1 1 -1 -1 6.4974 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3543 atoms have been selected out of 3617 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1735 576 575 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 93 31 31 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 1.12 Total of12876 atoms and 4283 groups and 4277 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3617 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1194 Number of atoms = 3617 Number of groups = 1199 Number of bonds = 3610 Number of angles = 1298 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1196 Number of HB donors = 2370 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1194 Number of atoms = 3617 Number of groups = 1199 Number of bonds = 3610 Number of angles = 1298 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1196 Number of HB donors = 2370 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.962" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1194" Evaluating: 1194-7 Parameter: NUMWAT <- "1187" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1187" Comparing "1081" and "1187". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.962" Parameter: BOX -> "32.962" Parameter: BOX -> "32.962" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.96200 B = 32.96200 C = 32.96200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9980 2 1 -1 0 -1 2.1104 3 1 -1 1 -1 5.1379 4 1 0 -1 -1 4.8743 5 1 0 0 -1 1.1043 6 1 0 1 -1 2.0500 7 1 -1 -1 0 4.9201 8 1 -1 0 0 1.2500 9 1 -1 1 0 4.8783 10 1 0 -1 0 0.9588 11 1 0 1 0 0.9588 12 1 -1 -1 1 5.7953 13 1 -1 0 1 1.9056 14 1 -1 1 1 6.4944 15 1 0 -1 1 2.0500 16 1 0 0 1 1.1043 17 1 0 1 1 4.8743 18 1 1 1 1 5.9980 19 1 1 0 1 2.1104 20 1 1 -1 1 5.1379 21 1 1 1 0 4.9201 22 1 1 0 0 1.2500 23 1 1 -1 0 4.8783 24 1 1 1 -1 5.7953 25 1 1 0 -1 1.9056 26 1 1 -1 -1 6.4944 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3543 atoms have been selected out of 3617 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1735 576 575 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 93 31 31 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 1.12 Total of12876 atoms and 4283 groups and 4277 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3617 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1194 Number of atoms = 3617 Number of groups = 1199 Number of bonds = 3610 Number of angles = 1298 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1196 Number of HB donors = 2370 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1194 Number of atoms = 3617 Number of groups = 1199 Number of bonds = 3610 Number of angles = 1298 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1196 Number of HB donors = 2370 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.96" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1194" Evaluating: 1194-7 Parameter: NUMWAT <- "1187" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1187" Comparing "1081" and "1187". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.96" Parameter: BOX -> "32.96" Parameter: BOX -> "32.96" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.96000 B = 32.96000 C = 32.96000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9966 2 1 -1 0 -1 2.1077 3 1 -1 1 -1 5.1345 4 1 0 -1 -1 4.8747 5 1 0 0 -1 1.1025 6 1 0 1 -1 2.0473 7 1 -1 -1 0 4.9182 8 1 -1 0 0 1.2482 9 1 -1 1 0 4.8758 10 1 0 -1 0 0.9570 11 1 0 1 0 0.9570 12 1 -1 -1 1 5.7925 13 1 -1 0 1 1.9033 14 1 -1 1 1 6.4914 15 1 0 -1 1 2.0473 16 1 0 0 1 1.1025 17 1 0 1 1 4.8747 18 1 1 1 1 5.9966 19 1 1 0 1 2.1077 20 1 1 -1 1 5.1345 21 1 1 1 0 4.9182 22 1 1 0 0 1.2482 23 1 1 -1 0 4.8758 24 1 1 1 -1 5.7925 25 1 1 0 -1 1.9033 26 1 1 -1 -1 6.4914 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3543 atoms have been selected out of 3617 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1738 577 576 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 96 32 32 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 1.12 Total of12882 atoms and 4285 groups and 4279 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3617 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1194 Number of atoms = 3617 Number of groups = 1199 Number of bonds = 3610 Number of angles = 1298 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1196 Number of HB donors = 2370 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1194 Number of atoms = 3617 Number of groups = 1199 Number of bonds = 3610 Number of angles = 1298 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1196 Number of HB donors = 2370 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.958" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1194" Evaluating: 1194-7 Parameter: NUMWAT <- "1187" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1187" Comparing "1081" and "1187". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.958" Parameter: BOX -> "32.958" Parameter: BOX -> "32.958" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.95800 B = 32.95800 C = 32.95800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9951 2 1 -1 0 -1 2.1051 3 1 -1 1 -1 5.1310 4 1 0 -1 -1 4.8751 5 1 0 0 -1 1.1007 6 1 0 1 -1 2.0447 7 1 -1 -1 0 4.9163 8 1 -1 0 0 1.2465 9 1 -1 1 0 4.8733 10 1 0 -1 0 0.9551 11 1 0 1 0 0.9551 12 1 -1 -1 1 5.7896 13 1 -1 0 1 1.9010 14 1 -1 1 1 6.4884 15 1 0 -1 1 2.0447 16 1 0 0 1 1.1007 17 1 0 1 1 4.8751 18 1 1 1 1 5.9951 19 1 1 0 1 2.1051 20 1 1 -1 1 5.1310 21 1 1 1 0 4.9163 22 1 1 0 0 1.2465 23 1 1 -1 0 4.8733 24 1 1 1 -1 5.7896 25 1 1 0 -1 1.9010 26 1 1 -1 -1 6.4884 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3543 atoms have been selected out of 3617 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1738 577 576 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 96 32 32 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 1.12 Total of12882 atoms and 4285 groups and 4279 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3617 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1194 Number of atoms = 3617 Number of groups = 1199 Number of bonds = 3610 Number of angles = 1298 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1196 Number of HB donors = 2370 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1194 Number of atoms = 3617 Number of groups = 1199 Number of bonds = 3610 Number of angles = 1298 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1196 Number of HB donors = 2370 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.956" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1194" Evaluating: 1194-7 Parameter: NUMWAT <- "1187" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1187" Comparing "1081" and "1187". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.956" Parameter: BOX -> "32.956" Parameter: BOX -> "32.956" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.95600 B = 32.95600 C = 32.95600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9936 2 1 -1 0 -1 2.1025 3 1 -1 1 -1 5.1276 4 1 0 -1 -1 4.8756 5 1 0 0 -1 1.0989 6 1 0 1 -1 2.0421 7 1 -1 -1 0 4.9144 8 1 -1 0 0 1.2448 9 1 -1 1 0 4.8708 10 1 0 -1 0 0.9532 11 1 0 1 0 0.9532 12 1 -1 -1 1 5.7868 13 1 -1 0 1 1.8987 14 1 -1 1 1 6.4854 15 1 0 -1 1 2.0421 16 1 0 0 1 1.0989 17 1 0 1 1 4.8756 18 1 1 1 1 5.9936 19 1 1 0 1 2.1025 20 1 1 -1 1 5.1276 21 1 1 1 0 4.9144 22 1 1 0 0 1.2448 23 1 1 -1 0 4.8708 24 1 1 1 -1 5.7868 25 1 1 0 -1 1.8987 26 1 1 -1 -1 6.4854 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3543 atoms have been selected out of 3617 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 95 OPERATED ON BY TRANSFORMATION C016 RESIDUE 393 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1551 517 517 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1738 577 576 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1650 550 550 0.00 12 C012 has 105 35 35 0.00 13 C013 has 480 160 160 0.00 14 C014 has 111 37 37 1.12 Total of12909 atoms and 4294 groups and 4288 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3617 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1192 Number of atoms = 3611 Number of groups = 1197 Number of bonds = 3604 Number of angles = 1296 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1194 Number of HB donors = 2366 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1192 Number of atoms = 3611 Number of groups = 1197 Number of bonds = 3604 Number of angles = 1296 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1194 Number of HB donors = 2366 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.954" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1192" Evaluating: 1192-7 Parameter: NUMWAT <- "1185" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1185" Comparing "1081" and "1185". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.954" Parameter: BOX -> "32.954" Parameter: BOX -> "32.954" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.95400 B = 32.95400 C = 32.95400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9921 2 1 -1 0 -1 2.0998 3 1 -1 1 -1 5.1242 4 1 0 -1 -1 4.8760 5 1 0 0 -1 1.0972 6 1 0 1 -1 2.0394 7 1 -1 -1 0 4.9124 8 1 -1 0 0 1.2431 9 1 -1 1 0 4.8683 10 1 0 -1 0 0.9513 11 1 0 1 0 0.9513 12 1 -1 -1 1 5.7839 13 1 -1 0 1 1.8965 14 1 -1 1 1 6.4824 15 1 0 -1 1 2.0394 16 1 0 0 1 1.0972 17 1 0 1 1 4.8760 18 1 1 1 1 5.9921 19 1 1 0 1 2.0998 20 1 1 -1 1 5.1242 21 1 1 1 0 4.9124 22 1 1 0 0 1.2431 23 1 1 -1 0 4.8683 24 1 1 1 -1 5.7839 25 1 1 0 -1 1.8965 26 1 1 -1 -1 6.4824 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3537 atoms have been selected out of 3611 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 435 145 145 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1738 577 576 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 96 32 32 0.00 13 C013 has 477 159 159 0.00 14 C014 has 111 37 37 1.11 Total of12876 atoms and 4283 groups and 4277 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3611 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1192 Number of atoms = 3611 Number of groups = 1197 Number of bonds = 3604 Number of angles = 1296 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1194 Number of HB donors = 2366 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1192 Number of atoms = 3611 Number of groups = 1197 Number of bonds = 3604 Number of angles = 1296 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1194 Number of HB donors = 2366 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.952" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1192" Evaluating: 1192-7 Parameter: NUMWAT <- "1185" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1185" Comparing "1081" and "1185". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.952" Parameter: BOX -> "32.952" Parameter: BOX -> "32.952" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.95200 B = 32.95200 C = 32.95200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9907 2 1 -1 0 -1 2.0972 3 1 -1 1 -1 5.1207 4 1 0 -1 -1 4.8764 5 1 0 0 -1 1.0954 6 1 0 1 -1 2.0368 7 1 -1 -1 0 4.9105 8 1 -1 0 0 1.2413 9 1 -1 1 0 4.8658 10 1 0 -1 0 0.9495 11 1 0 1 0 0.9495 12 1 -1 -1 1 5.7811 13 1 -1 0 1 1.8942 14 1 -1 1 1 6.4794 15 1 0 -1 1 2.0368 16 1 0 0 1 1.0954 17 1 0 1 1 4.8764 18 1 1 1 1 5.9907 19 1 1 0 1 2.0972 20 1 1 -1 1 5.1207 21 1 1 1 0 4.9105 22 1 1 0 0 1.2413 23 1 1 -1 0 4.8658 24 1 1 1 -1 5.7811 25 1 1 0 -1 1.8942 26 1 1 -1 -1 6.4794 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3537 atoms have been selected out of 3611 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 741 247 247 0.00 3 C003 has 105 35 35 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 435 145 145 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1738 577 576 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 96 32 32 0.00 13 C013 has 480 160 160 0.00 14 C014 has 114 38 38 1.11 Total of12882 atoms and 4285 groups and 4279 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3611 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1192 Number of atoms = 3611 Number of groups = 1197 Number of bonds = 3604 Number of angles = 1296 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1194 Number of HB donors = 2366 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1192 Number of atoms = 3611 Number of groups = 1197 Number of bonds = 3604 Number of angles = 1296 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1194 Number of HB donors = 2366 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.95" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1192" Evaluating: 1192-7 Parameter: NUMWAT <- "1185" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1185" Comparing "1081" and "1185". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.95" Parameter: BOX -> "32.95" Parameter: BOX -> "32.95" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.95000 B = 32.95000 C = 32.95000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9892 2 1 -1 0 -1 2.0946 3 1 -1 1 -1 5.1173 4 1 0 -1 -1 4.8768 5 1 0 0 -1 1.0936 6 1 0 1 -1 2.0341 7 1 -1 -1 0 4.9086 8 1 -1 0 0 1.2396 9 1 -1 1 0 4.8633 10 1 0 -1 0 0.9476 11 1 0 1 0 0.9476 12 1 -1 -1 1 5.7783 13 1 -1 0 1 1.8919 14 1 -1 1 1 6.4764 15 1 0 -1 1 2.0341 16 1 0 0 1 1.0936 17 1 0 1 1 4.8768 18 1 1 1 1 5.9892 19 1 1 0 1 2.0946 20 1 1 -1 1 5.1173 21 1 1 1 0 4.9086 22 1 1 0 0 1.2396 23 1 1 -1 0 4.8633 24 1 1 1 -1 5.7783 25 1 1 0 -1 1.8919 26 1 1 -1 -1 6.4764 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3537 atoms have been selected out of 3611 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 744 248 248 0.00 3 C003 has 105 35 35 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 435 145 145 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1738 577 576 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1647 549 549 0.00 12 C012 has 96 32 32 0.00 13 C013 has 480 160 160 0.00 14 C014 has 114 38 38 1.11 Total of12885 atoms and 4286 groups and 4280 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3611 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1192 Number of atoms = 3611 Number of groups = 1197 Number of bonds = 3604 Number of angles = 1296 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1194 Number of HB donors = 2366 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1192 Number of atoms = 3611 Number of groups = 1197 Number of bonds = 3604 Number of angles = 1296 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1194 Number of HB donors = 2366 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.948" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1192" Evaluating: 1192-7 Parameter: NUMWAT <- "1185" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1185" Comparing "1081" and "1185". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.948" Parameter: BOX -> "32.948" Parameter: BOX -> "32.948" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.94800 B = 32.94800 C = 32.94800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9877 2 1 -1 0 -1 2.0919 3 1 -1 1 -1 5.1139 4 1 0 -1 -1 4.8773 5 1 0 0 -1 1.0918 6 1 0 1 -1 2.0315 7 1 -1 -1 0 4.9067 8 1 -1 0 0 1.2379 9 1 -1 1 0 4.8608 10 1 0 -1 0 0.9457 11 1 0 1 0 0.9457 12 1 -1 -1 1 5.7754 13 1 -1 0 1 1.8897 14 1 -1 1 1 6.4734 15 1 0 -1 1 2.0315 16 1 0 0 1 1.0918 17 1 0 1 1 4.8773 18 1 1 1 1 5.9877 19 1 1 0 1 2.0919 20 1 1 -1 1 5.1139 21 1 1 1 0 4.9067 22 1 1 0 0 1.2379 23 1 1 -1 0 4.8608 24 1 1 1 -1 5.7754 25 1 1 0 -1 1.8897 26 1 1 -1 -1 6.4734 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3537 atoms have been selected out of 3611 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 266 OPERATED ON BY TRANSFORMATION C016 RESIDUE 609 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1548 516 516 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1738 577 576 0.00 9 C009 has 486 162 162 0.00 10 C010 has 1644 548 548 0.00 12 C012 has 96 32 32 0.00 13 C013 has 477 159 159 0.00 14 C014 has 111 37 37 1.11 Total of12888 atoms and 4287 groups and 4281 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3611 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1190 Number of atoms = 3605 Number of groups = 1195 Number of bonds = 3598 Number of angles = 1294 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1192 Number of HB donors = 2362 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1190 Number of atoms = 3605 Number of groups = 1195 Number of bonds = 3598 Number of angles = 1294 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1192 Number of HB donors = 2362 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.946" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1190" Evaluating: 1190-7 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1183" Comparing "1081" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.946" Parameter: BOX -> "32.946" Parameter: BOX -> "32.946" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.94600 B = 32.94600 C = 32.94600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9863 2 1 -1 0 -1 2.0893 3 1 -1 1 -1 5.1105 4 1 0 -1 -1 4.8777 5 1 0 0 -1 1.0901 6 1 0 1 -1 2.0289 7 1 -1 -1 0 4.9048 8 1 -1 0 0 1.2362 9 1 -1 1 0 4.8583 10 1 0 -1 0 0.9439 11 1 0 1 0 0.9439 12 1 -1 -1 1 5.7726 13 1 -1 0 1 1.8874 14 1 -1 1 1 6.4704 15 1 0 -1 1 2.0289 16 1 0 0 1 1.0901 17 1 0 1 1 4.8777 18 1 1 1 1 5.9863 19 1 1 0 1 2.0893 20 1 1 -1 1 5.1105 21 1 1 1 0 4.9048 22 1 1 0 0 1.2362 23 1 1 -1 0 4.8583 24 1 1 1 -1 5.7726 25 1 1 0 -1 1.8874 26 1 1 -1 -1 6.4704 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3531 atoms have been selected out of 3605 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 744 248 248 0.00 3 C003 has 105 35 35 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 435 145 145 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1735 576 575 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1641 547 547 0.00 12 C012 has 96 32 32 0.00 13 C013 has 477 159 159 0.00 14 C014 has 111 37 37 1.11 Total of12861 atoms and 4278 groups and 4272 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3605 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1190 Number of atoms = 3605 Number of groups = 1195 Number of bonds = 3598 Number of angles = 1294 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1192 Number of HB donors = 2362 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1190 Number of atoms = 3605 Number of groups = 1195 Number of bonds = 3598 Number of angles = 1294 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1192 Number of HB donors = 2362 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.944" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1190" Evaluating: 1190-7 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1183" Comparing "1081" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.944" Parameter: BOX -> "32.944" Parameter: BOX -> "32.944" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.94400 B = 32.94400 C = 32.94400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9848 2 1 -1 0 -1 2.0867 3 1 -1 1 -1 5.1070 4 1 0 -1 -1 4.8782 5 1 0 0 -1 1.0883 6 1 0 1 -1 2.0262 7 1 -1 -1 0 4.9029 8 1 -1 0 0 1.2345 9 1 -1 1 0 4.8557 10 1 0 -1 0 0.9420 11 1 0 1 0 0.9420 12 1 -1 -1 1 5.7698 13 1 -1 0 1 1.8851 14 1 -1 1 1 6.4673 15 1 0 -1 1 2.0262 16 1 0 0 1 1.0883 17 1 0 1 1 4.8782 18 1 1 1 1 5.9848 19 1 1 0 1 2.0867 20 1 1 -1 1 5.1070 21 1 1 1 0 4.9029 22 1 1 0 0 1.2345 23 1 1 -1 0 4.8557 24 1 1 1 -1 5.7698 25 1 1 0 -1 1.8851 26 1 1 -1 -1 6.4673 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3531 atoms have been selected out of 3605 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 744 248 248 0.00 3 C003 has 105 35 35 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1738 577 576 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1641 547 547 0.00 12 C012 has 96 32 32 0.00 13 C013 has 477 159 159 0.00 14 C014 has 111 37 37 1.10 Total of12870 atoms and 4281 groups and 4275 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3605 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1190 Number of atoms = 3605 Number of groups = 1195 Number of bonds = 3598 Number of angles = 1294 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1192 Number of HB donors = 2362 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1190 Number of atoms = 3605 Number of groups = 1195 Number of bonds = 3598 Number of angles = 1294 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1192 Number of HB donors = 2362 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.942" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1190" Evaluating: 1190-7 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1183" Comparing "1081" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.942" Parameter: BOX -> "32.942" Parameter: BOX -> "32.942" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.94200 B = 32.94200 C = 32.94200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9834 2 1 -1 0 -1 2.0840 3 1 -1 1 -1 5.1036 4 1 0 -1 -1 4.8786 5 1 0 0 -1 1.0865 6 1 0 1 -1 2.0236 7 1 -1 -1 0 4.9010 8 1 -1 0 0 1.2327 9 1 -1 1 0 4.8532 10 1 0 -1 0 0.9401 11 1 0 1 0 0.9401 12 1 -1 -1 1 5.7669 13 1 -1 0 1 1.8829 14 1 -1 1 1 6.4643 15 1 0 -1 1 2.0236 16 1 0 0 1 1.0865 17 1 0 1 1 4.8786 18 1 1 1 1 5.9834 19 1 1 0 1 2.0840 20 1 1 -1 1 5.1036 21 1 1 1 0 4.9010 22 1 1 0 0 1.2327 23 1 1 -1 0 4.8532 24 1 1 1 -1 5.7669 25 1 1 0 -1 1.8829 26 1 1 -1 -1 6.4643 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3531 atoms have been selected out of 3605 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 744 248 248 0.00 3 C003 has 105 35 35 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1738 577 576 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1641 547 547 0.00 12 C012 has 96 32 32 0.00 13 C013 has 477 159 159 0.00 14 C014 has 111 37 37 1.10 Total of12870 atoms and 4281 groups and 4275 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3605 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1190 Number of atoms = 3605 Number of groups = 1195 Number of bonds = 3598 Number of angles = 1294 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1192 Number of HB donors = 2362 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1190 Number of atoms = 3605 Number of groups = 1195 Number of bonds = 3598 Number of angles = 1294 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1192 Number of HB donors = 2362 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.94" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1190" Evaluating: 1190-7 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1183" Comparing "1081" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.94" Parameter: BOX -> "32.94" Parameter: BOX -> "32.94" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.94000 B = 32.94000 C = 32.94000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9819 2 1 -1 0 -1 2.0814 3 1 -1 1 -1 5.1002 4 1 0 -1 -1 4.8790 5 1 0 0 -1 1.0848 6 1 0 1 -1 2.0209 7 1 -1 -1 0 4.8990 8 1 -1 0 0 1.2310 9 1 -1 1 0 4.8507 10 1 0 -1 0 0.9382 11 1 0 1 0 0.9382 12 1 -1 -1 1 5.7641 13 1 -1 0 1 1.8806 14 1 -1 1 1 6.4613 15 1 0 -1 1 2.0209 16 1 0 0 1 1.0848 17 1 0 1 1 4.8790 18 1 1 1 1 5.9819 19 1 1 0 1 2.0814 20 1 1 -1 1 5.1002 21 1 1 1 0 4.8990 22 1 1 0 0 1.2310 23 1 1 -1 0 4.8507 24 1 1 1 -1 5.7641 25 1 1 0 -1 1.8806 26 1 1 -1 -1 6.4613 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3531 atoms have been selected out of 3605 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 744 248 248 0.00 3 C003 has 105 35 35 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1738 577 576 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1641 547 547 0.00 12 C012 has 96 32 32 0.00 13 C013 has 477 159 159 0.00 14 C014 has 111 37 37 1.10 Total of12870 atoms and 4281 groups and 4275 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3605 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1190 Number of atoms = 3605 Number of groups = 1195 Number of bonds = 3598 Number of angles = 1294 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1192 Number of HB donors = 2362 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1190 Number of atoms = 3605 Number of groups = 1195 Number of bonds = 3598 Number of angles = 1294 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1192 Number of HB donors = 2362 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.938" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1190" Evaluating: 1190-7 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1183" Comparing "1081" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.938" Parameter: BOX -> "32.938" Parameter: BOX -> "32.938" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.93800 B = 32.93800 C = 32.93800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9804 2 1 -1 0 -1 2.0788 3 1 -1 1 -1 5.0968 4 1 0 -1 -1 4.8795 5 1 0 0 -1 1.0830 6 1 0 1 -1 2.0183 7 1 -1 -1 0 4.8971 8 1 -1 0 0 1.2293 9 1 -1 1 0 4.8482 10 1 0 -1 0 0.9364 11 1 0 1 0 0.9364 12 1 -1 -1 1 5.7613 13 1 -1 0 1 1.8784 14 1 -1 1 1 6.4583 15 1 0 -1 1 2.0183 16 1 0 0 1 1.0830 17 1 0 1 1 4.8795 18 1 1 1 1 5.9804 19 1 1 0 1 2.0788 20 1 1 -1 1 5.0968 21 1 1 1 0 4.8971 22 1 1 0 0 1.2293 23 1 1 -1 0 4.8482 24 1 1 1 -1 5.7613 25 1 1 0 -1 1.8784 26 1 1 -1 -1 6.4583 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3531 atoms have been selected out of 3605 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 744 248 248 0.00 3 C003 has 105 35 35 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1738 577 576 0.00 9 C009 has 483 161 161 0.00 10 C010 has 1641 547 547 0.00 12 C012 has 96 32 32 0.00 13 C013 has 477 159 159 0.00 14 C014 has 111 37 37 1.10 Total of12870 atoms and 4281 groups and 4275 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3605 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1190 Number of atoms = 3605 Number of groups = 1195 Number of bonds = 3598 Number of angles = 1294 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1192 Number of HB donors = 2362 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1190 Number of atoms = 3605 Number of groups = 1195 Number of bonds = 3598 Number of angles = 1294 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1192 Number of HB donors = 2362 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.936" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1190" Evaluating: 1190-7 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1183" Comparing "1081" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.936" Parameter: BOX -> "32.936" Parameter: BOX -> "32.936" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.93600 B = 32.93600 C = 32.93600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9790 2 1 -1 0 -1 2.0761 3 1 -1 1 -1 5.0933 4 1 0 -1 -1 4.8799 5 1 0 0 -1 1.0812 6 1 0 1 -1 2.0157 7 1 -1 -1 0 4.8952 8 1 -1 0 0 1.2276 9 1 -1 1 0 4.8457 10 1 0 -1 0 0.9345 11 1 0 1 0 0.9345 12 1 -1 -1 1 5.7584 13 1 -1 0 1 1.8761 14 1 -1 1 1 6.4553 15 1 0 -1 1 2.0157 16 1 0 0 1 1.0812 17 1 0 1 1 4.8799 18 1 1 1 1 5.9790 19 1 1 0 1 2.0761 20 1 1 -1 1 5.0933 21 1 1 1 0 4.8952 22 1 1 0 0 1.2276 23 1 1 -1 0 4.8457 24 1 1 1 -1 5.7584 25 1 1 0 -1 1.8761 26 1 1 -1 -1 6.4553 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3531 atoms have been selected out of 3605 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 919 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1073 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 747 249 249 0.00 3 C003 has 105 35 35 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1551 517 517 0.00 6 C006 has 438 146 146 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1738 577 576 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1635 545 545 0.00 12 C012 has 96 32 32 0.00 13 C013 has 477 159 159 0.00 14 C014 has 111 37 37 1.10 Total of12873 atoms and 4282 groups and 4276 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3605 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1188 Number of atoms = 3599 Number of groups = 1193 Number of bonds = 3592 Number of angles = 1292 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1190 Number of HB donors = 2358 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1188 Number of atoms = 3599 Number of groups = 1193 Number of bonds = 3592 Number of angles = 1292 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1190 Number of HB donors = 2358 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.934" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1188" Evaluating: 1188-7 Parameter: NUMWAT <- "1181" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1181" Comparing "1081" and "1181". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.934" Parameter: BOX -> "32.934" Parameter: BOX -> "32.934" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.93400 B = 32.93400 C = 32.93400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9775 2 1 -1 0 -1 2.0735 3 1 -1 1 -1 5.0899 4 1 0 -1 -1 4.8804 5 1 0 0 -1 1.0794 6 1 0 1 -1 2.0130 7 1 -1 -1 0 4.8933 8 1 -1 0 0 1.1457 9 1 -1 1 0 1.8339 10 1 0 -1 0 0.9326 11 1 0 1 0 0.9326 12 1 -1 -1 1 5.7556 13 1 -1 0 1 1.8738 14 1 -1 1 1 6.4523 15 1 0 -1 1 2.0130 16 1 0 0 1 1.0794 17 1 0 1 1 4.8804 18 1 1 1 1 5.9775 19 1 1 0 1 2.0735 20 1 1 -1 1 5.0899 21 1 1 1 0 4.8933 22 1 1 0 0 1.1457 23 1 1 -1 0 1.8339 24 1 1 1 -1 5.7556 25 1 1 0 -1 1.8738 26 1 1 -1 -1 6.4523 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3525 atoms have been selected out of 3599 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 744 248 248 0.00 3 C003 has 105 35 35 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1548 516 516 0.00 6 C006 has 438 146 146 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1735 576 575 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1635 545 545 0.00 12 C012 has 96 32 32 0.00 13 C013 has 477 159 159 0.00 14 C014 has 111 37 37 1.09 Total of12837 atoms and 4270 groups and 4264 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3599 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1188 Number of atoms = 3599 Number of groups = 1193 Number of bonds = 3592 Number of angles = 1292 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1190 Number of HB donors = 2358 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1188 Number of atoms = 3599 Number of groups = 1193 Number of bonds = 3592 Number of angles = 1292 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1190 Number of HB donors = 2358 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.932" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1188" Evaluating: 1188-7 Parameter: NUMWAT <- "1181" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1181" Comparing "1081" and "1181". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.932" Parameter: BOX -> "32.932" Parameter: BOX -> "32.932" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.93200 B = 32.93200 C = 32.93200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9761 2 1 -1 0 -1 2.0709 3 1 -1 1 -1 5.0865 4 1 0 -1 -1 4.8808 5 1 0 0 -1 1.0777 6 1 0 1 -1 2.0104 7 1 -1 -1 0 4.8914 8 1 -1 0 0 1.1447 9 1 -1 1 0 1.8317 10 1 0 -1 0 0.9308 11 1 0 1 0 0.9308 12 1 -1 -1 1 5.7528 13 1 -1 0 1 1.8716 14 1 -1 1 1 6.4493 15 1 0 -1 1 2.0104 16 1 0 0 1 1.0777 17 1 0 1 1 4.8808 18 1 1 1 1 5.9761 19 1 1 0 1 2.0709 20 1 1 -1 1 5.0865 21 1 1 1 0 4.8914 22 1 1 0 0 1.1447 23 1 1 -1 0 1.8317 24 1 1 1 -1 5.7528 25 1 1 0 -1 1.8716 26 1 1 -1 -1 6.4493 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3525 atoms have been selected out of 3599 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 744 248 248 0.00 3 C003 has 105 35 35 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1548 516 516 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1735 576 575 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1635 545 545 0.00 12 C012 has 96 32 32 0.00 13 C013 has 477 159 159 0.00 14 C014 has 111 37 37 1.09 Total of12840 atoms and 4271 groups and 4265 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3599 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1188 Number of atoms = 3599 Number of groups = 1193 Number of bonds = 3592 Number of angles = 1292 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1190 Number of HB donors = 2358 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1188 Number of atoms = 3599 Number of groups = 1193 Number of bonds = 3592 Number of angles = 1292 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1190 Number of HB donors = 2358 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.93" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1188" Evaluating: 1188-7 Parameter: NUMWAT <- "1181" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1181" Comparing "1081" and "1181". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.93" Parameter: BOX -> "32.93" Parameter: BOX -> "32.93" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.93000 B = 32.93000 C = 32.93000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9746 2 1 -1 0 -1 2.0683 3 1 -1 1 -1 5.0830 4 1 0 -1 -1 4.8813 5 1 0 0 -1 1.0759 6 1 0 1 -1 2.0077 7 1 -1 -1 0 4.8895 8 1 -1 0 0 1.1436 9 1 -1 1 0 1.8294 10 1 0 -1 0 0.9289 11 1 0 1 0 0.9289 12 1 -1 -1 1 5.7499 13 1 -1 0 1 1.8693 14 1 -1 1 1 6.4463 15 1 0 -1 1 2.0077 16 1 0 0 1 1.0759 17 1 0 1 1 4.8813 18 1 1 1 1 5.9746 19 1 1 0 1 2.0683 20 1 1 -1 1 5.0830 21 1 1 1 0 4.8895 22 1 1 0 0 1.1436 23 1 1 -1 0 1.8294 24 1 1 1 -1 5.7499 25 1 1 0 -1 1.8693 26 1 1 -1 -1 6.4463 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3525 atoms have been selected out of 3599 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 747 249 249 0.00 3 C003 has 105 35 35 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1548 516 516 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1735 576 575 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1635 545 545 0.00 12 C012 has 96 32 32 0.00 13 C013 has 477 159 159 0.00 14 C014 has 111 37 37 1.09 Total of12843 atoms and 4272 groups and 4266 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3599 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1188 Number of atoms = 3599 Number of groups = 1193 Number of bonds = 3592 Number of angles = 1292 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1190 Number of HB donors = 2358 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1188 Number of atoms = 3599 Number of groups = 1193 Number of bonds = 3592 Number of angles = 1292 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1190 Number of HB donors = 2358 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.928" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1188" Evaluating: 1188-7 Parameter: NUMWAT <- "1181" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1181" Comparing "1081" and "1181". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.928" Parameter: BOX -> "32.928" Parameter: BOX -> "32.928" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.92800 B = 32.92800 C = 32.92800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9732 2 1 -1 0 -1 2.0656 3 1 -1 1 -1 5.0796 4 1 0 -1 -1 4.8817 5 1 0 0 -1 1.0741 6 1 0 1 -1 2.0051 7 1 -1 -1 0 4.8876 8 1 -1 0 0 1.1426 9 1 -1 1 0 1.8271 10 1 0 -1 0 0.9270 11 1 0 1 0 0.9270 12 1 -1 -1 1 5.7471 13 1 -1 0 1 1.8671 14 1 -1 1 1 6.4433 15 1 0 -1 1 2.0051 16 1 0 0 1 1.0741 17 1 0 1 1 4.8817 18 1 1 1 1 5.9732 19 1 1 0 1 2.0656 20 1 1 -1 1 5.0796 21 1 1 1 0 4.8876 22 1 1 0 0 1.1426 23 1 1 -1 0 1.8271 24 1 1 1 -1 5.7471 25 1 1 0 -1 1.8671 26 1 1 -1 -1 6.4433 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3525 atoms have been selected out of 3599 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 747 249 249 0.00 3 C003 has 105 35 35 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1548 516 516 0.00 6 C006 has 438 146 146 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1735 576 575 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1635 545 545 0.00 12 C012 has 96 32 32 0.00 13 C013 has 477 159 159 0.00 14 C014 has 111 37 37 1.09 Total of12846 atoms and 4273 groups and 4267 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3599 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1188 Number of atoms = 3599 Number of groups = 1193 Number of bonds = 3592 Number of angles = 1292 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1190 Number of HB donors = 2358 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1188 Number of atoms = 3599 Number of groups = 1193 Number of bonds = 3592 Number of angles = 1292 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1190 Number of HB donors = 2358 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.926" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1188" Evaluating: 1188-7 Parameter: NUMWAT <- "1181" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1181" Comparing "1081" and "1181". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.926" Parameter: BOX -> "32.926" Parameter: BOX -> "32.926" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.92600 B = 32.92600 C = 32.92600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9717 2 1 -1 0 -1 2.0630 3 1 -1 1 -1 5.0762 4 1 0 -1 -1 4.8822 5 1 0 0 -1 1.0724 6 1 0 1 -1 2.0025 7 1 -1 -1 0 4.8857 8 1 -1 0 0 1.1415 9 1 -1 1 0 1.8249 10 1 0 -1 0 0.9252 11 1 0 1 0 0.9252 12 1 -1 -1 1 5.7443 13 1 -1 0 1 1.8648 14 1 -1 1 1 6.4403 15 1 0 -1 1 2.0025 16 1 0 0 1 1.0724 17 1 0 1 1 4.8822 18 1 1 1 1 5.9717 19 1 1 0 1 2.0630 20 1 1 -1 1 5.0762 21 1 1 1 0 4.8857 22 1 1 0 0 1.1415 23 1 1 -1 0 1.8249 24 1 1 1 -1 5.7443 25 1 1 0 -1 1.8648 26 1 1 -1 -1 6.4403 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3525 atoms have been selected out of 3599 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 190 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 747 249 249 0.00 3 C003 has 105 35 35 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1548 516 516 0.00 6 C006 has 438 146 146 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1735 576 575 0.00 9 C009 has 468 156 156 0.00 10 C010 has 1632 544 544 0.00 12 C012 has 99 33 33 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 1.09 Total of12843 atoms and 4272 groups and 4266 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3599 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1187 Number of atoms = 3596 Number of groups = 1192 Number of bonds = 3589 Number of angles = 1291 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1189 Number of HB donors = 2356 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1187 Number of atoms = 3596 Number of groups = 1192 Number of bonds = 3589 Number of angles = 1291 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1189 Number of HB donors = 2356 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.924" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1187" Evaluating: 1187-7 Parameter: NUMWAT <- "1180" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1180" Comparing "1081" and "1180". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.924" Parameter: BOX -> "32.924" Parameter: BOX -> "32.924" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.92400 B = 32.92400 C = 32.92400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9703 2 1 -1 0 -1 2.0604 3 1 -1 1 -1 5.0728 4 1 0 -1 -1 4.8826 5 1 0 0 -1 1.0706 6 1 0 1 -1 1.9998 7 1 -1 -1 0 4.8838 8 1 -1 0 0 1.1405 9 1 -1 1 0 1.8226 10 1 0 -1 0 0.9233 11 1 0 1 0 0.9233 12 1 -1 -1 1 5.7414 13 1 -1 0 1 1.8626 14 1 -1 1 1 6.4373 15 1 0 -1 1 1.9998 16 1 0 0 1 1.0706 17 1 0 1 1 4.8826 18 1 1 1 1 5.9703 19 1 1 0 1 2.0604 20 1 1 -1 1 5.0728 21 1 1 1 0 4.8838 22 1 1 0 0 1.1405 23 1 1 -1 0 1.8226 24 1 1 1 -1 5.7414 25 1 1 0 -1 1.8626 26 1 1 -1 -1 6.4373 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3522 atoms have been selected out of 3596 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 747 249 249 0.00 3 C003 has 105 35 35 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1548 516 516 0.00 6 C006 has 438 146 146 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1732 575 574 0.00 9 C009 has 468 156 156 0.00 10 C010 has 1629 543 543 0.00 12 C012 has 96 32 32 0.00 13 C013 has 474 158 158 0.00 14 C014 has 108 36 36 1.08 Total of12825 atoms and 4266 groups and 4260 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3596 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1187 Number of atoms = 3596 Number of groups = 1192 Number of bonds = 3589 Number of angles = 1291 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1189 Number of HB donors = 2356 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1187 Number of atoms = 3596 Number of groups = 1192 Number of bonds = 3589 Number of angles = 1291 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1189 Number of HB donors = 2356 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.922" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1187" Evaluating: 1187-7 Parameter: NUMWAT <- "1180" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1180" Comparing "1081" and "1180". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.922" Parameter: BOX -> "32.922" Parameter: BOX -> "32.922" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.92200 B = 32.92200 C = 32.92200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9688 2 1 -1 0 -1 2.0577 3 1 -1 1 -1 5.0693 4 1 0 -1 -1 4.8831 5 1 0 0 -1 1.0689 6 1 0 1 -1 1.9972 7 1 -1 -1 0 4.8819 8 1 -1 0 0 1.1394 9 1 -1 1 0 1.8204 10 1 0 -1 0 0.9214 11 1 0 1 0 0.9214 12 1 -1 -1 1 5.7386 13 1 -1 0 1 1.8603 14 1 -1 1 1 6.4343 15 1 0 -1 1 1.9972 16 1 0 0 1 1.0689 17 1 0 1 1 4.8831 18 1 1 1 1 5.9688 19 1 1 0 1 2.0577 20 1 1 -1 1 5.0693 21 1 1 1 0 4.8819 22 1 1 0 0 1.1394 23 1 1 -1 0 1.8204 24 1 1 1 -1 5.7386 25 1 1 0 -1 1.8603 26 1 1 -1 -1 6.4343 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3522 atoms have been selected out of 3596 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 747 249 249 0.00 3 C003 has 105 35 35 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1548 516 516 0.00 6 C006 has 438 146 146 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1732 575 574 0.00 9 C009 has 468 156 156 0.00 10 C010 has 1629 543 543 0.00 12 C012 has 96 32 32 0.00 13 C013 has 474 158 158 0.00 14 C014 has 108 36 36 1.08 Total of12825 atoms and 4266 groups and 4260 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3596 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1187 Number of atoms = 3596 Number of groups = 1192 Number of bonds = 3589 Number of angles = 1291 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1189 Number of HB donors = 2356 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1187 Number of atoms = 3596 Number of groups = 1192 Number of bonds = 3589 Number of angles = 1291 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1189 Number of HB donors = 2356 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.92" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1187" Evaluating: 1187-7 Parameter: NUMWAT <- "1180" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1180" Comparing "1081" and "1180". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.92" Parameter: BOX -> "32.92" Parameter: BOX -> "32.92" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.92000 B = 32.92000 C = 32.92000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9674 2 1 -1 0 -1 2.0551 3 1 -1 1 -1 5.0659 4 1 0 -1 -1 4.8835 5 1 0 0 -1 1.0671 6 1 0 1 -1 1.9946 7 1 -1 -1 0 4.8800 8 1 -1 0 0 1.1384 9 1 -1 1 0 1.8181 10 1 0 -1 0 0.9196 11 1 0 1 0 0.9196 12 1 -1 -1 1 5.7358 13 1 -1 0 1 1.8581 14 1 -1 1 1 6.4313 15 1 0 -1 1 1.9946 16 1 0 0 1 1.0671 17 1 0 1 1 4.8835 18 1 1 1 1 5.9674 19 1 1 0 1 2.0551 20 1 1 -1 1 5.0659 21 1 1 1 0 4.8800 22 1 1 0 0 1.1384 23 1 1 -1 0 1.8181 24 1 1 1 -1 5.7358 25 1 1 0 -1 1.8581 26 1 1 -1 -1 6.4313 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3522 atoms have been selected out of 3596 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 747 249 249 0.00 3 C003 has 105 35 35 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1548 516 516 0.00 6 C006 has 438 146 146 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1735 576 575 0.00 9 C009 has 468 156 156 0.00 10 C010 has 1629 543 543 0.00 12 C012 has 96 32 32 0.00 13 C013 has 474 158 158 0.00 14 C014 has 108 36 36 1.08 Total of12828 atoms and 4267 groups and 4261 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3596 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1187 Number of atoms = 3596 Number of groups = 1192 Number of bonds = 3589 Number of angles = 1291 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1189 Number of HB donors = 2356 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1187 Number of atoms = 3596 Number of groups = 1192 Number of bonds = 3589 Number of angles = 1291 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1189 Number of HB donors = 2356 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.918" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1187" Evaluating: 1187-7 Parameter: NUMWAT <- "1180" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1180" Comparing "1081" and "1180". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.918" Parameter: BOX -> "32.918" Parameter: BOX -> "32.918" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.91800 B = 32.91800 C = 32.91800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9660 2 1 -1 0 -1 2.0525 3 1 -1 1 -1 5.0625 4 1 0 -1 -1 4.8840 5 1 0 0 -1 1.0653 6 1 0 1 -1 1.9919 7 1 -1 -1 0 4.8781 8 1 -1 0 0 1.1373 9 1 -1 1 0 1.8159 10 1 0 -1 0 0.9177 11 1 0 1 0 0.9177 12 1 -1 -1 1 5.7330 13 1 -1 0 1 1.8559 14 1 -1 1 1 6.4283 15 1 0 -1 1 1.9919 16 1 0 0 1 1.0653 17 1 0 1 1 4.8840 18 1 1 1 1 5.9660 19 1 1 0 1 2.0525 20 1 1 -1 1 5.0625 21 1 1 1 0 4.8781 22 1 1 0 0 1.1373 23 1 1 -1 0 1.8159 24 1 1 1 -1 5.7330 25 1 1 0 -1 1.8559 26 1 1 -1 -1 6.4283 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3522 atoms have been selected out of 3596 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 747 249 249 0.00 3 C003 has 105 35 35 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1548 516 516 0.00 6 C006 has 438 146 146 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1735 576 575 0.00 9 C009 has 468 156 156 0.00 10 C010 has 1629 543 543 0.00 12 C012 has 96 32 32 0.00 13 C013 has 474 158 158 0.00 14 C014 has 108 36 36 1.08 Total of12828 atoms and 4267 groups and 4261 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3596 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1187 Number of atoms = 3596 Number of groups = 1192 Number of bonds = 3589 Number of angles = 1291 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1189 Number of HB donors = 2356 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1187 Number of atoms = 3596 Number of groups = 1192 Number of bonds = 3589 Number of angles = 1291 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1189 Number of HB donors = 2356 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.916" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1187" Evaluating: 1187-7 Parameter: NUMWAT <- "1180" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1180" Comparing "1081" and "1180". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.916" Parameter: BOX -> "32.916" Parameter: BOX -> "32.916" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.91600 B = 32.91600 C = 32.91600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9645 2 1 -1 0 -1 2.0499 3 1 -1 1 -1 5.0591 4 1 0 -1 -1 4.8844 5 1 0 0 -1 1.0636 6 1 0 1 -1 1.9893 7 1 -1 -1 0 4.8762 8 1 -1 0 0 1.1363 9 1 -1 1 0 1.8137 10 1 0 -1 0 0.9159 11 1 0 1 0 0.9159 12 1 -1 -1 1 5.7301 13 1 -1 0 1 1.8536 14 1 -1 1 1 6.4253 15 1 0 -1 1 1.9893 16 1 0 0 1 1.0636 17 1 0 1 1 4.8844 18 1 1 1 1 5.9645 19 1 1 0 1 2.0499 20 1 1 -1 1 5.0591 21 1 1 1 0 4.8762 22 1 1 0 0 1.1363 23 1 1 -1 0 1.8137 24 1 1 1 -1 5.7301 25 1 1 0 -1 1.8536 26 1 1 -1 -1 6.4253 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3522 atoms have been selected out of 3596 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 747 249 249 0.00 3 C003 has 105 35 35 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1548 516 516 0.00 6 C006 has 438 146 146 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1735 576 575 0.00 9 C009 has 468 156 156 0.00 10 C010 has 1629 543 543 0.00 12 C012 has 96 32 32 0.00 13 C013 has 474 158 158 0.00 14 C014 has 108 36 36 1.08 Total of12828 atoms and 4267 groups and 4261 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3596 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1187 Number of atoms = 3596 Number of groups = 1192 Number of bonds = 3589 Number of angles = 1291 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1189 Number of HB donors = 2356 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1187 Number of atoms = 3596 Number of groups = 1192 Number of bonds = 3589 Number of angles = 1291 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1189 Number of HB donors = 2356 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.914" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1187" Evaluating: 1187-7 Parameter: NUMWAT <- "1180" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1180" Comparing "1081" and "1180". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.914" Parameter: BOX -> "32.914" Parameter: BOX -> "32.914" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.91400 B = 32.91400 C = 32.91400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9631 2 1 -1 0 -1 2.0473 3 1 -1 1 -1 5.0556 4 1 0 -1 -1 4.8849 5 1 0 0 -1 1.0618 6 1 0 1 -1 1.9867 7 1 -1 -1 0 4.8743 8 1 -1 0 0 1.1353 9 1 -1 1 0 1.8114 10 1 0 -1 0 0.9140 11 1 0 1 0 0.9140 12 1 -1 -1 1 5.7273 13 1 -1 0 1 1.8514 14 1 -1 1 1 6.4223 15 1 0 -1 1 1.9867 16 1 0 0 1 1.0618 17 1 0 1 1 4.8849 18 1 1 1 1 5.9631 19 1 1 0 1 2.0473 20 1 1 -1 1 5.0556 21 1 1 1 0 4.8743 22 1 1 0 0 1.1353 23 1 1 -1 0 1.8114 24 1 1 1 -1 5.7273 25 1 1 0 -1 1.8514 26 1 1 -1 -1 6.4223 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3522 atoms have been selected out of 3596 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 453 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 747 249 249 0.00 3 C003 has 105 35 35 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1548 516 516 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1738 577 576 0.00 9 C009 has 468 156 156 0.00 10 C010 has 1626 542 542 0.00 12 C012 has 96 32 32 0.00 13 C013 has 474 158 158 0.00 14 C014 has 108 36 36 1.07 Total of12825 atoms and 4266 groups and 4260 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3596 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1186 Number of atoms = 3593 Number of groups = 1191 Number of bonds = 3586 Number of angles = 1290 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1188 Number of HB donors = 2354 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1186 Number of atoms = 3593 Number of groups = 1191 Number of bonds = 3586 Number of angles = 1290 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1188 Number of HB donors = 2354 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.912" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1186" Evaluating: 1186-7 Parameter: NUMWAT <- "1179" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1179" Comparing "1081" and "1179". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.912" Parameter: BOX -> "32.912" Parameter: BOX -> "32.912" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.91200 B = 32.91200 C = 32.91200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9616 2 1 -1 0 -1 2.0446 3 1 -1 1 -1 5.0522 4 1 0 -1 -1 4.8854 5 1 0 0 -1 1.0601 6 1 0 1 -1 1.9840 7 1 -1 -1 0 4.8724 8 1 -1 0 0 1.1342 9 1 -1 1 0 1.8092 10 1 0 -1 0 0.9121 11 1 0 1 0 0.9121 12 1 -1 -1 1 5.7245 13 1 -1 0 1 1.8491 14 1 -1 1 1 6.4193 15 1 0 -1 1 1.9840 16 1 0 0 1 1.0601 17 1 0 1 1 4.8854 18 1 1 1 1 5.9616 19 1 1 0 1 2.0446 20 1 1 -1 1 5.0522 21 1 1 1 0 4.8724 22 1 1 0 0 1.1342 23 1 1 -1 0 1.8092 24 1 1 1 -1 5.7245 25 1 1 0 -1 1.8491 26 1 1 -1 -1 6.4193 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3519 atoms have been selected out of 3593 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 747 249 249 0.00 3 C003 has 105 35 35 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1548 516 516 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1735 576 575 0.00 9 C009 has 468 156 156 0.00 10 C010 has 1626 542 542 0.00 12 C012 has 96 32 32 0.00 13 C013 has 474 158 158 0.00 14 C014 has 108 36 36 1.07 Total of12819 atoms and 4264 groups and 4258 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3593 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1186 Number of atoms = 3593 Number of groups = 1191 Number of bonds = 3586 Number of angles = 1290 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1188 Number of HB donors = 2354 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1186 Number of atoms = 3593 Number of groups = 1191 Number of bonds = 3586 Number of angles = 1290 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1188 Number of HB donors = 2354 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.91" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1186" Evaluating: 1186-7 Parameter: NUMWAT <- "1179" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1179" Comparing "1081" and "1179". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.91" Parameter: BOX -> "32.91" Parameter: BOX -> "32.91" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.91000 B = 32.91000 C = 32.91000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9602 2 1 -1 0 -1 2.0420 3 1 -1 1 -1 5.0488 4 1 0 -1 -1 4.8858 5 1 0 0 -1 1.0583 6 1 0 1 -1 1.9814 7 1 -1 -1 0 4.8705 8 1 -1 0 0 1.1332 9 1 -1 1 0 1.8069 10 1 0 -1 0 0.9103 11 1 0 1 0 0.9103 12 1 -1 -1 1 5.7217 13 1 -1 0 1 1.8469 14 1 -1 1 1 6.4163 15 1 0 -1 1 1.9814 16 1 0 0 1 1.0583 17 1 0 1 1 4.8858 18 1 1 1 1 5.9602 19 1 1 0 1 2.0420 20 1 1 -1 1 5.0488 21 1 1 1 0 4.8705 22 1 1 0 0 1.1332 23 1 1 -1 0 1.8069 24 1 1 1 -1 5.7217 25 1 1 0 -1 1.8469 26 1 1 -1 -1 6.4163 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3519 atoms have been selected out of 3593 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 747 249 249 0.00 3 C003 has 105 35 35 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1548 516 516 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1735 576 575 0.00 9 C009 has 468 156 156 0.00 10 C010 has 1626 542 542 0.00 12 C012 has 96 32 32 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 1.07 Total of12822 atoms and 4265 groups and 4259 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3593 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1186 Number of atoms = 3593 Number of groups = 1191 Number of bonds = 3586 Number of angles = 1290 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1188 Number of HB donors = 2354 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1186 Number of atoms = 3593 Number of groups = 1191 Number of bonds = 3586 Number of angles = 1290 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1188 Number of HB donors = 2354 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.908" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1186" Evaluating: 1186-7 Parameter: NUMWAT <- "1179" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1179" Comparing "1081" and "1179". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.908" Parameter: BOX -> "32.908" Parameter: BOX -> "32.908" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.90800 B = 32.90800 C = 32.90800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9588 2 1 -1 0 -1 2.0394 3 1 -1 1 -1 5.0454 4 1 0 -1 -1 4.8863 5 1 0 0 -1 1.0565 6 1 0 1 -1 1.9788 7 1 -1 -1 0 4.8686 8 1 -1 0 0 1.1322 9 1 -1 1 0 1.8047 10 1 0 -1 0 0.9084 11 1 0 1 0 0.9084 12 1 -1 -1 1 5.7188 13 1 -1 0 1 1.8447 14 1 -1 1 1 6.4133 15 1 0 -1 1 1.9788 16 1 0 0 1 1.0565 17 1 0 1 1 4.8863 18 1 1 1 1 5.9588 19 1 1 0 1 2.0394 20 1 1 -1 1 5.0454 21 1 1 1 0 4.8686 22 1 1 0 0 1.1322 23 1 1 -1 0 1.8047 24 1 1 1 -1 5.7188 25 1 1 0 -1 1.8447 26 1 1 -1 -1 6.4133 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3519 atoms have been selected out of 3593 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 802 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 744 248 248 0.00 3 C003 has 105 35 35 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1548 516 516 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1744 579 578 0.00 9 C009 has 465 155 155 0.00 10 C010 has 1626 542 542 0.00 12 C012 has 96 32 32 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 1.07 Total of12825 atoms and 4266 groups and 4260 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3593 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1185 Number of atoms = 3590 Number of groups = 1190 Number of bonds = 3583 Number of angles = 1289 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1187 Number of HB donors = 2352 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1185 Number of atoms = 3590 Number of groups = 1190 Number of bonds = 3583 Number of angles = 1289 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1187 Number of HB donors = 2352 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.906" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1185" Evaluating: 1185-7 Parameter: NUMWAT <- "1178" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1178" Comparing "1081" and "1178". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.906" Parameter: BOX -> "32.906" Parameter: BOX -> "32.906" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.90600 B = 32.90600 C = 32.90600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9573 2 1 -1 0 -1 2.0368 3 1 -1 1 -1 5.0419 4 1 0 -1 -1 4.8868 5 1 0 0 -1 1.0548 6 1 0 1 -1 1.9761 7 1 -1 -1 0 4.8667 8 1 -1 0 0 1.1311 9 1 -1 1 0 1.8025 10 1 0 -1 0 0.9066 11 1 0 1 0 0.9066 12 1 -1 -1 1 5.7160 13 1 -1 0 1 1.8424 14 1 -1 1 1 6.4103 15 1 0 -1 1 1.9761 16 1 0 0 1 1.0548 17 1 0 1 1 4.8868 18 1 1 1 1 5.9573 19 1 1 0 1 2.0368 20 1 1 -1 1 5.0419 21 1 1 1 0 4.8667 22 1 1 0 0 1.1311 23 1 1 -1 0 1.8025 24 1 1 1 -1 5.7160 25 1 1 0 -1 1.8424 26 1 1 -1 -1 6.4103 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3516 atoms have been selected out of 3590 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 744 248 248 0.00 3 C003 has 105 35 35 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1732 575 574 0.00 9 C009 has 465 155 155 0.00 10 C010 has 1626 542 542 0.00 12 C012 has 96 32 32 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 1.07 Total of12807 atoms and 4260 groups and 4254 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3590 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1185 Number of atoms = 3590 Number of groups = 1190 Number of bonds = 3583 Number of angles = 1289 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1187 Number of HB donors = 2352 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1185 Number of atoms = 3590 Number of groups = 1190 Number of bonds = 3583 Number of angles = 1289 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1187 Number of HB donors = 2352 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.904" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1185" Evaluating: 1185-7 Parameter: NUMWAT <- "1178" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1178" Comparing "1081" and "1178". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.904" Parameter: BOX -> "32.904" Parameter: BOX -> "32.904" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.90400 B = 32.90400 C = 32.90400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9559 2 1 -1 0 -1 2.0341 3 1 -1 1 -1 5.0385 4 1 0 -1 -1 4.8872 5 1 0 0 -1 1.0530 6 1 0 1 -1 1.9735 7 1 -1 -1 0 4.8648 8 1 -1 0 0 1.1301 9 1 -1 1 0 1.8002 10 1 0 -1 0 0.9047 11 1 0 1 0 0.9047 12 1 -1 -1 1 5.7132 13 1 -1 0 1 1.8402 14 1 -1 1 1 6.4073 15 1 0 -1 1 1.9735 16 1 0 0 1 1.0530 17 1 0 1 1 4.8872 18 1 1 1 1 5.9559 19 1 1 0 1 2.0341 20 1 1 -1 1 5.0385 21 1 1 1 0 4.8648 22 1 1 0 0 1.1301 23 1 1 -1 0 1.8002 24 1 1 1 -1 5.7132 25 1 1 0 -1 1.8402 26 1 1 -1 -1 6.4073 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3516 atoms have been selected out of 3590 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 744 248 248 0.00 3 C003 has 108 36 36 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1732 575 574 0.00 9 C009 has 468 156 156 0.00 10 C010 has 1626 542 542 0.00 12 C012 has 96 32 32 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 1.06 Total of12813 atoms and 4262 groups and 4256 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3590 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1185 Number of atoms = 3590 Number of groups = 1190 Number of bonds = 3583 Number of angles = 1289 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1187 Number of HB donors = 2352 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1185 Number of atoms = 3590 Number of groups = 1190 Number of bonds = 3583 Number of angles = 1289 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1187 Number of HB donors = 2352 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.902" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1185" Evaluating: 1185-7 Parameter: NUMWAT <- "1178" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1178" Comparing "1081" and "1178". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.902" Parameter: BOX -> "32.902" Parameter: BOX -> "32.902" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.90200 B = 32.90200 C = 32.90200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9545 2 1 -1 0 -1 2.0315 3 1 -1 1 -1 5.0351 4 1 0 -1 -1 4.8877 5 1 0 0 -1 1.0513 6 1 0 1 -1 1.9709 7 1 -1 -1 0 4.8629 8 1 -1 0 0 1.1291 9 1 -1 1 0 1.7980 10 1 0 -1 0 0.9028 11 1 0 1 0 0.9028 12 1 -1 -1 1 5.7104 13 1 -1 0 1 1.8380 14 1 -1 1 1 6.4043 15 1 0 -1 1 1.9709 16 1 0 0 1 1.0513 17 1 0 1 1 4.8877 18 1 1 1 1 5.9545 19 1 1 0 1 2.0315 20 1 1 -1 1 5.0351 21 1 1 1 0 4.8629 22 1 1 0 0 1.1291 23 1 1 -1 0 1.7980 24 1 1 1 -1 5.7104 25 1 1 0 -1 1.8380 26 1 1 -1 -1 6.4043 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3516 atoms have been selected out of 3590 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 744 248 248 0.00 3 C003 has 108 36 36 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1732 575 574 0.00 9 C009 has 468 156 156 0.00 10 C010 has 1626 542 542 0.00 12 C012 has 96 32 32 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 1.06 Total of12813 atoms and 4262 groups and 4256 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3590 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1185 Number of atoms = 3590 Number of groups = 1190 Number of bonds = 3583 Number of angles = 1289 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1187 Number of HB donors = 2352 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1185 Number of atoms = 3590 Number of groups = 1190 Number of bonds = 3583 Number of angles = 1289 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1187 Number of HB donors = 2352 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.9" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1185" Evaluating: 1185-7 Parameter: NUMWAT <- "1178" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1178" Comparing "1081" and "1178". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.9" Parameter: BOX -> "32.9" Parameter: BOX -> "32.9" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.90000 B = 32.90000 C = 32.90000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9531 2 1 -1 0 -1 2.0289 3 1 -1 1 -1 5.0316 4 1 0 -1 -1 4.8882 5 1 0 0 -1 1.0495 6 1 0 1 -1 1.9683 7 1 -1 -1 0 4.8610 8 1 -1 0 0 1.1281 9 1 -1 1 0 1.7958 10 1 0 -1 0 0.9010 11 1 0 1 0 0.9010 12 1 -1 -1 1 5.7076 13 1 -1 0 1 1.8357 14 1 -1 1 1 6.4013 15 1 0 -1 1 1.9683 16 1 0 0 1 1.0495 17 1 0 1 1 4.8882 18 1 1 1 1 5.9531 19 1 1 0 1 2.0289 20 1 1 -1 1 5.0316 21 1 1 1 0 4.8610 22 1 1 0 0 1.1281 23 1 1 -1 0 1.7958 24 1 1 1 -1 5.7076 25 1 1 0 -1 1.8357 26 1 1 -1 -1 6.4013 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3516 atoms have been selected out of 3590 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 744 248 248 0.00 3 C003 has 108 36 36 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1732 575 574 0.00 9 C009 has 468 156 156 0.00 10 C010 has 1626 542 542 0.00 12 C012 has 96 32 32 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 1.06 Total of12813 atoms and 4262 groups and 4256 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3590 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1185 Number of atoms = 3590 Number of groups = 1190 Number of bonds = 3583 Number of angles = 1289 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1187 Number of HB donors = 2352 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1185 Number of atoms = 3590 Number of groups = 1190 Number of bonds = 3583 Number of angles = 1289 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1187 Number of HB donors = 2352 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.898" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1185" Evaluating: 1185-7 Parameter: NUMWAT <- "1178" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1178" Comparing "1081" and "1178". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.898" Parameter: BOX -> "32.898" Parameter: BOX -> "32.898" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.89800 B = 32.89800 C = 32.89800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9516 2 1 -1 0 -1 2.0263 3 1 -1 1 -1 5.0282 4 1 0 -1 -1 4.8887 5 1 0 0 -1 1.0478 6 1 0 1 -1 1.9656 7 1 -1 -1 0 4.8591 8 1 -1 0 0 1.1271 9 1 -1 1 0 1.7935 10 1 0 -1 0 0.8991 11 1 0 1 0 0.8991 12 1 -1 -1 1 5.7047 13 1 -1 0 1 1.8335 14 1 -1 1 1 6.3983 15 1 0 -1 1 1.9656 16 1 0 0 1 1.0478 17 1 0 1 1 4.8887 18 1 1 1 1 5.9516 19 1 1 0 1 2.0263 20 1 1 -1 1 5.0282 21 1 1 1 0 4.8591 22 1 1 0 0 1.1271 23 1 1 -1 0 1.7935 24 1 1 1 -1 5.7047 25 1 1 0 -1 1.8335 26 1 1 -1 -1 6.3983 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3516 atoms have been selected out of 3590 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 993 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 438 146 146 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1732 575 574 0.00 9 C009 has 468 156 156 0.00 10 C010 has 1626 542 542 0.00 12 C012 has 96 32 32 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 1.06 Total of12825 atoms and 4266 groups and 4260 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3590 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1184 Number of atoms = 3587 Number of groups = 1189 Number of bonds = 3580 Number of angles = 1288 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1186 Number of HB donors = 2350 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1184 Number of atoms = 3587 Number of groups = 1189 Number of bonds = 3580 Number of angles = 1288 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1186 Number of HB donors = 2350 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.896" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1184" Evaluating: 1184-7 Parameter: NUMWAT <- "1177" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1177" Comparing "1081" and "1177". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.896" Parameter: BOX -> "32.896" Parameter: BOX -> "32.896" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.89600 B = 32.89600 C = 32.89600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9502 2 1 -1 0 -1 2.0237 3 1 -1 1 -1 5.0248 4 1 0 -1 -1 4.8891 5 1 0 0 -1 1.0460 6 1 0 1 -1 1.9630 7 1 -1 -1 0 4.8572 8 1 -1 0 0 1.1261 9 1 -1 1 0 1.7913 10 1 0 -1 0 0.8973 11 1 0 1 0 0.8973 12 1 -1 -1 1 5.7019 13 1 -1 0 1 1.8313 14 1 -1 1 1 6.3953 15 1 0 -1 1 1.9630 16 1 0 0 1 1.0460 17 1 0 1 1 4.8891 18 1 1 1 1 5.9502 19 1 1 0 1 2.0237 20 1 1 -1 1 5.0248 21 1 1 1 0 4.8572 22 1 1 0 0 1.1261 23 1 1 -1 0 1.7913 24 1 1 1 -1 5.7019 25 1 1 0 -1 1.8313 26 1 1 -1 -1 6.3953 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3513 atoms have been selected out of 3587 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 744 248 248 0.00 3 C003 has 108 36 36 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1542 514 514 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1729 574 573 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 96 32 32 0.00 13 C013 has 477 159 159 0.00 14 C014 has 108 36 36 1.06 Total of12804 atoms and 4259 groups and 4253 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3587 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1184 Number of atoms = 3587 Number of groups = 1189 Number of bonds = 3580 Number of angles = 1288 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1186 Number of HB donors = 2350 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1184 Number of atoms = 3587 Number of groups = 1189 Number of bonds = 3580 Number of angles = 1288 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1186 Number of HB donors = 2350 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.894" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1184" Evaluating: 1184-7 Parameter: NUMWAT <- "1177" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1177" Comparing "1081" and "1177". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.894" Parameter: BOX -> "32.894" Parameter: BOX -> "32.894" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.89400 B = 32.89400 C = 32.89400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9488 2 1 -1 0 -1 2.0211 3 1 -1 1 -1 5.0214 4 1 0 -1 -1 4.8896 5 1 0 0 -1 1.0443 6 1 0 1 -1 1.9604 7 1 -1 -1 0 4.8553 8 1 -1 0 0 1.1250 9 1 -1 1 0 1.7891 10 1 0 -1 0 0.8954 11 1 0 1 0 0.8954 12 1 -1 -1 1 5.6991 13 1 -1 0 1 1.8291 14 1 -1 1 1 6.3923 15 1 0 -1 1 1.9604 16 1 0 0 1 1.0443 17 1 0 1 1 4.8896 18 1 1 1 1 5.9488 19 1 1 0 1 2.0211 20 1 1 -1 1 5.0214 21 1 1 1 0 4.8553 22 1 1 0 0 1.1250 23 1 1 -1 0 1.7891 24 1 1 1 -1 5.6991 25 1 1 0 -1 1.8291 26 1 1 -1 -1 6.3923 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3513 atoms have been selected out of 3587 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 744 248 248 0.00 3 C003 has 108 36 36 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1729 574 573 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 96 32 32 0.00 13 C013 has 477 159 159 0.00 14 C014 has 111 37 37 1.05 Total of12810 atoms and 4261 groups and 4255 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3587 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1184 Number of atoms = 3587 Number of groups = 1189 Number of bonds = 3580 Number of angles = 1288 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1186 Number of HB donors = 2350 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1184 Number of atoms = 3587 Number of groups = 1189 Number of bonds = 3580 Number of angles = 1288 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1186 Number of HB donors = 2350 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.892" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1184" Evaluating: 1184-7 Parameter: NUMWAT <- "1177" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1177" Comparing "1081" and "1177". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.892" Parameter: BOX -> "32.892" Parameter: BOX -> "32.892" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.89200 B = 32.89200 C = 32.89200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9474 2 1 -1 0 -1 2.0184 3 1 -1 1 -1 5.0179 4 1 0 -1 -1 4.8901 5 1 0 0 -1 1.0425 6 1 0 1 -1 1.9577 7 1 -1 -1 0 4.8534 8 1 -1 0 0 1.1240 9 1 -1 1 0 1.7868 10 1 0 -1 0 0.8935 11 1 0 1 0 0.8935 12 1 -1 -1 1 5.6963 13 1 -1 0 1 1.8268 14 1 -1 1 1 6.3893 15 1 0 -1 1 1.9577 16 1 0 0 1 1.0425 17 1 0 1 1 4.8901 18 1 1 1 1 5.9474 19 1 1 0 1 2.0184 20 1 1 -1 1 5.0179 21 1 1 1 0 4.8534 22 1 1 0 0 1.1240 23 1 1 -1 0 1.7868 24 1 1 1 -1 5.6963 25 1 1 0 -1 1.8268 26 1 1 -1 -1 6.3893 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3513 atoms have been selected out of 3587 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 744 248 248 0.00 3 C003 has 108 36 36 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1729 574 573 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 96 32 32 0.00 13 C013 has 480 160 160 0.00 14 C014 has 111 37 37 1.05 Total of12813 atoms and 4262 groups and 4256 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3587 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1184 Number of atoms = 3587 Number of groups = 1189 Number of bonds = 3580 Number of angles = 1288 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1186 Number of HB donors = 2350 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1184 Number of atoms = 3587 Number of groups = 1189 Number of bonds = 3580 Number of angles = 1288 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1186 Number of HB donors = 2350 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.89" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1184" Evaluating: 1184-7 Parameter: NUMWAT <- "1177" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1177" Comparing "1081" and "1177". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.89" Parameter: BOX -> "32.89" Parameter: BOX -> "32.89" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.89000 B = 32.89000 C = 32.89000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9459 2 1 -1 0 -1 2.0158 3 1 -1 1 -1 5.0145 4 1 0 -1 -1 4.8906 5 1 0 0 -1 1.0408 6 1 0 1 -1 1.9551 7 1 -1 -1 0 4.8516 8 1 -1 0 0 1.1230 9 1 -1 1 0 1.7846 10 1 0 -1 0 0.8917 11 1 0 1 0 0.8917 12 1 -1 -1 1 5.6935 13 1 -1 0 1 1.8246 14 1 -1 1 1 6.3863 15 1 0 -1 1 1.9551 16 1 0 0 1 1.0408 17 1 0 1 1 4.8906 18 1 1 1 1 5.9459 19 1 1 0 1 2.0158 20 1 1 -1 1 5.0145 21 1 1 1 0 4.8516 22 1 1 0 0 1.1230 23 1 1 -1 0 1.7846 24 1 1 1 -1 5.6935 25 1 1 0 -1 1.8246 26 1 1 -1 -1 6.3863 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3513 atoms have been selected out of 3587 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1729 574 573 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 96 32 32 0.00 13 C013 has 480 160 160 0.00 14 C014 has 111 37 37 1.05 Total of12819 atoms and 4264 groups and 4258 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3587 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1184 Number of atoms = 3587 Number of groups = 1189 Number of bonds = 3580 Number of angles = 1288 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1186 Number of HB donors = 2350 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1184 Number of atoms = 3587 Number of groups = 1189 Number of bonds = 3580 Number of angles = 1288 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1186 Number of HB donors = 2350 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.888" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1184" Evaluating: 1184-7 Parameter: NUMWAT <- "1177" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1177" Comparing "1081" and "1177". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.888" Parameter: BOX -> "32.888" Parameter: BOX -> "32.888" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.88800 B = 32.88800 C = 32.88800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9445 2 1 -1 0 -1 2.0132 3 1 -1 1 -1 5.0111 4 1 0 -1 -1 4.8911 5 1 0 0 -1 1.0390 6 1 0 1 -1 1.9525 7 1 -1 -1 0 4.8497 8 1 -1 0 0 1.1220 9 1 -1 1 0 1.7824 10 1 0 -1 0 0.8898 11 1 0 1 0 0.8898 12 1 -1 -1 1 5.6906 13 1 -1 0 1 1.8224 14 1 -1 1 1 6.3833 15 1 0 -1 1 1.9525 16 1 0 0 1 1.0390 17 1 0 1 1 4.8911 18 1 1 1 1 5.9445 19 1 1 0 1 2.0132 20 1 1 -1 1 5.0111 21 1 1 1 0 4.8497 22 1 1 0 0 1.1220 23 1 1 -1 0 1.7824 24 1 1 1 -1 5.6906 25 1 1 0 -1 1.8224 26 1 1 -1 -1 6.3833 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3513 atoms have been selected out of 3587 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 943 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 438 146 146 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1723 572 571 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1626 542 542 0.00 12 C012 has 96 32 32 0.00 13 C013 has 480 160 160 0.00 14 C014 has 111 37 37 1.05 Total of12825 atoms and 4266 groups and 4260 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3587 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1183 Number of atoms = 3584 Number of groups = 1188 Number of bonds = 3577 Number of angles = 1287 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1185 Number of HB donors = 2348 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1183 Number of atoms = 3584 Number of groups = 1188 Number of bonds = 3577 Number of angles = 1287 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1185 Number of HB donors = 2348 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.886" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1183" Evaluating: 1183-7 Parameter: NUMWAT <- "1176" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1176" Comparing "1081" and "1176". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.886" Parameter: BOX -> "32.886" Parameter: BOX -> "32.886" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.88600 B = 32.88600 C = 32.88600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9431 2 1 -1 0 -1 2.0106 3 1 -1 1 -1 5.0077 4 1 0 -1 -1 4.8915 5 1 0 0 -1 1.0373 6 1 0 1 -1 1.9499 7 1 -1 -1 0 4.8478 8 1 -1 0 0 1.1210 9 1 -1 1 0 1.7802 10 1 0 -1 0 0.8880 11 1 0 1 0 0.8880 12 1 -1 -1 1 5.6878 13 1 -1 0 1 1.8202 14 1 -1 1 1 6.3804 15 1 0 -1 1 1.9499 16 1 0 0 1 1.0373 17 1 0 1 1 4.8915 18 1 1 1 1 5.9431 19 1 1 0 1 2.0106 20 1 1 -1 1 5.0077 21 1 1 1 0 4.8478 22 1 1 0 0 1.1210 23 1 1 -1 0 1.7802 24 1 1 1 -1 5.6878 25 1 1 0 -1 1.8202 26 1 1 -1 -1 6.3804 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3510 atoms have been selected out of 3584 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1542 514 514 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1720 571 570 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 96 32 32 0.00 13 C013 has 480 160 160 0.00 14 C014 has 111 37 37 1.05 Total of12801 atoms and 4258 groups and 4252 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3584 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1183 Number of atoms = 3584 Number of groups = 1188 Number of bonds = 3577 Number of angles = 1287 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1185 Number of HB donors = 2348 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1183 Number of atoms = 3584 Number of groups = 1188 Number of bonds = 3577 Number of angles = 1287 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1185 Number of HB donors = 2348 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.884" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1183" Evaluating: 1183-7 Parameter: NUMWAT <- "1176" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1176" Comparing "1081" and "1176". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.884" Parameter: BOX -> "32.884" Parameter: BOX -> "32.884" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.88400 B = 32.88400 C = 32.88400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9417 2 1 -1 0 -1 2.0080 3 1 -1 1 -1 5.0042 4 1 0 -1 -1 4.8920 5 1 0 0 -1 1.0355 6 1 0 1 -1 1.9472 7 1 -1 -1 0 4.8459 8 1 -1 0 0 1.1200 9 1 -1 1 0 1.7780 10 1 0 -1 0 0.8861 11 1 0 1 0 0.8861 12 1 -1 -1 1 5.6850 13 1 -1 0 1 1.8180 14 1 -1 1 1 6.3774 15 1 0 -1 1 1.9472 16 1 0 0 1 1.0355 17 1 0 1 1 4.8920 18 1 1 1 1 5.9417 19 1 1 0 1 2.0080 20 1 1 -1 1 5.0042 21 1 1 1 0 4.8459 22 1 1 0 0 1.1200 23 1 1 -1 0 1.7780 24 1 1 1 -1 5.6850 25 1 1 0 -1 1.8180 26 1 1 -1 -1 6.3774 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3510 atoms have been selected out of 3584 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1542 514 514 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1720 571 570 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 96 32 32 0.00 13 C013 has 483 161 161 0.00 14 C014 has 111 37 37 1.04 Total of12804 atoms and 4259 groups and 4253 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3584 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1183 Number of atoms = 3584 Number of groups = 1188 Number of bonds = 3577 Number of angles = 1287 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1185 Number of HB donors = 2348 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1183 Number of atoms = 3584 Number of groups = 1188 Number of bonds = 3577 Number of angles = 1287 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1185 Number of HB donors = 2348 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.882" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1183" Evaluating: 1183-7 Parameter: NUMWAT <- "1176" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1176" Comparing "1081" and "1176". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.882" Parameter: BOX -> "32.882" Parameter: BOX -> "32.882" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.88200 B = 32.88200 C = 32.88200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9403 2 1 -1 0 -1 2.0054 3 1 -1 1 -1 5.0008 4 1 0 -1 -1 4.8925 5 1 0 0 -1 1.0338 6 1 0 1 -1 1.9446 7 1 -1 -1 0 4.8440 8 1 -1 0 0 1.1190 9 1 -1 1 0 1.7758 10 1 0 -1 0 0.8843 11 1 0 1 0 0.8843 12 1 -1 -1 1 5.6822 13 1 -1 0 1 1.8158 14 1 -1 1 1 6.3744 15 1 0 -1 1 1.9446 16 1 0 0 1 1.0338 17 1 0 1 1 4.8925 18 1 1 1 1 5.9403 19 1 1 0 1 2.0054 20 1 1 -1 1 5.0008 21 1 1 1 0 4.8440 22 1 1 0 0 1.1190 23 1 1 -1 0 1.7758 24 1 1 1 -1 5.6822 25 1 1 0 -1 1.8158 26 1 1 -1 -1 6.3744 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3510 atoms have been selected out of 3584 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1542 514 514 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1720 571 570 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 96 32 32 0.00 13 C013 has 483 161 161 0.00 14 C014 has 111 37 37 1.04 Total of12804 atoms and 4259 groups and 4253 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3584 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1183 Number of atoms = 3584 Number of groups = 1188 Number of bonds = 3577 Number of angles = 1287 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1185 Number of HB donors = 2348 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1183 Number of atoms = 3584 Number of groups = 1188 Number of bonds = 3577 Number of angles = 1287 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1185 Number of HB donors = 2348 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.88" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1183" Evaluating: 1183-7 Parameter: NUMWAT <- "1176" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1176" Comparing "1081" and "1176". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.88" Parameter: BOX -> "32.88" Parameter: BOX -> "32.88" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.88000 B = 32.88000 C = 32.88000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9389 2 1 -1 0 -1 2.0027 3 1 -1 1 -1 4.9974 4 1 0 -1 -1 4.8930 5 1 0 0 -1 1.0320 6 1 0 1 -1 1.9420 7 1 -1 -1 0 4.8421 8 1 -1 0 0 1.1181 9 1 -1 1 0 1.7735 10 1 0 -1 0 0.8824 11 1 0 1 0 0.8824 12 1 -1 -1 1 5.6794 13 1 -1 0 1 1.8135 14 1 -1 1 1 6.3714 15 1 0 -1 1 1.9420 16 1 0 0 1 1.0320 17 1 0 1 1 4.8930 18 1 1 1 1 5.9389 19 1 1 0 1 2.0027 20 1 1 -1 1 4.9974 21 1 1 1 0 4.8421 22 1 1 0 0 1.1181 23 1 1 -1 0 1.7735 24 1 1 1 -1 5.6794 25 1 1 0 -1 1.8135 26 1 1 -1 -1 6.3714 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3510 atoms have been selected out of 3584 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1542 514 514 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1720 571 570 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 96 32 32 0.00 13 C013 has 486 162 162 0.00 14 C014 has 111 37 37 1.04 Total of12807 atoms and 4260 groups and 4254 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3584 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1183 Number of atoms = 3584 Number of groups = 1188 Number of bonds = 3577 Number of angles = 1287 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1185 Number of HB donors = 2348 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1183 Number of atoms = 3584 Number of groups = 1188 Number of bonds = 3577 Number of angles = 1287 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1185 Number of HB donors = 2348 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.878" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1183" Evaluating: 1183-7 Parameter: NUMWAT <- "1176" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1176" Comparing "1081" and "1176". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.878" Parameter: BOX -> "32.878" Parameter: BOX -> "32.878" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.87800 B = 32.87800 C = 32.87800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9375 2 1 -1 0 -1 2.0001 3 1 -1 1 -1 4.9940 4 1 0 -1 -1 4.8935 5 1 0 0 -1 1.0303 6 1 0 1 -1 1.9394 7 1 -1 -1 0 4.8402 8 1 -1 0 0 1.1171 9 1 -1 1 0 1.7713 10 1 0 -1 0 0.8806 11 1 0 1 0 0.8806 12 1 -1 -1 1 5.6766 13 1 -1 0 1 1.8113 14 1 -1 1 1 6.3684 15 1 0 -1 1 1.9394 16 1 0 0 1 1.0303 17 1 0 1 1 4.8935 18 1 1 1 1 5.9375 19 1 1 0 1 2.0001 20 1 1 -1 1 4.9940 21 1 1 1 0 4.8402 22 1 1 0 0 1.1171 23 1 1 -1 0 1.7713 24 1 1 1 -1 5.6766 25 1 1 0 -1 1.8113 26 1 1 -1 -1 6.3684 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3510 atoms have been selected out of 3584 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 961 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1545 515 515 0.00 6 C006 has 438 146 146 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1720 571 570 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 96 32 32 0.00 13 C013 has 486 162 162 0.00 14 C014 has 111 37 37 1.04 Total of12807 atoms and 4260 groups and 4254 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3584 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.876" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1182" Evaluating: 1182-7 Parameter: NUMWAT <- "1175" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1175" Comparing "1081" and "1175". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.876" Parameter: BOX -> "32.876" Parameter: BOX -> "32.876" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.87600 B = 32.87600 C = 32.87600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9361 2 1 -1 0 -1 1.9975 3 1 -1 1 -1 4.9905 4 1 0 -1 -1 4.8940 5 1 0 0 -1 1.0285 6 1 0 1 -1 1.9368 7 1 -1 -1 0 4.8384 8 1 -1 0 0 1.1161 9 1 -1 1 0 1.7691 10 1 0 -1 0 0.8787 11 1 0 1 0 0.8787 12 1 -1 -1 1 5.6738 13 1 -1 0 1 1.8091 14 1 -1 1 1 6.3654 15 1 0 -1 1 1.9368 16 1 0 0 1 1.0285 17 1 0 1 1 4.8940 18 1 1 1 1 5.9361 19 1 1 0 1 1.9975 20 1 1 -1 1 4.9905 21 1 1 1 0 4.8384 22 1 1 0 0 1.1161 23 1 1 -1 0 1.7691 24 1 1 1 -1 5.6738 25 1 1 0 -1 1.8091 26 1 1 -1 -1 6.3654 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3507 atoms have been selected out of 3581 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1539 513 513 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1720 571 570 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1620 540 540 0.00 12 C012 has 96 32 32 0.00 13 C013 has 486 162 162 0.00 14 C014 has 111 37 37 1.04 Total of12792 atoms and 4255 groups and 4249 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3581 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.874" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1182" Evaluating: 1182-7 Parameter: NUMWAT <- "1175" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1175" Comparing "1081" and "1175". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.874" Parameter: BOX -> "32.874" Parameter: BOX -> "32.874" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.87400 B = 32.87400 C = 32.87400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9347 2 1 -1 0 -1 1.9949 3 1 -1 1 -1 4.9871 4 1 0 -1 -1 4.8945 5 1 0 0 -1 1.0268 6 1 0 1 -1 1.9341 7 1 -1 -1 0 4.8365 8 1 -1 0 0 1.1151 9 1 -1 1 0 1.7669 10 1 0 -1 0 0.8769 11 1 0 1 0 0.8769 12 1 -1 -1 1 5.6710 13 1 -1 0 1 1.8069 14 1 -1 1 1 6.3624 15 1 0 -1 1 1.9341 16 1 0 0 1 1.0268 17 1 0 1 1 4.8945 18 1 1 1 1 5.9347 19 1 1 0 1 1.9949 20 1 1 -1 1 4.9871 21 1 1 1 0 4.8365 22 1 1 0 0 1.1151 23 1 1 -1 0 1.7669 24 1 1 1 -1 5.6710 25 1 1 0 -1 1.8069 26 1 1 -1 -1 6.3624 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3507 atoms have been selected out of 3581 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1539 513 513 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1720 571 570 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1620 540 540 0.00 12 C012 has 96 32 32 0.00 13 C013 has 486 162 162 0.00 14 C014 has 111 37 37 1.03 Total of12792 atoms and 4255 groups and 4249 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3581 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.872" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1182" Evaluating: 1182-7 Parameter: NUMWAT <- "1175" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1175" Comparing "1081" and "1175". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.872" Parameter: BOX -> "32.872" Parameter: BOX -> "32.872" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.87200 B = 32.87200 C = 32.87200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9333 2 1 -1 0 -1 1.9923 3 1 -1 1 -1 4.9837 4 1 0 -1 -1 4.8950 5 1 0 0 -1 1.0251 6 1 0 1 -1 1.9315 7 1 -1 -1 0 4.8346 8 1 -1 0 0 1.1141 9 1 -1 1 0 1.7647 10 1 0 -1 0 0.8750 11 1 0 1 0 0.8750 12 1 -1 -1 1 5.6681 13 1 -1 0 1 1.8047 14 1 -1 1 1 6.3594 15 1 0 -1 1 1.9315 16 1 0 0 1 1.0251 17 1 0 1 1 4.8950 18 1 1 1 1 5.9333 19 1 1 0 1 1.9923 20 1 1 -1 1 4.9837 21 1 1 1 0 4.8346 22 1 1 0 0 1.1141 23 1 1 -1 0 1.7647 24 1 1 1 -1 5.6681 25 1 1 0 -1 1.8047 26 1 1 -1 -1 6.3594 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3507 atoms have been selected out of 3581 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1539 513 513 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1720 571 570 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1620 540 540 0.00 12 C012 has 96 32 32 0.00 13 C013 has 486 162 162 0.00 14 C014 has 111 37 37 1.03 Total of12795 atoms and 4256 groups and 4250 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3581 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.87" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1182" Evaluating: 1182-7 Parameter: NUMWAT <- "1175" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1175" Comparing "1081" and "1175". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.87" Parameter: BOX -> "32.87" Parameter: BOX -> "32.87" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.87000 B = 32.87000 C = 32.87000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9319 2 1 -1 0 -1 1.9897 3 1 -1 1 -1 4.9803 4 1 0 -1 -1 4.8955 5 1 0 0 -1 1.0233 6 1 0 1 -1 1.9289 7 1 -1 -1 0 4.8327 8 1 -1 0 0 1.1131 9 1 -1 1 0 1.7625 10 1 0 -1 0 0.8732 11 1 0 1 0 0.8732 12 1 -1 -1 1 5.6653 13 1 -1 0 1 1.8025 14 1 -1 1 1 6.3564 15 1 0 -1 1 1.9289 16 1 0 0 1 1.0233 17 1 0 1 1 4.8955 18 1 1 1 1 5.9319 19 1 1 0 1 1.9897 20 1 1 -1 1 4.9803 21 1 1 1 0 4.8327 22 1 1 0 0 1.1131 23 1 1 -1 0 1.7625 24 1 1 1 -1 5.6653 25 1 1 0 -1 1.8025 26 1 1 -1 -1 6.3564 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3507 atoms have been selected out of 3581 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1539 513 513 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1720 571 570 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 96 32 32 0.00 13 C013 has 486 162 162 0.00 14 C014 has 111 37 37 1.03 Total of12798 atoms and 4257 groups and 4251 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3581 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.868" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1182" Evaluating: 1182-7 Parameter: NUMWAT <- "1175" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1175" Comparing "1081" and "1175". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.868" Parameter: BOX -> "32.868" Parameter: BOX -> "32.868" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.86800 B = 32.86800 C = 32.86800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9305 2 1 -1 0 -1 1.9871 3 1 -1 1 -1 4.9768 4 1 0 -1 -1 4.8960 5 1 0 0 -1 1.0216 6 1 0 1 -1 1.9263 7 1 -1 -1 0 4.8308 8 1 -1 0 0 1.1122 9 1 -1 1 0 1.7603 10 1 0 -1 0 0.8713 11 1 0 1 0 0.8713 12 1 -1 -1 1 5.6625 13 1 -1 0 1 1.8003 14 1 -1 1 1 6.3534 15 1 0 -1 1 1.9263 16 1 0 0 1 1.0216 17 1 0 1 1 4.8960 18 1 1 1 1 5.9305 19 1 1 0 1 1.9871 20 1 1 -1 1 4.9768 21 1 1 1 0 4.8308 22 1 1 0 0 1.1122 23 1 1 -1 0 1.7603 24 1 1 1 -1 5.6625 25 1 1 0 -1 1.8003 26 1 1 -1 -1 6.3534 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3507 atoms have been selected out of 3581 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1539 513 513 0.00 6 C006 has 438 146 146 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1720 571 570 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 99 33 33 0.00 13 C013 has 489 163 163 0.00 14 C014 has 111 37 37 1.03 Total of12804 atoms and 4259 groups and 4253 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3581 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.866" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1182" Evaluating: 1182-7 Parameter: NUMWAT <- "1175" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1175" Comparing "1081" and "1175". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.866" Parameter: BOX -> "32.866" Parameter: BOX -> "32.866" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.86600 B = 32.86600 C = 32.86600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9291 2 1 -1 0 -1 1.9845 3 1 -1 1 -1 4.9734 4 1 0 -1 -1 4.8965 5 1 0 0 -1 1.0199 6 1 0 1 -1 1.9236 7 1 -1 -1 0 4.8290 8 1 -1 0 0 1.1112 9 1 -1 1 0 1.7581 10 1 0 -1 0 0.8695 11 1 0 1 0 0.8695 12 1 -1 -1 1 5.6597 13 1 -1 0 1 1.7981 14 1 -1 1 1 6.3504 15 1 0 -1 1 1.9236 16 1 0 0 1 1.0199 17 1 0 1 1 4.8965 18 1 1 1 1 5.9291 19 1 1 0 1 1.9845 20 1 1 -1 1 4.9734 21 1 1 1 0 4.8290 22 1 1 0 0 1.1112 23 1 1 -1 0 1.7581 24 1 1 1 -1 5.6597 25 1 1 0 -1 1.7981 26 1 1 -1 -1 6.3504 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3507 atoms have been selected out of 3581 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1539 513 513 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1720 571 570 0.00 9 C009 has 471 157 157 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 99 33 33 0.00 13 C013 has 489 163 163 0.00 14 C014 has 111 37 37 1.03 Total of12807 atoms and 4260 groups and 4254 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3581 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.864" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1182" Evaluating: 1182-7 Parameter: NUMWAT <- "1175" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1175" Comparing "1081" and "1175". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.864" Parameter: BOX -> "32.864" Parameter: BOX -> "32.864" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.86400 B = 32.86400 C = 32.86400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9277 2 1 -1 0 -1 1.9819 3 1 -1 1 -1 4.9700 4 1 0 -1 -1 4.8970 5 1 0 0 -1 1.0181 6 1 0 1 -1 1.9210 7 1 -1 -1 0 4.8271 8 1 -1 0 0 1.1102 9 1 -1 1 0 1.7559 10 1 0 -1 0 0.8676 11 1 0 1 0 0.8676 12 1 -1 -1 1 5.6569 13 1 -1 0 1 1.7959 14 1 -1 1 1 6.3475 15 1 0 -1 1 1.9210 16 1 0 0 1 1.0181 17 1 0 1 1 4.8970 18 1 1 1 1 5.9277 19 1 1 0 1 1.9819 20 1 1 -1 1 4.9700 21 1 1 1 0 4.8271 22 1 1 0 0 1.1102 23 1 1 -1 0 1.7559 24 1 1 1 -1 5.6569 25 1 1 0 -1 1.7959 26 1 1 -1 -1 6.3475 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3507 atoms have been selected out of 3581 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1539 513 513 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1720 571 570 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 99 33 33 0.00 13 C013 has 489 163 163 0.00 14 C014 has 111 37 37 1.02 Total of12810 atoms and 4261 groups and 4255 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3581 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.862" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1182" Evaluating: 1182-7 Parameter: NUMWAT <- "1175" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1175" Comparing "1081" and "1175". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.862" Parameter: BOX -> "32.862" Parameter: BOX -> "32.862" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.86200 B = 32.86200 C = 32.86200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9263 2 1 -1 0 -1 1.9793 3 1 -1 1 -1 4.9666 4 1 0 -1 -1 4.8975 5 1 0 0 -1 1.0164 6 1 0 1 -1 1.9184 7 1 -1 -1 0 4.8252 8 1 -1 0 0 1.1093 9 1 -1 1 0 1.7537 10 1 0 -1 0 0.8658 11 1 0 1 0 0.8658 12 1 -1 -1 1 5.6541 13 1 -1 0 1 1.7937 14 1 -1 1 1 6.3445 15 1 0 -1 1 1.9184 16 1 0 0 1 1.0164 17 1 0 1 1 4.8975 18 1 1 1 1 5.9263 19 1 1 0 1 1.9793 20 1 1 -1 1 4.9666 21 1 1 1 0 4.8252 22 1 1 0 0 1.1093 23 1 1 -1 0 1.7537 24 1 1 1 -1 5.6541 25 1 1 0 -1 1.7937 26 1 1 -1 -1 6.3445 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3507 atoms have been selected out of 3581 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1539 513 513 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1720 571 570 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 99 33 33 0.00 13 C013 has 489 163 163 0.00 14 C014 has 111 37 37 1.02 Total of12810 atoms and 4261 groups and 4255 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3581 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.86" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1182" Evaluating: 1182-7 Parameter: NUMWAT <- "1175" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1175" Comparing "1081" and "1175". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.86" Parameter: BOX -> "32.86" Parameter: BOX -> "32.86" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.86000 B = 32.86000 C = 32.86000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9249 2 1 -1 0 -1 1.9766 3 1 -1 1 -1 4.9631 4 1 0 -1 -1 4.8980 5 1 0 0 -1 1.0146 6 1 0 1 -1 1.9158 7 1 -1 -1 0 4.8233 8 1 -1 0 0 1.1083 9 1 -1 1 0 1.7515 10 1 0 -1 0 0.8639 11 1 0 1 0 0.8639 12 1 -1 -1 1 5.6513 13 1 -1 0 1 1.7915 14 1 -1 1 1 6.3415 15 1 0 -1 1 1.9158 16 1 0 0 1 1.0146 17 1 0 1 1 4.8980 18 1 1 1 1 5.9249 19 1 1 0 1 1.9766 20 1 1 -1 1 4.9631 21 1 1 1 0 4.8233 22 1 1 0 0 1.1083 23 1 1 -1 0 1.7515 24 1 1 1 -1 5.6513 25 1 1 0 -1 1.7915 26 1 1 -1 -1 6.3415 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3507 atoms have been selected out of 3581 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1542 514 514 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1723 572 571 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 99 33 33 0.00 13 C013 has 489 163 163 0.00 14 C014 has 111 37 37 1.02 Total of12819 atoms and 4264 groups and 4258 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3581 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.858" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1182" Evaluating: 1182-7 Parameter: NUMWAT <- "1175" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1175" Comparing "1081" and "1175". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.858" Parameter: BOX -> "32.858" Parameter: BOX -> "32.858" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.85800 B = 32.85800 C = 32.85800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9235 2 1 -1 0 -1 1.9740 3 1 -1 1 -1 4.9597 4 1 0 -1 -1 4.8985 5 1 0 0 -1 1.0129 6 1 0 1 -1 1.9132 7 1 -1 -1 0 4.8215 8 1 -1 0 0 1.1073 9 1 -1 1 0 1.7493 10 1 0 -1 0 0.8621 11 1 0 1 0 0.8621 12 1 -1 -1 1 5.6485 13 1 -1 0 1 1.7893 14 1 -1 1 1 6.3385 15 1 0 -1 1 1.9132 16 1 0 0 1 1.0129 17 1 0 1 1 4.8985 18 1 1 1 1 5.9235 19 1 1 0 1 1.9740 20 1 1 -1 1 4.9597 21 1 1 1 0 4.8215 22 1 1 0 0 1.1073 23 1 1 -1 0 1.7493 24 1 1 1 -1 5.6485 25 1 1 0 -1 1.7893 26 1 1 -1 -1 6.3385 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3507 atoms have been selected out of 3581 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1542 514 514 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1723 572 571 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 99 33 33 0.00 13 C013 has 489 163 163 0.00 14 C014 has 111 37 37 1.02 Total of12822 atoms and 4265 groups and 4259 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3581 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.856" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1182" Evaluating: 1182-7 Parameter: NUMWAT <- "1175" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1175" Comparing "1081" and "1175". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.856" Parameter: BOX -> "32.856" Parameter: BOX -> "32.856" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.85600 B = 32.85600 C = 32.85600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9221 2 1 -1 0 -1 1.9714 3 1 -1 1 -1 4.9563 4 1 0 -1 -1 4.8990 5 1 0 0 -1 1.0112 6 1 0 1 -1 1.9106 7 1 -1 -1 0 4.8196 8 1 -1 0 0 1.1064 9 1 -1 1 0 1.7471 10 1 0 -1 0 0.8603 11 1 0 1 0 0.8603 12 1 -1 -1 1 5.6457 13 1 -1 0 1 1.7871 14 1 -1 1 1 6.3355 15 1 0 -1 1 1.9106 16 1 0 0 1 1.0112 17 1 0 1 1 4.8990 18 1 1 1 1 5.9221 19 1 1 0 1 1.9714 20 1 1 -1 1 4.9563 21 1 1 1 0 4.8196 22 1 1 0 0 1.1064 23 1 1 -1 0 1.7471 24 1 1 1 -1 5.6457 25 1 1 0 -1 1.7871 26 1 1 -1 -1 6.3355 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3507 atoms have been selected out of 3581 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1542 514 514 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1726 573 572 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 99 33 33 0.00 13 C013 has 489 163 163 0.00 14 C014 has 111 37 37 1.02 Total of12825 atoms and 4266 groups and 4260 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3581 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.854" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1182" Evaluating: 1182-7 Parameter: NUMWAT <- "1175" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1175" Comparing "1081" and "1175". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.854" Parameter: BOX -> "32.854" Parameter: BOX -> "32.854" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.85400 B = 32.85400 C = 32.85400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9207 2 1 -1 0 -1 1.9688 3 1 -1 1 -1 4.9529 4 1 0 -1 -1 4.8995 5 1 0 0 -1 1.0094 6 1 0 1 -1 1.9079 7 1 -1 -1 0 4.8177 8 1 -1 0 0 1.1054 9 1 -1 1 0 1.7449 10 1 0 -1 0 0.8584 11 1 0 1 0 0.8584 12 1 -1 -1 1 5.6429 13 1 -1 0 1 1.7849 14 1 -1 1 1 6.3325 15 1 0 -1 1 1.9079 16 1 0 0 1 1.0094 17 1 0 1 1 4.8995 18 1 1 1 1 5.9207 19 1 1 0 1 1.9688 20 1 1 -1 1 4.9529 21 1 1 1 0 4.8177 22 1 1 0 0 1.1054 23 1 1 -1 0 1.7449 24 1 1 1 -1 5.6429 25 1 1 0 -1 1.7849 26 1 1 -1 -1 6.3325 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3507 atoms have been selected out of 3581 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1542 514 514 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1729 574 573 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 99 33 33 0.00 13 C013 has 489 163 163 0.00 14 C014 has 111 37 37 1.01 Total of12831 atoms and 4268 groups and 4262 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3581 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.852" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1182" Evaluating: 1182-7 Parameter: NUMWAT <- "1175" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1175" Comparing "1081" and "1175". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.852" Parameter: BOX -> "32.852" Parameter: BOX -> "32.852" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.85200 B = 32.85200 C = 32.85200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9193 2 1 -1 0 -1 1.9662 3 1 -1 1 -1 4.9494 4 1 0 -1 -1 4.9000 5 1 0 0 -1 1.0077 6 1 0 1 -1 1.9053 7 1 -1 -1 0 4.8159 8 1 -1 0 0 1.1045 9 1 -1 1 0 1.7427 10 1 0 -1 0 0.8566 11 1 0 1 0 0.8566 12 1 -1 -1 1 5.6401 13 1 -1 0 1 1.7828 14 1 -1 1 1 6.3295 15 1 0 -1 1 1.9053 16 1 0 0 1 1.0077 17 1 0 1 1 4.9000 18 1 1 1 1 5.9193 19 1 1 0 1 1.9662 20 1 1 -1 1 4.9494 21 1 1 1 0 4.8159 22 1 1 0 0 1.1045 23 1 1 -1 0 1.7427 24 1 1 1 -1 5.6401 25 1 1 0 -1 1.7828 26 1 1 -1 -1 6.3295 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3507 atoms have been selected out of 3581 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1542 514 514 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1729 574 573 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 99 33 33 0.00 13 C013 has 489 163 163 0.00 14 C014 has 111 37 37 1.01 Total of12834 atoms and 4269 groups and 4263 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3581 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.85" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1182" Evaluating: 1182-7 Parameter: NUMWAT <- "1175" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1175" Comparing "1081" and "1175". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.85" Parameter: BOX -> "32.85" Parameter: BOX -> "32.85" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.85000 B = 32.85000 C = 32.85000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9179 2 1 -1 0 -1 1.9636 3 1 -1 1 -1 4.9460 4 1 0 -1 -1 4.9005 5 1 0 0 -1 1.0060 6 1 0 1 -1 1.9027 7 1 -1 -1 0 4.8140 8 1 -1 0 0 1.1035 9 1 -1 1 0 1.7405 10 1 0 -1 0 0.8547 11 1 0 1 0 0.8547 12 1 -1 -1 1 5.6373 13 1 -1 0 1 1.7806 14 1 -1 1 1 6.3266 15 1 0 -1 1 1.9027 16 1 0 0 1 1.0060 17 1 0 1 1 4.9005 18 1 1 1 1 5.9179 19 1 1 0 1 1.9636 20 1 1 -1 1 4.9460 21 1 1 1 0 4.8140 22 1 1 0 0 1.1035 23 1 1 -1 0 1.7405 24 1 1 1 -1 5.6373 25 1 1 0 -1 1.7806 26 1 1 -1 -1 6.3266 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3507 atoms have been selected out of 3581 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1542 514 514 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1729 574 573 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 99 33 33 0.00 13 C013 has 489 163 163 0.00 14 C014 has 111 37 37 1.01 Total of12834 atoms and 4269 groups and 4263 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3581 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1182 Number of atoms = 3581 Number of groups = 1187 Number of bonds = 3574 Number of angles = 1286 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1184 Number of HB donors = 2346 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.848" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1182" Evaluating: 1182-7 Parameter: NUMWAT <- "1175" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1175" Comparing "1081" and "1175". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.848" Parameter: BOX -> "32.848" Parameter: BOX -> "32.848" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.84800 B = 32.84800 C = 32.84800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9166 2 1 -1 0 -1 1.9610 3 1 -1 1 -1 4.9426 4 1 0 -1 -1 4.9010 5 1 0 0 -1 1.0043 6 1 0 1 -1 1.9001 7 1 -1 -1 0 4.8121 8 1 -1 0 0 1.1026 9 1 -1 1 0 1.7384 10 1 0 -1 0 0.8529 11 1 0 1 0 0.8529 12 1 -1 -1 1 5.6345 13 1 -1 0 1 1.7784 14 1 -1 1 1 6.3236 15 1 0 -1 1 1.9001 16 1 0 0 1 1.0043 17 1 0 1 1 4.9010 18 1 1 1 1 5.9166 19 1 1 0 1 1.9610 20 1 1 -1 1 4.9426 21 1 1 1 0 4.8121 22 1 1 0 0 1.1026 23 1 1 -1 0 1.7384 24 1 1 1 -1 5.6345 25 1 1 0 -1 1.7784 26 1 1 -1 -1 6.3236 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3507 atoms have been selected out of 3581 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 36 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 753 251 251 0.00 3 C003 has 108 36 36 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1542 514 514 0.00 6 C006 has 441 147 147 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1726 573 572 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1626 542 542 0.00 12 C012 has 99 33 33 0.00 13 C013 has 489 163 163 0.00 14 C014 has 111 37 37 1.01 Total of12837 atoms and 4270 groups and 4264 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3581 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1181 Number of atoms = 3578 Number of groups = 1186 Number of bonds = 3571 Number of angles = 1285 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1183 Number of HB donors = 2344 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1181 Number of atoms = 3578 Number of groups = 1186 Number of bonds = 3571 Number of angles = 1285 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1183 Number of HB donors = 2344 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.846" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1181" Evaluating: 1181-7 Parameter: NUMWAT <- "1174" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1174" Comparing "1081" and "1174". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.846" Parameter: BOX -> "32.846" Parameter: BOX -> "32.846" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.84600 B = 32.84600 C = 32.84600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9152 2 1 -1 0 -1 1.9584 3 1 -1 1 -1 4.9392 4 1 0 -1 -1 4.9015 5 1 0 0 -1 1.0025 6 1 0 1 -1 1.8975 7 1 -1 -1 0 4.8102 8 1 -1 0 0 1.1016 9 1 -1 1 0 1.7362 10 1 0 -1 0 0.8511 11 1 0 1 0 0.8511 12 1 -1 -1 1 5.6317 13 1 -1 0 1 1.7762 14 1 -1 1 1 6.3206 15 1 0 -1 1 1.8975 16 1 0 0 1 1.0025 17 1 0 1 1 4.9015 18 1 1 1 1 5.9152 19 1 1 0 1 1.9584 20 1 1 -1 1 4.9392 21 1 1 1 0 4.8102 22 1 1 0 0 1.1016 23 1 1 -1 0 1.7362 24 1 1 1 -1 5.6317 25 1 1 0 -1 1.7762 26 1 1 -1 -1 6.3206 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3504 atoms have been selected out of 3578 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 756 252 252 0.00 3 C003 has 108 36 36 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1542 514 514 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1726 573 572 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 99 33 33 0.00 13 C013 has 489 163 163 0.00 14 C014 has 111 37 37 1.01 Total of12831 atoms and 4268 groups and 4262 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3578 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1181 Number of atoms = 3578 Number of groups = 1186 Number of bonds = 3571 Number of angles = 1285 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1183 Number of HB donors = 2344 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1181 Number of atoms = 3578 Number of groups = 1186 Number of bonds = 3571 Number of angles = 1285 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1183 Number of HB donors = 2344 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.844" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1181" Evaluating: 1181-7 Parameter: NUMWAT <- "1174" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1174" Comparing "1081" and "1174". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.844" Parameter: BOX -> "32.844" Parameter: BOX -> "32.844" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.84400 B = 32.84400 C = 32.84400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9138 2 1 -1 0 -1 1.9558 3 1 -1 1 -1 4.9357 4 1 0 -1 -1 4.9021 5 1 0 0 -1 1.0008 6 1 0 1 -1 1.8949 7 1 -1 -1 0 4.8084 8 1 -1 0 0 1.1007 9 1 -1 1 0 1.7340 10 1 0 -1 0 0.8492 11 1 0 1 0 0.8492 12 1 -1 -1 1 5.6289 13 1 -1 0 1 1.7740 14 1 -1 1 1 6.3176 15 1 0 -1 1 1.8949 16 1 0 0 1 1.0008 17 1 0 1 1 4.9021 18 1 1 1 1 5.9138 19 1 1 0 1 1.9558 20 1 1 -1 1 4.9357 21 1 1 1 0 4.8084 22 1 1 0 0 1.1007 23 1 1 -1 0 1.7340 24 1 1 1 -1 5.6289 25 1 1 0 -1 1.7740 26 1 1 -1 -1 6.3176 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3504 atoms have been selected out of 3578 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 756 252 252 0.00 3 C003 has 108 36 36 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1542 514 514 0.00 6 C006 has 441 147 147 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1726 573 572 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 99 33 33 0.00 13 C013 has 489 163 163 0.00 14 C014 has 111 37 37 1.00 Total of12834 atoms and 4269 groups and 4263 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3578 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1181 Number of atoms = 3578 Number of groups = 1186 Number of bonds = 3571 Number of angles = 1285 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1183 Number of HB donors = 2344 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1181 Number of atoms = 3578 Number of groups = 1186 Number of bonds = 3571 Number of angles = 1285 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1183 Number of HB donors = 2344 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.842" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1181" Evaluating: 1181-7 Parameter: NUMWAT <- "1174" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1174" Comparing "1081" and "1174". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.842" Parameter: BOX -> "32.842" Parameter: BOX -> "32.842" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.84200 B = 32.84200 C = 32.84200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9124 2 1 -1 0 -1 1.9532 3 1 -1 1 -1 4.9323 4 1 0 -1 -1 4.9026 5 1 0 0 -1 0.9991 6 1 0 1 -1 1.8923 7 1 -1 -1 0 4.8065 8 1 -1 0 0 1.0998 9 1 -1 1 0 1.7318 10 1 0 -1 0 0.8474 11 1 0 1 0 0.8474 12 1 -1 -1 1 5.6261 13 1 -1 0 1 1.7719 14 1 -1 1 1 6.3146 15 1 0 -1 1 1.8923 16 1 0 0 1 0.9991 17 1 0 1 1 4.9026 18 1 1 1 1 5.9124 19 1 1 0 1 1.9532 20 1 1 -1 1 4.9323 21 1 1 1 0 4.8065 22 1 1 0 0 1.0998 23 1 1 -1 0 1.7318 24 1 1 1 -1 5.6261 25 1 1 0 -1 1.7719 26 1 1 -1 -1 6.3146 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3504 atoms have been selected out of 3578 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 756 252 252 0.00 3 C003 has 108 36 36 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1542 514 514 0.00 6 C006 has 441 147 147 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1726 573 572 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 99 33 33 0.00 13 C013 has 489 163 163 0.00 14 C014 has 111 37 37 1.00 Total of12837 atoms and 4270 groups and 4264 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3578 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1181 Number of atoms = 3578 Number of groups = 1186 Number of bonds = 3571 Number of angles = 1285 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1183 Number of HB donors = 2344 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1181 Number of atoms = 3578 Number of groups = 1186 Number of bonds = 3571 Number of angles = 1285 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1183 Number of HB donors = 2344 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.84" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1181" Evaluating: 1181-7 Parameter: NUMWAT <- "1174" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1174" Comparing "1081" and "1174". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.84" Parameter: BOX -> "32.84" Parameter: BOX -> "32.84" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.84000 B = 32.84000 C = 32.84000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9111 2 1 -1 0 -1 1.9506 3 1 -1 1 -1 4.9289 4 1 0 -1 -1 4.9031 5 1 0 0 -1 0.9973 6 1 0 1 -1 1.8897 7 1 -1 -1 0 4.8046 8 1 -1 0 0 1.0988 9 1 -1 1 0 1.7296 10 1 0 -1 0 0.8455 11 1 0 1 0 0.8455 12 1 -1 -1 1 5.6233 13 1 -1 0 1 1.7697 14 1 -1 1 1 6.3116 15 1 0 -1 1 1.8897 16 1 0 0 1 0.9973 17 1 0 1 1 4.9031 18 1 1 1 1 5.9111 19 1 1 0 1 1.9506 20 1 1 -1 1 4.9289 21 1 1 1 0 4.8046 22 1 1 0 0 1.0988 23 1 1 -1 0 1.7296 24 1 1 1 -1 5.6233 25 1 1 0 -1 1.7697 26 1 1 -1 -1 6.3116 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3504 atoms have been selected out of 3578 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 108 36 36 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1542 514 514 0.00 6 C006 has 441 147 147 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1726 573 572 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 99 33 33 0.00 13 C013 has 489 163 163 0.00 14 C014 has 111 37 37 1.00 Total of12840 atoms and 4271 groups and 4265 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3578 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1181 Number of atoms = 3578 Number of groups = 1186 Number of bonds = 3571 Number of angles = 1285 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1183 Number of HB donors = 2344 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1181 Number of atoms = 3578 Number of groups = 1186 Number of bonds = 3571 Number of angles = 1285 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1183 Number of HB donors = 2344 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.838" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1181" Evaluating: 1181-7 Parameter: NUMWAT <- "1174" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1174" Comparing "1081" and "1174". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.838" Parameter: BOX -> "32.838" Parameter: BOX -> "32.838" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.83800 B = 32.83800 C = 32.83800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9097 2 1 -1 0 -1 1.9480 3 1 -1 1 -1 4.9255 4 1 0 -1 -1 4.9036 5 1 0 0 -1 0.9956 6 1 0 1 -1 1.8870 7 1 -1 -1 0 4.8028 8 1 -1 0 0 1.0979 9 1 -1 1 0 1.7275 10 1 0 -1 0 0.8437 11 1 0 1 0 0.8437 12 1 -1 -1 1 5.6205 13 1 -1 0 1 1.7675 14 1 -1 1 1 6.3087 15 1 0 -1 1 1.8870 16 1 0 0 1 0.9956 17 1 0 1 1 4.9036 18 1 1 1 1 5.9097 19 1 1 0 1 1.9480 20 1 1 -1 1 4.9255 21 1 1 1 0 4.8028 22 1 1 0 0 1.0979 23 1 1 -1 0 1.7275 24 1 1 1 -1 5.6205 25 1 1 0 -1 1.7675 26 1 1 -1 -1 6.3087 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3504 atoms have been selected out of 3578 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 108 36 36 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1542 514 514 0.00 6 C006 has 441 147 147 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1726 573 572 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 99 33 33 0.00 13 C013 has 489 163 163 0.00 14 C014 has 111 37 37 1.00 Total of12840 atoms and 4271 groups and 4265 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3578 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1181 Number of atoms = 3578 Number of groups = 1186 Number of bonds = 3571 Number of angles = 1285 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1183 Number of HB donors = 2344 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1181 Number of atoms = 3578 Number of groups = 1186 Number of bonds = 3571 Number of angles = 1285 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1183 Number of HB donors = 2344 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.836" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1181" Evaluating: 1181-7 Parameter: NUMWAT <- "1174" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1174" Comparing "1081" and "1174". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.836" Parameter: BOX -> "32.836" Parameter: BOX -> "32.836" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.83600 B = 32.83600 C = 32.83600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9083 2 1 -1 0 -1 1.9454 3 1 -1 1 -1 4.9220 4 1 0 -1 -1 4.9041 5 1 0 0 -1 0.9939 6 1 0 1 -1 1.8844 7 1 -1 -1 0 4.8009 8 1 -1 0 0 1.0970 9 1 -1 1 0 1.7253 10 1 0 -1 0 0.8419 11 1 0 1 0 0.8419 12 1 -1 -1 1 5.6177 13 1 -1 0 1 1.7653 14 1 -1 1 1 6.3057 15 1 0 -1 1 1.8844 16 1 0 0 1 0.9939 17 1 0 1 1 4.9041 18 1 1 1 1 5.9083 19 1 1 0 1 1.9454 20 1 1 -1 1 4.9220 21 1 1 1 0 4.8009 22 1 1 0 0 1.0970 23 1 1 -1 0 1.7253 24 1 1 1 -1 5.6177 25 1 1 0 -1 1.7653 26 1 1 -1 -1 6.3057 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3504 atoms have been selected out of 3578 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 627 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 762 254 254 0.00 3 C003 has 108 36 36 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1539 513 513 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1729 574 573 0.00 9 C009 has 477 159 159 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 99 33 33 0.00 13 C013 has 489 163 163 0.00 14 C014 has 111 37 37 1.00 Total of12843 atoms and 4272 groups and 4266 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3578 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1180 Number of atoms = 3575 Number of groups = 1185 Number of bonds = 3568 Number of angles = 1284 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1182 Number of HB donors = 2342 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1180 Number of atoms = 3575 Number of groups = 1185 Number of bonds = 3568 Number of angles = 1284 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1182 Number of HB donors = 2342 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.834" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1180" Evaluating: 1180-7 Parameter: NUMWAT <- "1173" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1173" Comparing "1081" and "1173". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.834" Parameter: BOX -> "32.834" Parameter: BOX -> "32.834" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.83400 B = 32.83400 C = 32.83400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9069 2 1 -1 0 -1 1.9428 3 1 -1 1 -1 4.9186 4 1 0 -1 -1 4.9047 5 1 0 0 -1 0.9922 6 1 0 1 -1 1.8818 7 1 -1 -1 0 4.7991 8 1 -1 0 0 1.0960 9 1 -1 1 0 1.7231 10 1 0 -1 0 0.8400 11 1 0 1 0 0.8400 12 1 -1 -1 1 5.6149 13 1 -1 0 1 1.7632 14 1 -1 1 1 6.3027 15 1 0 -1 1 1.8818 16 1 0 0 1 0.9922 17 1 0 1 1 4.9047 18 1 1 1 1 5.9069 19 1 1 0 1 1.9428 20 1 1 -1 1 4.9186 21 1 1 1 0 4.7991 22 1 1 0 0 1.0960 23 1 1 -1 0 1.7231 24 1 1 1 -1 5.6149 25 1 1 0 -1 1.7632 26 1 1 -1 -1 6.3027 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3501 atoms have been selected out of 3575 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 108 36 36 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1539 513 513 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1726 573 572 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 99 33 33 0.00 13 C013 has 489 163 163 0.00 14 C014 has 111 37 37 0.99 Total of12831 atoms and 4268 groups and 4262 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3575 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1180 Number of atoms = 3575 Number of groups = 1185 Number of bonds = 3568 Number of angles = 1284 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1182 Number of HB donors = 2342 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1180 Number of atoms = 3575 Number of groups = 1185 Number of bonds = 3568 Number of angles = 1284 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1182 Number of HB donors = 2342 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.832" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1180" Evaluating: 1180-7 Parameter: NUMWAT <- "1173" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1173" Comparing "1081" and "1173". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.832" Parameter: BOX -> "32.832" Parameter: BOX -> "32.832" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.83200 B = 32.83200 C = 32.83200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9056 2 1 -1 0 -1 1.9402 3 1 -1 1 -1 4.9152 4 1 0 -1 -1 4.9052 5 1 0 0 -1 0.9905 6 1 0 1 -1 1.8792 7 1 -1 -1 0 4.7972 8 1 -1 0 0 1.0951 9 1 -1 1 0 1.7209 10 1 0 -1 0 0.8382 11 1 0 1 0 0.8382 12 1 -1 -1 1 5.6121 13 1 -1 0 1 1.7610 14 1 -1 1 1 6.2997 15 1 0 -1 1 1.8792 16 1 0 0 1 0.9905 17 1 0 1 1 4.9052 18 1 1 1 1 5.9056 19 1 1 0 1 1.9402 20 1 1 -1 1 4.9152 21 1 1 1 0 4.7972 22 1 1 0 0 1.0951 23 1 1 -1 0 1.7209 24 1 1 1 -1 5.6121 25 1 1 0 -1 1.7610 26 1 1 -1 -1 6.2997 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3501 atoms have been selected out of 3575 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 108 36 36 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1539 513 513 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1726 573 572 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 99 33 33 0.00 13 C013 has 489 163 163 0.00 14 C014 has 111 37 37 0.99 Total of12831 atoms and 4268 groups and 4262 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3575 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1180 Number of atoms = 3575 Number of groups = 1185 Number of bonds = 3568 Number of angles = 1284 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1182 Number of HB donors = 2342 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1180 Number of atoms = 3575 Number of groups = 1185 Number of bonds = 3568 Number of angles = 1284 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1182 Number of HB donors = 2342 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.83" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1180" Evaluating: 1180-7 Parameter: NUMWAT <- "1173" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1173" Comparing "1081" and "1173". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.83" Parameter: BOX -> "32.83" Parameter: BOX -> "32.83" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.83000 B = 32.83000 C = 32.83000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9042 2 1 -1 0 -1 1.9376 3 1 -1 1 -1 4.9118 4 1 0 -1 -1 4.9057 5 1 0 0 -1 0.9887 6 1 0 1 -1 1.8766 7 1 -1 -1 0 4.7953 8 1 -1 0 0 1.0942 9 1 -1 1 0 1.7188 10 1 0 -1 0 0.8364 11 1 0 1 0 0.8364 12 1 -1 -1 1 5.6093 13 1 -1 0 1 1.7588 14 1 -1 1 1 6.2967 15 1 0 -1 1 1.8766 16 1 0 0 1 0.9887 17 1 0 1 1 4.9057 18 1 1 1 1 5.9042 19 1 1 0 1 1.9376 20 1 1 -1 1 4.9118 21 1 1 1 0 4.7953 22 1 1 0 0 1.0942 23 1 1 -1 0 1.7188 24 1 1 1 -1 5.6093 25 1 1 0 -1 1.7588 26 1 1 -1 -1 6.2967 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3501 atoms have been selected out of 3575 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 108 36 36 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1539 513 513 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1726 573 572 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 99 33 33 0.00 13 C013 has 489 163 163 0.00 14 C014 has 111 37 37 0.99 Total of12831 atoms and 4268 groups and 4262 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3575 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1180 Number of atoms = 3575 Number of groups = 1185 Number of bonds = 3568 Number of angles = 1284 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1182 Number of HB donors = 2342 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1180 Number of atoms = 3575 Number of groups = 1185 Number of bonds = 3568 Number of angles = 1284 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1182 Number of HB donors = 2342 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.828" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1180" Evaluating: 1180-7 Parameter: NUMWAT <- "1173" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1173" Comparing "1081" and "1173". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.828" Parameter: BOX -> "32.828" Parameter: BOX -> "32.828" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.82800 B = 32.82800 C = 32.82800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9028 2 1 -1 0 -1 1.9350 3 1 -1 1 -1 4.9083 4 1 0 -1 -1 4.9063 5 1 0 0 -1 0.9870 6 1 0 1 -1 1.8740 7 1 -1 -1 0 4.7935 8 1 -1 0 0 1.0933 9 1 -1 1 0 1.7166 10 1 0 -1 0 0.8345 11 1 0 1 0 0.8345 12 1 -1 -1 1 5.6065 13 1 -1 0 1 1.7567 14 1 -1 1 1 6.2938 15 1 0 -1 1 1.8740 16 1 0 0 1 0.9870 17 1 0 1 1 4.9063 18 1 1 1 1 5.9028 19 1 1 0 1 1.9350 20 1 1 -1 1 4.9083 21 1 1 1 0 4.7935 22 1 1 0 0 1.0933 23 1 1 -1 0 1.7166 24 1 1 1 -1 5.6065 25 1 1 0 -1 1.7567 26 1 1 -1 -1 6.2938 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3501 atoms have been selected out of 3575 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 108 36 36 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1539 513 513 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1726 573 572 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 99 33 33 0.00 13 C013 has 489 163 163 0.00 14 C014 has 111 37 37 0.99 Total of12831 atoms and 4268 groups and 4262 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3575 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1180 Number of atoms = 3575 Number of groups = 1185 Number of bonds = 3568 Number of angles = 1284 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1182 Number of HB donors = 2342 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1180 Number of atoms = 3575 Number of groups = 1185 Number of bonds = 3568 Number of angles = 1284 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1182 Number of HB donors = 2342 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.826" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1180" Evaluating: 1180-7 Parameter: NUMWAT <- "1173" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1173" Comparing "1081" and "1173". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.826" Parameter: BOX -> "32.826" Parameter: BOX -> "32.826" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.82600 B = 32.82600 C = 32.82600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9015 2 1 -1 0 -1 1.9324 3 1 -1 1 -1 4.9049 4 1 0 -1 -1 4.9068 5 1 0 0 -1 0.9853 6 1 0 1 -1 1.8714 7 1 -1 -1 0 4.7916 8 1 -1 0 0 1.0924 9 1 -1 1 0 1.7144 10 1 0 -1 0 0.8327 11 1 0 1 0 0.8327 12 1 -1 -1 1 5.6037 13 1 -1 0 1 1.7545 14 1 -1 1 1 6.2908 15 1 0 -1 1 1.8714 16 1 0 0 1 0.9853 17 1 0 1 1 4.9068 18 1 1 1 1 5.9015 19 1 1 0 1 1.9324 20 1 1 -1 1 4.9049 21 1 1 1 0 4.7916 22 1 1 0 0 1.0924 23 1 1 -1 0 1.7144 24 1 1 1 -1 5.6037 25 1 1 0 -1 1.7545 26 1 1 -1 -1 6.2908 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3501 atoms have been selected out of 3575 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 108 36 36 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1539 513 513 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1726 573 572 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 99 33 33 0.00 13 C013 has 489 163 163 0.00 14 C014 has 111 37 37 0.99 Total of12831 atoms and 4268 groups and 4262 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3575 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1180 Number of atoms = 3575 Number of groups = 1185 Number of bonds = 3568 Number of angles = 1284 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1182 Number of HB donors = 2342 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1180 Number of atoms = 3575 Number of groups = 1185 Number of bonds = 3568 Number of angles = 1284 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1182 Number of HB donors = 2342 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.824" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1180" Evaluating: 1180-7 Parameter: NUMWAT <- "1173" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1173" Comparing "1081" and "1173". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.824" Parameter: BOX -> "32.824" Parameter: BOX -> "32.824" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.82400 B = 32.82400 C = 32.82400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.9001 2 1 -1 0 -1 1.9298 3 1 -1 1 -1 4.9015 4 1 0 -1 -1 4.9073 5 1 0 0 -1 0.9836 6 1 0 1 -1 1.8688 7 1 -1 -1 0 4.7898 8 1 -1 0 0 1.0914 9 1 -1 1 0 1.7123 10 1 0 -1 0 0.8309 11 1 0 1 0 0.8309 12 1 -1 -1 1 5.6009 13 1 -1 0 1 1.7523 14 1 -1 1 1 6.2878 15 1 0 -1 1 1.8688 16 1 0 0 1 0.9836 17 1 0 1 1 4.9073 18 1 1 1 1 5.9001 19 1 1 0 1 1.9298 20 1 1 -1 1 4.9015 21 1 1 1 0 4.7898 22 1 1 0 0 1.0914 23 1 1 -1 0 1.7123 24 1 1 1 -1 5.6009 25 1 1 0 -1 1.7523 26 1 1 -1 -1 6.2878 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3501 atoms have been selected out of 3575 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 108 36 36 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1539 513 513 0.00 6 C006 has 441 147 147 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1726 573 572 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 99 33 33 0.00 13 C013 has 489 163 163 0.00 14 C014 has 111 37 37 0.98 Total of12834 atoms and 4269 groups and 4263 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3575 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1180 Number of atoms = 3575 Number of groups = 1185 Number of bonds = 3568 Number of angles = 1284 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1182 Number of HB donors = 2342 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1180 Number of atoms = 3575 Number of groups = 1185 Number of bonds = 3568 Number of angles = 1284 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1182 Number of HB donors = 2342 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.822" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1180" Evaluating: 1180-7 Parameter: NUMWAT <- "1173" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1173" Comparing "1081" and "1173". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.822" Parameter: BOX -> "32.822" Parameter: BOX -> "32.822" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.82200 B = 32.82200 C = 32.82200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8988 2 1 -1 0 -1 1.9272 3 1 -1 1 -1 4.8981 4 1 0 -1 -1 4.9079 5 1 0 0 -1 0.9819 6 1 0 1 -1 1.8662 7 1 -1 -1 0 4.7879 8 1 -1 0 0 1.0905 9 1 -1 1 0 1.7101 10 1 0 -1 0 0.8290 11 1 0 1 0 0.8290 12 1 -1 -1 1 5.5981 13 1 -1 0 1 1.7502 14 1 -1 1 1 6.2848 15 1 0 -1 1 1.8662 16 1 0 0 1 0.9819 17 1 0 1 1 4.9079 18 1 1 1 1 5.8988 19 1 1 0 1 1.9272 20 1 1 -1 1 4.8981 21 1 1 1 0 4.7879 22 1 1 0 0 1.0905 23 1 1 -1 0 1.7101 24 1 1 1 -1 5.5981 25 1 1 0 -1 1.7502 26 1 1 -1 -1 6.2848 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3501 atoms have been selected out of 3575 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 108 36 36 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1539 513 513 0.00 6 C006 has 441 147 147 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1726 573 572 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 99 33 33 0.00 13 C013 has 489 163 163 0.00 14 C014 has 111 37 37 0.98 Total of12840 atoms and 4271 groups and 4265 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3575 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1180 Number of atoms = 3575 Number of groups = 1185 Number of bonds = 3568 Number of angles = 1284 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1182 Number of HB donors = 2342 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1180 Number of atoms = 3575 Number of groups = 1185 Number of bonds = 3568 Number of angles = 1284 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1182 Number of HB donors = 2342 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.82" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1180" Evaluating: 1180-7 Parameter: NUMWAT <- "1173" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1173" Comparing "1081" and "1173". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.82" Parameter: BOX -> "32.82" Parameter: BOX -> "32.82" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.82000 B = 32.82000 C = 32.82000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8974 2 1 -1 0 -1 1.9246 3 1 -1 1 -1 4.8946 4 1 0 -1 -1 4.9084 5 1 0 0 -1 0.9802 6 1 0 1 -1 1.8636 7 1 -1 -1 0 4.7860 8 1 -1 0 0 1.0896 9 1 -1 1 0 1.7080 10 1 0 -1 0 0.8272 11 1 0 1 0 0.8272 12 1 -1 -1 1 5.5953 13 1 -1 0 1 1.7480 14 1 -1 1 1 6.2818 15 1 0 -1 1 1.8636 16 1 0 0 1 0.9802 17 1 0 1 1 4.9084 18 1 1 1 1 5.8974 19 1 1 0 1 1.9246 20 1 1 -1 1 4.8946 21 1 1 1 0 4.7860 22 1 1 0 0 1.0896 23 1 1 -1 0 1.7080 24 1 1 1 -1 5.5953 25 1 1 0 -1 1.7480 26 1 1 -1 -1 6.2818 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3501 atoms have been selected out of 3575 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 108 36 36 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1539 513 513 0.00 6 C006 has 441 147 147 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1726 573 572 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 99 33 33 0.00 13 C013 has 489 163 163 0.00 14 C014 has 111 37 37 0.98 Total of12843 atoms and 4272 groups and 4266 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3575 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1180 Number of atoms = 3575 Number of groups = 1185 Number of bonds = 3568 Number of angles = 1284 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1182 Number of HB donors = 2342 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1180 Number of atoms = 3575 Number of groups = 1185 Number of bonds = 3568 Number of angles = 1284 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1182 Number of HB donors = 2342 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.818" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1180" Evaluating: 1180-7 Parameter: NUMWAT <- "1173" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1173" Comparing "1081" and "1173". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.818" Parameter: BOX -> "32.818" Parameter: BOX -> "32.818" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.81800 B = 32.81800 C = 32.81800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8960 2 1 -1 0 -1 1.9220 3 1 -1 1 -1 4.8912 4 1 0 -1 -1 4.9089 5 1 0 0 -1 0.9784 6 1 0 1 -1 1.8610 7 1 -1 -1 0 4.7842 8 1 -1 0 0 1.0887 9 1 -1 1 0 1.7058 10 1 0 -1 0 0.8254 11 1 0 1 0 0.8254 12 1 -1 -1 1 5.5926 13 1 -1 0 1 1.7459 14 1 -1 1 1 6.2789 15 1 0 -1 1 1.8610 16 1 0 0 1 0.9784 17 1 0 1 1 4.9089 18 1 1 1 1 5.8960 19 1 1 0 1 1.9220 20 1 1 -1 1 4.8912 21 1 1 1 0 4.7842 22 1 1 0 0 1.0887 23 1 1 -1 0 1.7058 24 1 1 1 -1 5.5926 25 1 1 0 -1 1.7459 26 1 1 -1 -1 6.2789 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3501 atoms have been selected out of 3575 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 108 36 36 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1539 513 513 0.00 6 C006 has 441 147 147 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1726 573 572 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 99 33 33 0.00 13 C013 has 489 163 163 0.00 14 C014 has 111 37 37 0.98 Total of12843 atoms and 4272 groups and 4266 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3575 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1180 Number of atoms = 3575 Number of groups = 1185 Number of bonds = 3568 Number of angles = 1284 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1182 Number of HB donors = 2342 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1180 Number of atoms = 3575 Number of groups = 1185 Number of bonds = 3568 Number of angles = 1284 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1182 Number of HB donors = 2342 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.816" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1180" Evaluating: 1180-7 Parameter: NUMWAT <- "1173" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1173" Comparing "1081" and "1173". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.816" Parameter: BOX -> "32.816" Parameter: BOX -> "32.816" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.81600 B = 32.81600 C = 32.81600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8947 2 1 -1 0 -1 1.9194 3 1 -1 1 -1 4.8878 4 1 0 -1 -1 4.9095 5 1 0 0 -1 0.9767 6 1 0 1 -1 1.8584 7 1 -1 -1 0 4.7823 8 1 -1 0 0 1.0878 9 1 -1 1 0 1.7036 10 1 0 -1 0 0.8235 11 1 0 1 0 0.8235 12 1 -1 -1 1 5.5898 13 1 -1 0 1 1.7437 14 1 -1 1 1 6.2759 15 1 0 -1 1 1.8584 16 1 0 0 1 0.9767 17 1 0 1 1 4.9095 18 1 1 1 1 5.8947 19 1 1 0 1 1.9194 20 1 1 -1 1 4.8878 21 1 1 1 0 4.7823 22 1 1 0 0 1.0878 23 1 1 -1 0 1.7036 24 1 1 1 -1 5.5898 25 1 1 0 -1 1.7437 26 1 1 -1 -1 6.2759 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3501 atoms have been selected out of 3575 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 108 36 36 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1542 514 514 0.00 6 C006 has 441 147 147 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1726 573 572 0.00 9 C009 has 474 158 158 0.00 10 C010 has 1623 541 541 0.00 12 C012 has 99 33 33 0.00 13 C013 has 489 163 163 0.00 14 C014 has 111 37 37 0.98 Total of12846 atoms and 4273 groups and 4267 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3575 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1180 Number of atoms = 3575 Number of groups = 1185 Number of bonds = 3568 Number of angles = 1284 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1182 Number of HB donors = 2342 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1180 Number of atoms = 3575 Number of groups = 1185 Number of bonds = 3568 Number of angles = 1284 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1182 Number of HB donors = 2342 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.814" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1180" Evaluating: 1180-7 Parameter: NUMWAT <- "1173" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1173" Comparing "1081" and "1173". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.814" Parameter: BOX -> "32.814" Parameter: BOX -> "32.814" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.81400 B = 32.81400 C = 32.81400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8933 2 1 -1 0 -1 1.9168 3 1 -1 1 -1 4.8844 4 1 0 -1 -1 4.9100 5 1 0 0 -1 0.9750 6 1 0 1 -1 1.8558 7 1 -1 -1 0 4.7805 8 1 -1 0 0 1.0869 9 1 -1 1 0 1.7015 10 1 0 -1 0 0.8217 11 1 0 1 0 0.8217 12 1 -1 -1 1 5.5870 13 1 -1 0 1 1.7416 14 1 -1 1 1 6.2729 15 1 0 -1 1 1.8558 16 1 0 0 1 0.9750 17 1 0 1 1 4.9100 18 1 1 1 1 5.8933 19 1 1 0 1 1.9168 20 1 1 -1 1 4.8844 21 1 1 1 0 4.7805 22 1 1 0 0 1.0869 23 1 1 -1 0 1.7015 24 1 1 1 -1 5.5870 25 1 1 0 -1 1.7416 26 1 1 -1 -1 6.2729 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3501 atoms have been selected out of 3575 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 364 OPERATED ON BY TRANSFORMATION C010 RESIDUE 492 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 108 36 36 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1542 514 514 0.00 6 C006 has 441 147 147 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1726 573 572 0.00 9 C009 has 453 151 151 0.00 10 C010 has 1617 539 539 0.00 12 C012 has 96 32 32 0.00 13 C013 has 489 163 163 0.00 14 C014 has 114 38 38 0.97 Total of12816 atoms and 4263 groups and 4257 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3575 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1178 Number of atoms = 3569 Number of groups = 1183 Number of bonds = 3562 Number of angles = 1282 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2338 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1178 Number of atoms = 3569 Number of groups = 1183 Number of bonds = 3562 Number of angles = 1282 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2338 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.812" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1178" Evaluating: 1178-7 Parameter: NUMWAT <- "1171" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1171" Comparing "1081" and "1171". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.812" Parameter: BOX -> "32.812" Parameter: BOX -> "32.812" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.81200 B = 32.81200 C = 32.81200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8920 2 1 -1 0 -1 1.9143 3 1 -1 1 -1 4.8809 4 1 0 -1 -1 4.9105 5 1 0 0 -1 0.9733 6 1 0 1 -1 1.8532 7 1 -1 -1 0 4.7786 8 1 -1 0 0 1.1232 9 1 -1 1 0 4.6909 10 1 0 -1 0 0.8199 11 1 0 1 0 0.8199 12 1 -1 -1 1 5.5842 13 1 -1 0 1 1.7394 14 1 -1 1 1 6.2699 15 1 0 -1 1 1.8532 16 1 0 0 1 0.9733 17 1 0 1 1 4.9105 18 1 1 1 1 5.8920 19 1 1 0 1 1.9143 20 1 1 -1 1 4.8809 21 1 1 1 0 4.7786 22 1 1 0 0 1.1232 23 1 1 -1 0 4.6909 24 1 1 1 -1 5.5842 25 1 1 0 -1 1.7394 26 1 1 -1 -1 6.2699 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3495 atoms have been selected out of 3569 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 108 36 36 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1542 514 514 0.00 6 C006 has 441 147 147 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1723 572 571 0.00 9 C009 has 450 150 150 0.00 10 C010 has 1617 539 539 0.00 12 C012 has 96 32 32 0.00 13 C013 has 486 162 162 0.00 14 C014 has 111 37 37 0.97 Total of12798 atoms and 4257 groups and 4251 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3569 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1178 Number of atoms = 3569 Number of groups = 1183 Number of bonds = 3562 Number of angles = 1282 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2338 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1178 Number of atoms = 3569 Number of groups = 1183 Number of bonds = 3562 Number of angles = 1282 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2338 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.81" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1178" Evaluating: 1178-7 Parameter: NUMWAT <- "1171" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1171" Comparing "1081" and "1171". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.81" Parameter: BOX -> "32.81" Parameter: BOX -> "32.81" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.81000 B = 32.81000 C = 32.81000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8906 2 1 -1 0 -1 1.9117 3 1 -1 1 -1 4.8775 4 1 0 -1 -1 4.9111 5 1 0 0 -1 0.9716 6 1 0 1 -1 1.8506 7 1 -1 -1 0 4.7768 8 1 -1 0 0 1.1215 9 1 -1 1 0 4.6884 10 1 0 -1 0 0.8181 11 1 0 1 0 0.8181 12 1 -1 -1 1 5.5814 13 1 -1 0 1 1.7373 14 1 -1 1 1 6.2670 15 1 0 -1 1 1.8506 16 1 0 0 1 0.9716 17 1 0 1 1 4.9111 18 1 1 1 1 5.8906 19 1 1 0 1 1.9117 20 1 1 -1 1 4.8775 21 1 1 1 0 4.7768 22 1 1 0 0 1.1215 23 1 1 -1 0 4.6884 24 1 1 1 -1 5.5814 25 1 1 0 -1 1.7373 26 1 1 -1 -1 6.2670 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3495 atoms have been selected out of 3569 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 622 OPERATED ON BY TRANSFORMATION C022 RESIDUE 901 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1044 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 768 256 256 0.00 3 C003 has 108 36 36 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1536 512 512 0.00 6 C006 has 441 147 147 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1717 570 569 0.00 9 C009 has 450 150 150 0.00 10 C010 has 1614 538 538 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.97 Total of12768 atoms and 4247 groups and 4241 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 9 atoms have been selected out of 3569 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 3 residues deleted. DELTIC: 9 bonds deleted DELTIC: 3 angles deleted DELTIC: 6 donors deleted DELTIC: 3 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1175 Number of atoms = 3560 Number of groups = 1180 Number of bonds = 3553 Number of angles = 1279 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1177 Number of HB donors = 2332 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1175 Number of atoms = 3560 Number of groups = 1180 Number of bonds = 3553 Number of angles = 1279 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1177 Number of HB donors = 2332 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.808" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1175" Evaluating: 1175-7 Parameter: NUMWAT <- "1168" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1168" Comparing "1081" and "1168". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.808" Parameter: BOX -> "32.808" Parameter: BOX -> "32.808" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.80800 B = 32.80800 C = 32.80800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8893 2 1 -1 0 -1 1.9091 3 1 -1 1 -1 4.8741 4 1 0 -1 -1 4.9116 5 1 0 0 -1 0.9699 6 1 0 1 -1 1.8480 7 1 -1 -1 0 4.7749 8 1 -1 0 0 1.1199 9 1 -1 1 0 4.6859 10 1 0 -1 0 0.8162 11 1 0 1 0 0.8162 12 1 -1 -1 1 5.5786 13 1 -1 0 1 1.7351 14 1 -1 1 1 6.2640 15 1 0 -1 1 1.8480 16 1 0 0 1 0.9699 17 1 0 1 1 4.9116 18 1 1 1 1 5.8893 19 1 1 0 1 1.9091 20 1 1 -1 1 4.8741 21 1 1 1 0 4.7749 22 1 1 0 0 1.1199 23 1 1 -1 0 4.6859 24 1 1 1 -1 5.5786 25 1 1 0 -1 1.7351 26 1 1 -1 -1 6.2640 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3486 atoms have been selected out of 3560 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 756 252 252 0.00 3 C003 has 108 36 36 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1533 511 511 0.00 6 C006 has 441 147 147 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1711 568 567 0.00 9 C009 has 450 150 150 0.00 10 C010 has 1611 537 537 0.00 12 C012 has 96 32 32 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.97 Total of12726 atoms and 4233 groups and 4227 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3560 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1175 Number of atoms = 3560 Number of groups = 1180 Number of bonds = 3553 Number of angles = 1279 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1177 Number of HB donors = 2332 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1175 Number of atoms = 3560 Number of groups = 1180 Number of bonds = 3553 Number of angles = 1279 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1177 Number of HB donors = 2332 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.806" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1175" Evaluating: 1175-7 Parameter: NUMWAT <- "1168" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1168" Comparing "1081" and "1168". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.806" Parameter: BOX -> "32.806" Parameter: BOX -> "32.806" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.80600 B = 32.80600 C = 32.80600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8879 2 1 -1 0 -1 1.9065 3 1 -1 1 -1 4.8707 4 1 0 -1 -1 4.9122 5 1 0 0 -1 0.9682 6 1 0 1 -1 1.8454 7 1 -1 -1 0 4.7731 8 1 -1 0 0 1.1182 9 1 -1 1 0 4.6834 10 1 0 -1 0 0.8144 11 1 0 1 0 0.8144 12 1 -1 -1 1 5.5758 13 1 -1 0 1 1.7330 14 1 -1 1 1 6.2610 15 1 0 -1 1 1.8454 16 1 0 0 1 0.9682 17 1 0 1 1 4.9122 18 1 1 1 1 5.8879 19 1 1 0 1 1.9065 20 1 1 -1 1 4.8707 21 1 1 1 0 4.7731 22 1 1 0 0 1.1182 23 1 1 -1 0 4.6834 24 1 1 1 -1 5.5758 25 1 1 0 -1 1.7330 26 1 1 -1 -1 6.2610 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3486 atoms have been selected out of 3560 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 756 252 252 0.00 3 C003 has 108 36 36 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1533 511 511 0.00 6 C006 has 441 147 147 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1711 568 567 0.00 9 C009 has 450 150 150 0.00 10 C010 has 1611 537 537 0.00 12 C012 has 96 32 32 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.97 Total of12726 atoms and 4233 groups and 4227 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3560 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1175 Number of atoms = 3560 Number of groups = 1180 Number of bonds = 3553 Number of angles = 1279 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1177 Number of HB donors = 2332 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1175 Number of atoms = 3560 Number of groups = 1180 Number of bonds = 3553 Number of angles = 1279 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1177 Number of HB donors = 2332 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.804" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1175" Evaluating: 1175-7 Parameter: NUMWAT <- "1168" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1168" Comparing "1081" and "1168". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.804" Parameter: BOX -> "32.804" Parameter: BOX -> "32.804" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.80400 B = 32.80400 C = 32.80400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8866 2 1 -1 0 -1 1.9039 3 1 -1 1 -1 4.8673 4 1 0 -1 -1 4.9127 5 1 0 0 -1 0.9665 6 1 0 1 -1 1.8428 7 1 -1 -1 0 4.7712 8 1 -1 0 0 1.1166 9 1 -1 1 0 4.6809 10 1 0 -1 0 0.8126 11 1 0 1 0 0.8126 12 1 -1 -1 1 5.5730 13 1 -1 0 1 1.7308 14 1 -1 1 1 6.2580 15 1 0 -1 1 1.8428 16 1 0 0 1 0.9665 17 1 0 1 1 4.9127 18 1 1 1 1 5.8866 19 1 1 0 1 1.9039 20 1 1 -1 1 4.8673 21 1 1 1 0 4.7712 22 1 1 0 0 1.1166 23 1 1 -1 0 4.6809 24 1 1 1 -1 5.5730 25 1 1 0 -1 1.7308 26 1 1 -1 -1 6.2580 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3486 atoms have been selected out of 3560 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 756 252 252 0.00 3 C003 has 108 36 36 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1533 511 511 0.00 6 C006 has 441 147 147 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1711 568 567 0.00 9 C009 has 450 150 150 0.00 10 C010 has 1611 537 537 0.00 12 C012 has 96 32 32 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.96 Total of12726 atoms and 4233 groups and 4227 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3560 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1175 Number of atoms = 3560 Number of groups = 1180 Number of bonds = 3553 Number of angles = 1279 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1177 Number of HB donors = 2332 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1175 Number of atoms = 3560 Number of groups = 1180 Number of bonds = 3553 Number of angles = 1279 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1177 Number of HB donors = 2332 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.802" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1175" Evaluating: 1175-7 Parameter: NUMWAT <- "1168" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1168" Comparing "1081" and "1168". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.802" Parameter: BOX -> "32.802" Parameter: BOX -> "32.802" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.80200 B = 32.80200 C = 32.80200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8852 2 1 -1 0 -1 1.9013 3 1 -1 1 -1 4.8638 4 1 0 -1 -1 4.9133 5 1 0 0 -1 0.9648 6 1 0 1 -1 1.8402 7 1 -1 -1 0 4.7694 8 1 -1 0 0 1.1149 9 1 -1 1 0 4.6785 10 1 0 -1 0 0.8108 11 1 0 1 0 0.8108 12 1 -1 -1 1 5.5703 13 1 -1 0 1 1.7287 14 1 -1 1 1 6.2551 15 1 0 -1 1 1.8402 16 1 0 0 1 0.9648 17 1 0 1 1 4.9133 18 1 1 1 1 5.8852 19 1 1 0 1 1.9013 20 1 1 -1 1 4.8638 21 1 1 1 0 4.7694 22 1 1 0 0 1.1149 23 1 1 -1 0 4.6785 24 1 1 1 -1 5.5703 25 1 1 0 -1 1.7287 26 1 1 -1 -1 6.2551 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3486 atoms have been selected out of 3560 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1533 511 511 0.00 6 C006 has 441 147 147 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1711 568 567 0.00 9 C009 has 450 150 150 0.00 10 C010 has 1611 537 537 0.00 12 C012 has 96 32 32 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.96 Total of12732 atoms and 4235 groups and 4229 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3560 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1175 Number of atoms = 3560 Number of groups = 1180 Number of bonds = 3553 Number of angles = 1279 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1177 Number of HB donors = 2332 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1175 Number of atoms = 3560 Number of groups = 1180 Number of bonds = 3553 Number of angles = 1279 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1177 Number of HB donors = 2332 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.8" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1175" Evaluating: 1175-7 Parameter: NUMWAT <- "1168" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1168" Comparing "1081" and "1168". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.8" Parameter: BOX -> "32.8" Parameter: BOX -> "32.8" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.80000 B = 32.80000 C = 32.80000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8839 2 1 -1 0 -1 1.8987 3 1 -1 1 -1 4.8604 4 1 0 -1 -1 4.9138 5 1 0 0 -1 0.9631 6 1 0 1 -1 1.8376 7 1 -1 -1 0 4.7675 8 1 -1 0 0 1.1133 9 1 -1 1 0 4.6760 10 1 0 -1 0 0.8089 11 1 0 1 0 0.8089 12 1 -1 -1 1 5.5675 13 1 -1 0 1 1.7265 14 1 -1 1 1 6.2521 15 1 0 -1 1 1.8376 16 1 0 0 1 0.9631 17 1 0 1 1 4.9138 18 1 1 1 1 5.8839 19 1 1 0 1 1.8987 20 1 1 -1 1 4.8604 21 1 1 1 0 4.7675 22 1 1 0 0 1.1133 23 1 1 -1 0 4.6760 24 1 1 1 -1 5.5675 25 1 1 0 -1 1.7265 26 1 1 -1 -1 6.2521 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3486 atoms have been selected out of 3560 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1533 511 511 0.00 6 C006 has 441 147 147 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1711 568 567 0.00 9 C009 has 453 151 151 0.00 10 C010 has 1614 538 538 0.00 12 C012 has 96 32 32 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.96 Total of12738 atoms and 4237 groups and 4231 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3560 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1175 Number of atoms = 3560 Number of groups = 1180 Number of bonds = 3553 Number of angles = 1279 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1177 Number of HB donors = 2332 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1175 Number of atoms = 3560 Number of groups = 1180 Number of bonds = 3553 Number of angles = 1279 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1177 Number of HB donors = 2332 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.798" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1175" Evaluating: 1175-7 Parameter: NUMWAT <- "1168" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1168" Comparing "1081" and "1168". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.798" Parameter: BOX -> "32.798" Parameter: BOX -> "32.798" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.79800 B = 32.79800 C = 32.79800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8826 2 1 -1 0 -1 1.8961 3 1 -1 1 -1 4.8570 4 1 0 -1 -1 4.9144 5 1 0 0 -1 0.9614 6 1 0 1 -1 1.8350 7 1 -1 -1 0 4.7657 8 1 -1 0 0 1.1116 9 1 -1 1 0 4.6735 10 1 0 -1 0 0.8071 11 1 0 1 0 0.8071 12 1 -1 -1 1 5.5647 13 1 -1 0 1 1.7244 14 1 -1 1 1 6.2491 15 1 0 -1 1 1.8350 16 1 0 0 1 0.9614 17 1 0 1 1 4.9144 18 1 1 1 1 5.8826 19 1 1 0 1 1.8961 20 1 1 -1 1 4.8570 21 1 1 1 0 4.7657 22 1 1 0 0 1.1116 23 1 1 -1 0 4.6735 24 1 1 1 -1 5.5647 25 1 1 0 -1 1.7244 26 1 1 -1 -1 6.2491 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3486 atoms have been selected out of 3560 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1533 511 511 0.00 6 C006 has 441 147 147 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1714 569 568 0.00 9 C009 has 453 151 151 0.00 10 C010 has 1614 538 538 0.00 12 C012 has 96 32 32 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.96 Total of12741 atoms and 4238 groups and 4232 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3560 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1175 Number of atoms = 3560 Number of groups = 1180 Number of bonds = 3553 Number of angles = 1279 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1177 Number of HB donors = 2332 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1175 Number of atoms = 3560 Number of groups = 1180 Number of bonds = 3553 Number of angles = 1279 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1177 Number of HB donors = 2332 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.796" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1175" Evaluating: 1175-7 Parameter: NUMWAT <- "1168" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1168" Comparing "1081" and "1168". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.796" Parameter: BOX -> "32.796" Parameter: BOX -> "32.796" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.79600 B = 32.79600 C = 32.79600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8812 2 1 -1 0 -1 1.8935 3 1 -1 1 -1 4.8536 4 1 0 -1 -1 4.9149 5 1 0 0 -1 0.9597 6 1 0 1 -1 1.8324 7 1 -1 -1 0 4.7639 8 1 -1 0 0 1.1100 9 1 -1 1 0 4.6710 10 1 0 -1 0 0.8053 11 1 0 1 0 0.8053 12 1 -1 -1 1 5.5619 13 1 -1 0 1 1.7223 14 1 -1 1 1 6.2462 15 1 0 -1 1 1.8324 16 1 0 0 1 0.9597 17 1 0 1 1 4.9149 18 1 1 1 1 5.8812 19 1 1 0 1 1.8935 20 1 1 -1 1 4.8536 21 1 1 1 0 4.7639 22 1 1 0 0 1.1100 23 1 1 -1 0 4.6710 24 1 1 1 -1 5.5619 25 1 1 0 -1 1.7223 26 1 1 -1 -1 6.2462 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3486 atoms have been selected out of 3560 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1533 511 511 0.00 6 C006 has 441 147 147 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1714 569 568 0.00 9 C009 has 453 151 151 0.00 10 C010 has 1614 538 538 0.00 12 C012 has 96 32 32 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.96 Total of12741 atoms and 4238 groups and 4232 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3560 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1175 Number of atoms = 3560 Number of groups = 1180 Number of bonds = 3553 Number of angles = 1279 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1177 Number of HB donors = 2332 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1175 Number of atoms = 3560 Number of groups = 1180 Number of bonds = 3553 Number of angles = 1279 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1177 Number of HB donors = 2332 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.794" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1175" Evaluating: 1175-7 Parameter: NUMWAT <- "1168" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1168" Comparing "1081" and "1168". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.794" Parameter: BOX -> "32.794" Parameter: BOX -> "32.794" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.79400 B = 32.79400 C = 32.79400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8799 2 1 -1 0 -1 1.8910 3 1 -1 1 -1 4.8501 4 1 0 -1 -1 4.9155 5 1 0 0 -1 0.9580 6 1 0 1 -1 1.8298 7 1 -1 -1 0 4.7620 8 1 -1 0 0 1.1083 9 1 -1 1 0 4.6685 10 1 0 -1 0 0.8035 11 1 0 1 0 0.8035 12 1 -1 -1 1 5.5591 13 1 -1 0 1 1.7201 14 1 -1 1 1 6.2432 15 1 0 -1 1 1.8298 16 1 0 0 1 0.9580 17 1 0 1 1 4.9155 18 1 1 1 1 5.8799 19 1 1 0 1 1.8910 20 1 1 -1 1 4.8501 21 1 1 1 0 4.7620 22 1 1 0 0 1.1083 23 1 1 -1 0 4.6685 24 1 1 1 -1 5.5591 25 1 1 0 -1 1.7201 26 1 1 -1 -1 6.2432 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3486 atoms have been selected out of 3560 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1533 511 511 0.00 6 C006 has 444 148 148 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1714 569 568 0.00 9 C009 has 453 151 151 0.00 10 C010 has 1614 538 538 0.00 12 C012 has 96 32 32 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.95 Total of12744 atoms and 4239 groups and 4233 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3560 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1175 Number of atoms = 3560 Number of groups = 1180 Number of bonds = 3553 Number of angles = 1279 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1177 Number of HB donors = 2332 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1175 Number of atoms = 3560 Number of groups = 1180 Number of bonds = 3553 Number of angles = 1279 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1177 Number of HB donors = 2332 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.792" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1175" Evaluating: 1175-7 Parameter: NUMWAT <- "1168" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1168" Comparing "1081" and "1168". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.792" Parameter: BOX -> "32.792" Parameter: BOX -> "32.792" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.79200 B = 32.79200 C = 32.79200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8786 2 1 -1 0 -1 1.8884 3 1 -1 1 -1 4.8467 4 1 0 -1 -1 4.9135 5 1 0 0 -1 0.9563 6 1 0 1 -1 1.8272 7 1 -1 -1 0 4.7602 8 1 -1 0 0 1.1067 9 1 -1 1 0 4.6660 10 1 0 -1 0 0.8017 11 1 0 1 0 0.8017 12 1 -1 -1 1 5.5564 13 1 -1 0 1 1.7180 14 1 -1 1 1 6.2402 15 1 0 -1 1 1.8272 16 1 0 0 1 0.9563 17 1 0 1 1 4.9135 18 1 1 1 1 5.8786 19 1 1 0 1 1.8884 20 1 1 -1 1 4.8467 21 1 1 1 0 4.7602 22 1 1 0 0 1.1067 23 1 1 -1 0 4.6660 24 1 1 1 -1 5.5564 25 1 1 0 -1 1.7180 26 1 1 -1 -1 6.2402 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3486 atoms have been selected out of 3560 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1533 511 511 0.00 6 C006 has 444 148 148 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1714 569 568 0.00 9 C009 has 453 151 151 0.00 10 C010 has 1617 539 539 0.00 12 C012 has 96 32 32 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.95 Total of12747 atoms and 4240 groups and 4234 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3560 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1175 Number of atoms = 3560 Number of groups = 1180 Number of bonds = 3553 Number of angles = 1279 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1177 Number of HB donors = 2332 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1175 Number of atoms = 3560 Number of groups = 1180 Number of bonds = 3553 Number of angles = 1279 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1177 Number of HB donors = 2332 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.79" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1175" Evaluating: 1175-7 Parameter: NUMWAT <- "1168" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1168" Comparing "1081" and "1168". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.79" Parameter: BOX -> "32.79" Parameter: BOX -> "32.79" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.79000 B = 32.79000 C = 32.79000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8772 2 1 -1 0 -1 1.8858 3 1 -1 1 -1 4.8433 4 1 0 -1 -1 4.9116 5 1 0 0 -1 0.9546 6 1 0 1 -1 1.8246 7 1 -1 -1 0 4.7583 8 1 -1 0 0 1.1051 9 1 -1 1 0 4.6636 10 1 0 -1 0 0.7998 11 1 0 1 0 0.7998 12 1 -1 -1 1 5.5536 13 1 -1 0 1 1.7159 14 1 -1 1 1 6.2372 15 1 0 -1 1 1.8246 16 1 0 0 1 0.9546 17 1 0 1 1 4.9116 18 1 1 1 1 5.8772 19 1 1 0 1 1.8858 20 1 1 -1 1 4.8433 21 1 1 1 0 4.7583 22 1 1 0 0 1.1051 23 1 1 -1 0 4.6636 24 1 1 1 -1 5.5536 25 1 1 0 -1 1.7159 26 1 1 -1 -1 6.2372 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3486 atoms have been selected out of 3560 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 917 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1533 511 511 0.00 6 C006 has 447 149 149 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1714 569 568 0.00 9 C009 has 453 151 151 0.00 10 C010 has 1617 539 539 0.00 12 C012 has 96 32 32 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.95 Total of12750 atoms and 4241 groups and 4235 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3560 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1174 Number of atoms = 3557 Number of groups = 1179 Number of bonds = 3550 Number of angles = 1278 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1176 Number of HB donors = 2330 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1174 Number of atoms = 3557 Number of groups = 1179 Number of bonds = 3550 Number of angles = 1278 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1176 Number of HB donors = 2330 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.788" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1174" Evaluating: 1174-7 Parameter: NUMWAT <- "1167" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1167" Comparing "1081" and "1167". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.788" Parameter: BOX -> "32.788" Parameter: BOX -> "32.788" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.78800 B = 32.78800 C = 32.78800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8759 2 1 -1 0 -1 1.8832 3 1 -1 1 -1 4.8399 4 1 0 -1 -1 4.9096 5 1 0 0 -1 0.9529 6 1 0 1 -1 1.8220 7 1 -1 -1 0 4.7565 8 1 -1 0 0 1.1034 9 1 -1 1 0 4.6611 10 1 0 -1 0 0.7980 11 1 0 1 0 0.7980 12 1 -1 -1 1 5.5508 13 1 -1 0 1 1.7138 14 1 -1 1 1 6.2343 15 1 0 -1 1 1.8220 16 1 0 0 1 0.9529 17 1 0 1 1 4.9096 18 1 1 1 1 5.8759 19 1 1 0 1 1.8832 20 1 1 -1 1 4.8399 21 1 1 1 0 4.7565 22 1 1 0 0 1.1034 23 1 1 -1 0 4.6611 24 1 1 1 -1 5.5508 25 1 1 0 -1 1.7138 26 1 1 -1 -1 6.2343 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3483 atoms have been selected out of 3557 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1530 510 510 0.00 6 C006 has 447 149 149 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1714 569 568 0.00 9 C009 has 453 151 151 0.00 10 C010 has 1614 538 538 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.95 Total of12741 atoms and 4238 groups and 4232 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3557 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1174 Number of atoms = 3557 Number of groups = 1179 Number of bonds = 3550 Number of angles = 1278 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1176 Number of HB donors = 2330 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1174 Number of atoms = 3557 Number of groups = 1179 Number of bonds = 3550 Number of angles = 1278 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1176 Number of HB donors = 2330 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.786" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1174" Evaluating: 1174-7 Parameter: NUMWAT <- "1167" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1167" Comparing "1081" and "1167". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.786" Parameter: BOX -> "32.786" Parameter: BOX -> "32.786" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.78600 B = 32.78600 C = 32.78600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8746 2 1 -1 0 -1 1.8806 3 1 -1 1 -1 4.8364 4 1 0 -1 -1 4.9077 5 1 0 0 -1 0.9512 6 1 0 1 -1 1.8194 7 1 -1 -1 0 4.7546 8 1 -1 0 0 1.1018 9 1 -1 1 0 4.6586 10 1 0 -1 0 0.7962 11 1 0 1 0 0.7962 12 1 -1 -1 1 5.5480 13 1 -1 0 1 1.7116 14 1 -1 1 1 6.2313 15 1 0 -1 1 1.8194 16 1 0 0 1 0.9512 17 1 0 1 1 4.9077 18 1 1 1 1 5.8746 19 1 1 0 1 1.8806 20 1 1 -1 1 4.8364 21 1 1 1 0 4.7546 22 1 1 0 0 1.1018 23 1 1 -1 0 4.6586 24 1 1 1 -1 5.5480 25 1 1 0 -1 1.7116 26 1 1 -1 -1 6.2313 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3483 atoms have been selected out of 3557 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1530 510 510 0.00 6 C006 has 447 149 149 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1714 569 568 0.00 9 C009 has 453 151 151 0.00 10 C010 has 1614 538 538 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.95 Total of12741 atoms and 4238 groups and 4232 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3557 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1174 Number of atoms = 3557 Number of groups = 1179 Number of bonds = 3550 Number of angles = 1278 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1176 Number of HB donors = 2330 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1174 Number of atoms = 3557 Number of groups = 1179 Number of bonds = 3550 Number of angles = 1278 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1176 Number of HB donors = 2330 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.784" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1174" Evaluating: 1174-7 Parameter: NUMWAT <- "1167" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1167" Comparing "1081" and "1167". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.784" Parameter: BOX -> "32.784" Parameter: BOX -> "32.784" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.78400 B = 32.78400 C = 32.78400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8732 2 1 -1 0 -1 1.8780 3 1 -1 1 -1 4.8330 4 1 0 -1 -1 4.9057 5 1 0 0 -1 0.9495 6 1 0 1 -1 1.8168 7 1 -1 -1 0 4.7528 8 1 -1 0 0 1.1002 9 1 -1 1 0 4.6561 10 1 0 -1 0 0.7944 11 1 0 1 0 0.7944 12 1 -1 -1 1 5.5452 13 1 -1 0 1 1.7095 14 1 -1 1 1 6.2283 15 1 0 -1 1 1.8168 16 1 0 0 1 0.9495 17 1 0 1 1 4.9057 18 1 1 1 1 5.8732 19 1 1 0 1 1.8780 20 1 1 -1 1 4.8330 21 1 1 1 0 4.7528 22 1 1 0 0 1.1002 23 1 1 -1 0 4.6561 24 1 1 1 -1 5.5452 25 1 1 0 -1 1.7095 26 1 1 -1 -1 6.2283 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3483 atoms have been selected out of 3557 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1530 510 510 0.00 6 C006 has 447 149 149 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1714 569 568 0.00 9 C009 has 453 151 151 0.00 10 C010 has 1614 538 538 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.94 Total of12741 atoms and 4238 groups and 4232 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3557 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1174 Number of atoms = 3557 Number of groups = 1179 Number of bonds = 3550 Number of angles = 1278 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1176 Number of HB donors = 2330 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1174 Number of atoms = 3557 Number of groups = 1179 Number of bonds = 3550 Number of angles = 1278 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1176 Number of HB donors = 2330 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.782" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1174" Evaluating: 1174-7 Parameter: NUMWAT <- "1167" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1167" Comparing "1081" and "1167". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.782" Parameter: BOX -> "32.782" Parameter: BOX -> "32.782" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.78200 B = 32.78200 C = 32.78200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8719 2 1 -1 0 -1 1.8754 3 1 -1 1 -1 4.8296 4 1 0 -1 -1 4.9038 5 1 0 0 -1 0.9478 6 1 0 1 -1 1.8142 7 1 -1 -1 0 4.7510 8 1 -1 0 0 1.0985 9 1 -1 1 0 4.6536 10 1 0 -1 0 0.7926 11 1 0 1 0 0.7926 12 1 -1 -1 1 5.5425 13 1 -1 0 1 1.7074 14 1 -1 1 1 6.2254 15 1 0 -1 1 1.8142 16 1 0 0 1 0.9478 17 1 0 1 1 4.9038 18 1 1 1 1 5.8719 19 1 1 0 1 1.8754 20 1 1 -1 1 4.8296 21 1 1 1 0 4.7510 22 1 1 0 0 1.0985 23 1 1 -1 0 4.6536 24 1 1 1 -1 5.5425 25 1 1 0 -1 1.7074 26 1 1 -1 -1 6.2254 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3483 atoms have been selected out of 3557 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1530 510 510 0.00 6 C006 has 447 149 149 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1714 569 568 0.00 9 C009 has 453 151 151 0.00 10 C010 has 1614 538 538 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.94 Total of12744 atoms and 4239 groups and 4233 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3557 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1174 Number of atoms = 3557 Number of groups = 1179 Number of bonds = 3550 Number of angles = 1278 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1176 Number of HB donors = 2330 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1174 Number of atoms = 3557 Number of groups = 1179 Number of bonds = 3550 Number of angles = 1278 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1176 Number of HB donors = 2330 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.78" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1174" Evaluating: 1174-7 Parameter: NUMWAT <- "1167" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1167" Comparing "1081" and "1167". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.78" Parameter: BOX -> "32.78" Parameter: BOX -> "32.78" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.78000 B = 32.78000 C = 32.78000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8706 2 1 -1 0 -1 1.8729 3 1 -1 1 -1 4.8262 4 1 0 -1 -1 4.9018 5 1 0 0 -1 0.9461 6 1 0 1 -1 1.8116 7 1 -1 -1 0 4.7491 8 1 -1 0 0 1.0969 9 1 -1 1 0 4.6512 10 1 0 -1 0 0.7908 11 1 0 1 0 0.7908 12 1 -1 -1 1 5.5397 13 1 -1 0 1 1.7053 14 1 -1 1 1 6.2224 15 1 0 -1 1 1.8116 16 1 0 0 1 0.9461 17 1 0 1 1 4.9018 18 1 1 1 1 5.8706 19 1 1 0 1 1.8729 20 1 1 -1 1 4.8262 21 1 1 1 0 4.7491 22 1 1 0 0 1.0969 23 1 1 -1 0 4.6512 24 1 1 1 -1 5.5397 25 1 1 0 -1 1.7053 26 1 1 -1 -1 6.2224 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3483 atoms have been selected out of 3557 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 957 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1530 510 510 0.00 6 C006 has 450 150 150 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1714 569 568 0.00 9 C009 has 453 151 151 0.00 10 C010 has 1614 538 538 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.94 Total of12747 atoms and 4240 groups and 4234 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3557 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1173 Number of atoms = 3554 Number of groups = 1178 Number of bonds = 3547 Number of angles = 1277 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1175 Number of HB donors = 2328 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1173 Number of atoms = 3554 Number of groups = 1178 Number of bonds = 3547 Number of angles = 1277 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1175 Number of HB donors = 2328 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.778" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1173" Evaluating: 1173-7 Parameter: NUMWAT <- "1166" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1166" Comparing "1081" and "1166". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.778" Parameter: BOX -> "32.778" Parameter: BOX -> "32.778" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.77800 B = 32.77800 C = 32.77800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8693 2 1 -1 0 -1 1.8703 3 1 -1 1 -1 4.8227 4 1 0 -1 -1 4.8999 5 1 0 0 -1 0.9444 6 1 0 1 -1 1.8090 7 1 -1 -1 0 4.7473 8 1 -1 0 0 1.0953 9 1 -1 1 0 4.6487 10 1 0 -1 0 0.7889 11 1 0 1 0 0.7889 12 1 -1 -1 1 5.5369 13 1 -1 0 1 1.7032 14 1 -1 1 1 6.2194 15 1 0 -1 1 1.8090 16 1 0 0 1 0.9444 17 1 0 1 1 4.8999 18 1 1 1 1 5.8693 19 1 1 0 1 1.8703 20 1 1 -1 1 4.8227 21 1 1 1 0 4.7473 22 1 1 0 0 1.0953 23 1 1 -1 0 4.6487 24 1 1 1 -1 5.5369 25 1 1 0 -1 1.7032 26 1 1 -1 -1 6.2194 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3480 atoms have been selected out of 3554 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1527 509 509 0.00 6 C006 has 447 149 149 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1714 569 568 0.00 9 C009 has 453 151 151 0.00 10 C010 has 1611 537 537 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.94 Total of12732 atoms and 4235 groups and 4229 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3554 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1173 Number of atoms = 3554 Number of groups = 1178 Number of bonds = 3547 Number of angles = 1277 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1175 Number of HB donors = 2328 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1173 Number of atoms = 3554 Number of groups = 1178 Number of bonds = 3547 Number of angles = 1277 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1175 Number of HB donors = 2328 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.776" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1173" Evaluating: 1173-7 Parameter: NUMWAT <- "1166" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1166" Comparing "1081" and "1166". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.776" Parameter: BOX -> "32.776" Parameter: BOX -> "32.776" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.77600 B = 32.77600 C = 32.77600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8679 2 1 -1 0 -1 1.8677 3 1 -1 1 -1 4.8193 4 1 0 -1 -1 4.8979 5 1 0 0 -1 0.9427 6 1 0 1 -1 1.8064 7 1 -1 -1 0 4.7455 8 1 -1 0 0 1.0936 9 1 -1 1 0 4.6462 10 1 0 -1 0 0.7871 11 1 0 1 0 0.7871 12 1 -1 -1 1 5.5341 13 1 -1 0 1 1.7011 14 1 -1 1 1 6.2165 15 1 0 -1 1 1.8064 16 1 0 0 1 0.9427 17 1 0 1 1 4.8979 18 1 1 1 1 5.8679 19 1 1 0 1 1.8677 20 1 1 -1 1 4.8193 21 1 1 1 0 4.7455 22 1 1 0 0 1.0936 23 1 1 -1 0 4.6462 24 1 1 1 -1 5.5341 25 1 1 0 -1 1.7011 26 1 1 -1 -1 6.2165 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3480 atoms have been selected out of 3554 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1527 509 509 0.00 6 C006 has 447 149 149 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1714 569 568 0.00 9 C009 has 453 151 151 0.00 10 C010 has 1611 537 537 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.94 Total of12732 atoms and 4235 groups and 4229 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3554 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1173 Number of atoms = 3554 Number of groups = 1178 Number of bonds = 3547 Number of angles = 1277 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1175 Number of HB donors = 2328 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1173 Number of atoms = 3554 Number of groups = 1178 Number of bonds = 3547 Number of angles = 1277 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1175 Number of HB donors = 2328 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.774" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1173" Evaluating: 1173-7 Parameter: NUMWAT <- "1166" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1166" Comparing "1081" and "1166". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.774" Parameter: BOX -> "32.774" Parameter: BOX -> "32.774" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.77400 B = 32.77400 C = 32.77400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8666 2 1 -1 0 -1 1.8651 3 1 -1 1 -1 4.8159 4 1 0 -1 -1 4.8960 5 1 0 0 -1 0.9410 6 1 0 1 -1 1.8039 7 1 -1 -1 0 4.7436 8 1 -1 0 0 1.0920 9 1 -1 1 0 4.6437 10 1 0 -1 0 0.7853 11 1 0 1 0 0.7853 12 1 -1 -1 1 5.5314 13 1 -1 0 1 1.6989 14 1 -1 1 1 6.2135 15 1 0 -1 1 1.8039 16 1 0 0 1 0.9410 17 1 0 1 1 4.8960 18 1 1 1 1 5.8666 19 1 1 0 1 1.8651 20 1 1 -1 1 4.8159 21 1 1 1 0 4.7436 22 1 1 0 0 1.0920 23 1 1 -1 0 4.6437 24 1 1 1 -1 5.5314 25 1 1 0 -1 1.6989 26 1 1 -1 -1 6.2135 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3480 atoms have been selected out of 3554 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1527 509 509 0.00 6 C006 has 447 149 149 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1714 569 568 0.00 9 C009 has 456 152 152 0.00 10 C010 has 1611 537 537 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.93 Total of12735 atoms and 4236 groups and 4230 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3554 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1173 Number of atoms = 3554 Number of groups = 1178 Number of bonds = 3547 Number of angles = 1277 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1175 Number of HB donors = 2328 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1173 Number of atoms = 3554 Number of groups = 1178 Number of bonds = 3547 Number of angles = 1277 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1175 Number of HB donors = 2328 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.772" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1173" Evaluating: 1173-7 Parameter: NUMWAT <- "1166" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1166" Comparing "1081" and "1166". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.772" Parameter: BOX -> "32.772" Parameter: BOX -> "32.772" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.77200 B = 32.77200 C = 32.77200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8653 2 1 -1 0 -1 1.8626 3 1 -1 1 -1 4.8125 4 1 0 -1 -1 4.8940 5 1 0 0 -1 0.9394 6 1 0 1 -1 1.8013 7 1 -1 -1 0 4.7418 8 1 -1 0 0 1.0904 9 1 -1 1 0 4.6412 10 1 0 -1 0 0.7835 11 1 0 1 0 0.7835 12 1 -1 -1 1 5.5286 13 1 -1 0 1 1.6968 14 1 -1 1 1 6.2105 15 1 0 -1 1 1.8013 16 1 0 0 1 0.9394 17 1 0 1 1 4.8940 18 1 1 1 1 5.8653 19 1 1 0 1 1.8626 20 1 1 -1 1 4.8125 21 1 1 1 0 4.7418 22 1 1 0 0 1.0904 23 1 1 -1 0 4.6412 24 1 1 1 -1 5.5286 25 1 1 0 -1 1.6968 26 1 1 -1 -1 6.2105 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3480 atoms have been selected out of 3554 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1527 509 509 0.00 6 C006 has 447 149 149 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1714 569 568 0.00 9 C009 has 456 152 152 0.00 10 C010 has 1611 537 537 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.93 Total of12735 atoms and 4236 groups and 4230 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3554 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1173 Number of atoms = 3554 Number of groups = 1178 Number of bonds = 3547 Number of angles = 1277 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1175 Number of HB donors = 2328 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1173 Number of atoms = 3554 Number of groups = 1178 Number of bonds = 3547 Number of angles = 1277 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1175 Number of HB donors = 2328 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.77" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1173" Evaluating: 1173-7 Parameter: NUMWAT <- "1166" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1166" Comparing "1081" and "1166". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.77" Parameter: BOX -> "32.77" Parameter: BOX -> "32.77" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.77000 B = 32.77000 C = 32.77000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8640 2 1 -1 0 -1 1.8600 3 1 -1 1 -1 4.8091 4 1 0 -1 -1 4.8921 5 1 0 0 -1 0.9377 6 1 0 1 -1 1.7987 7 1 -1 -1 0 4.7400 8 1 -1 0 0 1.0887 9 1 -1 1 0 4.6388 10 1 0 -1 0 0.7817 11 1 0 1 0 0.7817 12 1 -1 -1 1 5.5258 13 1 -1 0 1 1.6947 14 1 -1 1 1 6.2076 15 1 0 -1 1 1.7987 16 1 0 0 1 0.9377 17 1 0 1 1 4.8921 18 1 1 1 1 5.8640 19 1 1 0 1 1.8600 20 1 1 -1 1 4.8091 21 1 1 1 0 4.7400 22 1 1 0 0 1.0887 23 1 1 -1 0 4.6388 24 1 1 1 -1 5.5258 25 1 1 0 -1 1.6947 26 1 1 -1 -1 6.2076 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3480 atoms have been selected out of 3554 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1527 509 509 0.00 6 C006 has 450 150 150 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1717 570 569 0.00 9 C009 has 456 152 152 0.00 10 C010 has 1611 537 537 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.93 Total of12741 atoms and 4238 groups and 4232 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3554 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1173 Number of atoms = 3554 Number of groups = 1178 Number of bonds = 3547 Number of angles = 1277 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1175 Number of HB donors = 2328 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1173 Number of atoms = 3554 Number of groups = 1178 Number of bonds = 3547 Number of angles = 1277 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1175 Number of HB donors = 2328 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.768" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1173" Evaluating: 1173-7 Parameter: NUMWAT <- "1166" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1166" Comparing "1081" and "1166". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.768" Parameter: BOX -> "32.768" Parameter: BOX -> "32.768" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.76800 B = 32.76800 C = 32.76800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8627 2 1 -1 0 -1 1.8574 3 1 -1 1 -1 4.8056 4 1 0 -1 -1 4.8901 5 1 0 0 -1 0.9360 6 1 0 1 -1 1.7961 7 1 -1 -1 0 4.7381 8 1 -1 0 0 1.0871 9 1 -1 1 0 4.6363 10 1 0 -1 0 0.7799 11 1 0 1 0 0.7799 12 1 -1 -1 1 5.5231 13 1 -1 0 1 1.6926 14 1 -1 1 1 6.2046 15 1 0 -1 1 1.7961 16 1 0 0 1 0.9360 17 1 0 1 1 4.8901 18 1 1 1 1 5.8627 19 1 1 0 1 1.8574 20 1 1 -1 1 4.8056 21 1 1 1 0 4.7381 22 1 1 0 0 1.0871 23 1 1 -1 0 4.6363 24 1 1 1 -1 5.5231 25 1 1 0 -1 1.6926 26 1 1 -1 -1 6.2046 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3480 atoms have been selected out of 3554 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1530 510 510 0.00 6 C006 has 450 150 150 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1717 570 569 0.00 9 C009 has 456 152 152 0.00 10 C010 has 1611 537 537 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.93 Total of12744 atoms and 4239 groups and 4233 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3554 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1173 Number of atoms = 3554 Number of groups = 1178 Number of bonds = 3547 Number of angles = 1277 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1175 Number of HB donors = 2328 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1173 Number of atoms = 3554 Number of groups = 1178 Number of bonds = 3547 Number of angles = 1277 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1175 Number of HB donors = 2328 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.766" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1173" Evaluating: 1173-7 Parameter: NUMWAT <- "1166" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1166" Comparing "1081" and "1166". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.766" Parameter: BOX -> "32.766" Parameter: BOX -> "32.766" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.76600 B = 32.76600 C = 32.76600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8614 2 1 -1 0 -1 1.8548 3 1 -1 1 -1 4.8022 4 1 0 -1 -1 4.8882 5 1 0 0 -1 0.9343 6 1 0 1 -1 1.7935 7 1 -1 -1 0 4.7363 8 1 -1 0 0 1.0855 9 1 -1 1 0 4.6338 10 1 0 -1 0 0.7781 11 1 0 1 0 0.7781 12 1 -1 -1 1 5.5203 13 1 -1 0 1 1.6905 14 1 -1 1 1 6.2016 15 1 0 -1 1 1.7935 16 1 0 0 1 0.9343 17 1 0 1 1 4.8882 18 1 1 1 1 5.8614 19 1 1 0 1 1.8548 20 1 1 -1 1 4.8022 21 1 1 1 0 4.7363 22 1 1 0 0 1.0855 23 1 1 -1 0 4.6338 24 1 1 1 -1 5.5203 25 1 1 0 -1 1.6905 26 1 1 -1 -1 6.2016 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3480 atoms have been selected out of 3554 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1530 510 510 0.00 6 C006 has 450 150 150 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1717 570 569 0.00 9 C009 has 456 152 152 0.00 10 C010 has 1614 538 538 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.93 Total of12747 atoms and 4240 groups and 4234 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3554 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1173 Number of atoms = 3554 Number of groups = 1178 Number of bonds = 3547 Number of angles = 1277 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1175 Number of HB donors = 2328 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1173 Number of atoms = 3554 Number of groups = 1178 Number of bonds = 3547 Number of angles = 1277 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1175 Number of HB donors = 2328 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.764" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1173" Evaluating: 1173-7 Parameter: NUMWAT <- "1166" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1166" Comparing "1081" and "1166". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.764" Parameter: BOX -> "32.764" Parameter: BOX -> "32.764" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.76400 B = 32.76400 C = 32.76400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8601 2 1 -1 0 -1 1.8522 3 1 -1 1 -1 4.7988 4 1 0 -1 -1 4.8863 5 1 0 0 -1 0.9326 6 1 0 1 -1 1.7909 7 1 -1 -1 0 4.7345 8 1 -1 0 0 1.0839 9 1 -1 1 0 4.6313 10 1 0 -1 0 0.7763 11 1 0 1 0 0.7763 12 1 -1 -1 1 5.5175 13 1 -1 0 1 1.6884 14 1 -1 1 1 6.1987 15 1 0 -1 1 1.7909 16 1 0 0 1 0.9326 17 1 0 1 1 4.8863 18 1 1 1 1 5.8601 19 1 1 0 1 1.8522 20 1 1 -1 1 4.7988 21 1 1 1 0 4.7345 22 1 1 0 0 1.0839 23 1 1 -1 0 4.6313 24 1 1 1 -1 5.5175 25 1 1 0 -1 1.6884 26 1 1 -1 -1 6.1987 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3480 atoms have been selected out of 3554 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1530 510 510 0.00 6 C006 has 450 150 150 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1717 570 569 0.00 9 C009 has 456 152 152 0.00 10 C010 has 1614 538 538 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.92 Total of12750 atoms and 4241 groups and 4235 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3554 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1173 Number of atoms = 3554 Number of groups = 1178 Number of bonds = 3547 Number of angles = 1277 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1175 Number of HB donors = 2328 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1173 Number of atoms = 3554 Number of groups = 1178 Number of bonds = 3547 Number of angles = 1277 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1175 Number of HB donors = 2328 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.762" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1173" Evaluating: 1173-7 Parameter: NUMWAT <- "1166" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1166" Comparing "1081" and "1166". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.762" Parameter: BOX -> "32.762" Parameter: BOX -> "32.762" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.76200 B = 32.76200 C = 32.76200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8588 2 1 -1 0 -1 1.8497 3 1 -1 1 -1 4.7954 4 1 0 -1 -1 4.8843 5 1 0 0 -1 0.9309 6 1 0 1 -1 1.7883 7 1 -1 -1 0 4.7326 8 1 -1 0 0 1.0822 9 1 -1 1 0 4.6289 10 1 0 -1 0 0.7745 11 1 0 1 0 0.7745 12 1 -1 -1 1 5.5147 13 1 -1 0 1 1.6863 14 1 -1 1 1 6.1957 15 1 0 -1 1 1.7883 16 1 0 0 1 0.9309 17 1 0 1 1 4.8843 18 1 1 1 1 5.8588 19 1 1 0 1 1.8497 20 1 1 -1 1 4.7954 21 1 1 1 0 4.7326 22 1 1 0 0 1.0822 23 1 1 -1 0 4.6289 24 1 1 1 -1 5.5147 25 1 1 0 -1 1.6863 26 1 1 -1 -1 6.1957 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3480 atoms have been selected out of 3554 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1530 510 510 0.00 6 C006 has 450 150 150 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1717 570 569 0.00 9 C009 has 456 152 152 0.00 10 C010 has 1614 538 538 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.92 Total of12750 atoms and 4241 groups and 4235 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3554 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1173 Number of atoms = 3554 Number of groups = 1178 Number of bonds = 3547 Number of angles = 1277 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1175 Number of HB donors = 2328 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1173 Number of atoms = 3554 Number of groups = 1178 Number of bonds = 3547 Number of angles = 1277 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1175 Number of HB donors = 2328 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.76" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1173" Evaluating: 1173-7 Parameter: NUMWAT <- "1166" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1166" Comparing "1081" and "1166". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.76" Parameter: BOX -> "32.76" Parameter: BOX -> "32.76" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.76000 B = 32.76000 C = 32.76000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8575 2 1 -1 0 -1 1.8471 3 1 -1 1 -1 4.7919 4 1 0 -1 -1 4.8824 5 1 0 0 -1 0.9293 6 1 0 1 -1 1.7858 7 1 -1 -1 0 4.7308 8 1 -1 0 0 1.0806 9 1 -1 1 0 4.6264 10 1 0 -1 0 0.7727 11 1 0 1 0 0.7727 12 1 -1 -1 1 5.5120 13 1 -1 0 1 1.6842 14 1 -1 1 1 6.1928 15 1 0 -1 1 1.7858 16 1 0 0 1 0.9293 17 1 0 1 1 4.8824 18 1 1 1 1 5.8575 19 1 1 0 1 1.8471 20 1 1 -1 1 4.7919 21 1 1 1 0 4.7308 22 1 1 0 0 1.0806 23 1 1 -1 0 4.6264 24 1 1 1 -1 5.5120 25 1 1 0 -1 1.6842 26 1 1 -1 -1 6.1928 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3480 atoms have been selected out of 3554 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1530 510 510 0.00 6 C006 has 450 150 150 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1717 570 569 0.00 9 C009 has 456 152 152 0.00 10 C010 has 1614 538 538 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.92 Total of12750 atoms and 4241 groups and 4235 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3554 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1173 Number of atoms = 3554 Number of groups = 1178 Number of bonds = 3547 Number of angles = 1277 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1175 Number of HB donors = 2328 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1173 Number of atoms = 3554 Number of groups = 1178 Number of bonds = 3547 Number of angles = 1277 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1175 Number of HB donors = 2328 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.758" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1173" Evaluating: 1173-7 Parameter: NUMWAT <- "1166" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1166" Comparing "1081" and "1166". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.758" Parameter: BOX -> "32.758" Parameter: BOX -> "32.758" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.75800 B = 32.75800 C = 32.75800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8561 2 1 -1 0 -1 1.8445 3 1 -1 1 -1 4.7885 4 1 0 -1 -1 4.8804 5 1 0 0 -1 0.9276 6 1 0 1 -1 1.7832 7 1 -1 -1 0 4.7290 8 1 -1 0 0 1.0790 9 1 -1 1 0 4.6239 10 1 0 -1 0 0.7709 11 1 0 1 0 0.7709 12 1 -1 -1 1 5.5092 13 1 -1 0 1 1.6821 14 1 -1 1 1 6.1898 15 1 0 -1 1 1.7832 16 1 0 0 1 0.9276 17 1 0 1 1 4.8804 18 1 1 1 1 5.8561 19 1 1 0 1 1.8445 20 1 1 -1 1 4.7885 21 1 1 1 0 4.7290 22 1 1 0 0 1.0790 23 1 1 -1 0 4.6239 24 1 1 1 -1 5.5092 25 1 1 0 -1 1.6821 26 1 1 -1 -1 6.1898 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3480 atoms have been selected out of 3554 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 272 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1530 510 510 0.00 6 C006 has 450 150 150 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1717 570 569 0.00 9 C009 has 453 151 151 0.00 10 C010 has 1617 539 539 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.92 Total of12750 atoms and 4241 groups and 4235 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3554 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1172 Number of atoms = 3551 Number of groups = 1177 Number of bonds = 3544 Number of angles = 1276 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1174 Number of HB donors = 2326 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1172 Number of atoms = 3551 Number of groups = 1177 Number of bonds = 3544 Number of angles = 1276 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1174 Number of HB donors = 2326 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.756" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1172" Evaluating: 1172-7 Parameter: NUMWAT <- "1165" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1165" Comparing "1081" and "1165". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.756" Parameter: BOX -> "32.756" Parameter: BOX -> "32.756" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.75600 B = 32.75600 C = 32.75600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8548 2 1 -1 0 -1 1.8420 3 1 -1 1 -1 4.7851 4 1 0 -1 -1 4.8785 5 1 0 0 -1 0.9259 6 1 0 1 -1 1.7806 7 1 -1 -1 0 4.7272 8 1 -1 0 0 1.0774 9 1 -1 1 0 4.6214 10 1 0 -1 0 0.7691 11 1 0 1 0 0.7691 12 1 -1 -1 1 5.5064 13 1 -1 0 1 1.6800 14 1 -1 1 1 6.1868 15 1 0 -1 1 1.7806 16 1 0 0 1 0.9259 17 1 0 1 1 4.8785 18 1 1 1 1 5.8548 19 1 1 0 1 1.8420 20 1 1 -1 1 4.7851 21 1 1 1 0 4.7272 22 1 1 0 0 1.0774 23 1 1 -1 0 4.6214 24 1 1 1 -1 5.5064 25 1 1 0 -1 1.6800 26 1 1 -1 -1 6.1868 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3477 atoms have been selected out of 3551 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1530 510 510 0.00 6 C006 has 450 150 150 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1714 569 568 0.00 9 C009 has 453 151 151 0.00 10 C010 has 1614 538 538 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.92 Total of12738 atoms and 4237 groups and 4231 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3551 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1172 Number of atoms = 3551 Number of groups = 1177 Number of bonds = 3544 Number of angles = 1276 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1174 Number of HB donors = 2326 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1172 Number of atoms = 3551 Number of groups = 1177 Number of bonds = 3544 Number of angles = 1276 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1174 Number of HB donors = 2326 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.754" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1172" Evaluating: 1172-7 Parameter: NUMWAT <- "1165" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1165" Comparing "1081" and "1165". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.754" Parameter: BOX -> "32.754" Parameter: BOX -> "32.754" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.75400 B = 32.75400 C = 32.75400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8535 2 1 -1 0 -1 1.8394 3 1 -1 1 -1 4.7817 4 1 0 -1 -1 4.8765 5 1 0 0 -1 0.9242 6 1 0 1 -1 1.7780 7 1 -1 -1 0 4.7253 8 1 -1 0 0 1.0758 9 1 -1 1 0 4.6190 10 1 0 -1 0 0.7673 11 1 0 1 0 0.7673 12 1 -1 -1 1 5.5037 13 1 -1 0 1 1.6779 14 1 -1 1 1 6.1839 15 1 0 -1 1 1.7780 16 1 0 0 1 0.9242 17 1 0 1 1 4.8765 18 1 1 1 1 5.8535 19 1 1 0 1 1.8394 20 1 1 -1 1 4.7817 21 1 1 1 0 4.7253 22 1 1 0 0 1.0758 23 1 1 -1 0 4.6190 24 1 1 1 -1 5.5037 25 1 1 0 -1 1.6779 26 1 1 -1 -1 6.1839 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3477 atoms have been selected out of 3551 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1530 510 510 0.00 6 C006 has 450 150 150 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1714 569 568 0.00 9 C009 has 453 151 151 0.00 10 C010 has 1614 538 538 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.91 Total of12738 atoms and 4237 groups and 4231 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3551 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1172 Number of atoms = 3551 Number of groups = 1177 Number of bonds = 3544 Number of angles = 1276 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1174 Number of HB donors = 2326 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1172 Number of atoms = 3551 Number of groups = 1177 Number of bonds = 3544 Number of angles = 1276 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1174 Number of HB donors = 2326 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.752" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1172" Evaluating: 1172-7 Parameter: NUMWAT <- "1165" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1165" Comparing "1081" and "1165". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.752" Parameter: BOX -> "32.752" Parameter: BOX -> "32.752" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.75200 B = 32.75200 C = 32.75200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8522 2 1 -1 0 -1 1.8368 3 1 -1 1 -1 4.7783 4 1 0 -1 -1 4.8746 5 1 0 0 -1 0.9226 6 1 0 1 -1 1.7754 7 1 -1 -1 0 4.7235 8 1 -1 0 0 1.0741 9 1 -1 1 0 4.6165 10 1 0 -1 0 0.7655 11 1 0 1 0 0.7655 12 1 -1 -1 1 5.5009 13 1 -1 0 1 1.6759 14 1 -1 1 1 6.1809 15 1 0 -1 1 1.7754 16 1 0 0 1 0.9226 17 1 0 1 1 4.8746 18 1 1 1 1 5.8522 19 1 1 0 1 1.8368 20 1 1 -1 1 4.7783 21 1 1 1 0 4.7235 22 1 1 0 0 1.0741 23 1 1 -1 0 4.6165 24 1 1 1 -1 5.5009 25 1 1 0 -1 1.6759 26 1 1 -1 -1 6.1809 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3477 atoms have been selected out of 3551 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1530 510 510 0.00 6 C006 has 450 150 150 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1714 569 568 0.00 9 C009 has 453 151 151 0.00 10 C010 has 1614 538 538 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.91 Total of12738 atoms and 4237 groups and 4231 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3551 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1172 Number of atoms = 3551 Number of groups = 1177 Number of bonds = 3544 Number of angles = 1276 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1174 Number of HB donors = 2326 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1172 Number of atoms = 3551 Number of groups = 1177 Number of bonds = 3544 Number of angles = 1276 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1174 Number of HB donors = 2326 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.75" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1172" Evaluating: 1172-7 Parameter: NUMWAT <- "1165" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1165" Comparing "1081" and "1165". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.75" Parameter: BOX -> "32.75" Parameter: BOX -> "32.75" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.75000 B = 32.75000 C = 32.75000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8509 2 1 -1 0 -1 1.8342 3 1 -1 1 -1 4.7748 4 1 0 -1 -1 4.8727 5 1 0 0 -1 0.9209 6 1 0 1 -1 1.7728 7 1 -1 -1 0 4.7217 8 1 -1 0 0 1.0725 9 1 -1 1 0 4.6140 10 1 0 -1 0 0.7637 11 1 0 1 0 0.7637 12 1 -1 -1 1 5.4981 13 1 -1 0 1 1.6738 14 1 -1 1 1 6.1780 15 1 0 -1 1 1.7728 16 1 0 0 1 0.9209 17 1 0 1 1 4.8727 18 1 1 1 1 5.8509 19 1 1 0 1 1.8342 20 1 1 -1 1 4.7748 21 1 1 1 0 4.7217 22 1 1 0 0 1.0725 23 1 1 -1 0 4.6140 24 1 1 1 -1 5.4981 25 1 1 0 -1 1.6738 26 1 1 -1 -1 6.1780 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3477 atoms have been selected out of 3551 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1530 510 510 0.00 6 C006 has 450 150 150 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1714 569 568 0.00 9 C009 has 453 151 151 0.00 10 C010 has 1614 538 538 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.91 Total of12738 atoms and 4237 groups and 4231 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3551 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1172 Number of atoms = 3551 Number of groups = 1177 Number of bonds = 3544 Number of angles = 1276 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1174 Number of HB donors = 2326 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1172 Number of atoms = 3551 Number of groups = 1177 Number of bonds = 3544 Number of angles = 1276 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1174 Number of HB donors = 2326 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.748" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1172" Evaluating: 1172-7 Parameter: NUMWAT <- "1165" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1165" Comparing "1081" and "1165". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.748" Parameter: BOX -> "32.748" Parameter: BOX -> "32.748" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.74800 B = 32.74800 C = 32.74800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8497 2 1 -1 0 -1 1.8317 3 1 -1 1 -1 4.7714 4 1 0 -1 -1 4.8707 5 1 0 0 -1 0.9192 6 1 0 1 -1 1.7703 7 1 -1 -1 0 4.7199 8 1 -1 0 0 1.0709 9 1 -1 1 0 4.6115 10 1 0 -1 0 0.7619 11 1 0 1 0 0.7619 12 1 -1 -1 1 5.4954 13 1 -1 0 1 1.6717 14 1 -1 1 1 6.1750 15 1 0 -1 1 1.7703 16 1 0 0 1 0.9192 17 1 0 1 1 4.8707 18 1 1 1 1 5.8497 19 1 1 0 1 1.8317 20 1 1 -1 1 4.7714 21 1 1 1 0 4.7199 22 1 1 0 0 1.0709 23 1 1 -1 0 4.6115 24 1 1 1 -1 5.4954 25 1 1 0 -1 1.6717 26 1 1 -1 -1 6.1750 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3477 atoms have been selected out of 3551 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 994 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1147 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 471 157 157 0.00 2 C002 has 756 252 252 0.00 3 C003 has 114 38 38 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1530 510 510 0.00 6 C006 has 456 152 152 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1714 569 568 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1620 540 540 0.00 12 C012 has 99 33 33 0.00 13 C013 has 468 156 156 0.00 14 C014 has 111 37 37 0.91 Total of12729 atoms and 4234 groups and 4228 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3551 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1170 Number of atoms = 3545 Number of groups = 1175 Number of bonds = 3538 Number of angles = 1274 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1172 Number of HB donors = 2322 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1170 Number of atoms = 3545 Number of groups = 1175 Number of bonds = 3538 Number of angles = 1274 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1172 Number of HB donors = 2322 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.746" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1170" Evaluating: 1170-7 Parameter: NUMWAT <- "1163" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1163" Comparing "1081" and "1163". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.746" Parameter: BOX -> "32.746" Parameter: BOX -> "32.746" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.74600 B = 32.74600 C = 32.74600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8484 2 1 -1 0 -1 1.8291 3 1 -1 1 -1 4.7680 4 1 0 -1 -1 4.8688 5 1 0 0 -1 0.9175 6 1 0 1 -1 1.7677 7 1 -1 -1 0 4.7181 8 1 -1 0 0 1.0693 9 1 -1 1 0 4.6091 10 1 0 -1 0 0.7601 11 1 0 1 0 0.7601 12 1 -1 -1 1 5.4926 13 1 -1 0 1 1.6696 14 1 -1 1 1 6.1720 15 1 0 -1 1 1.7677 16 1 0 0 1 0.9175 17 1 0 1 1 4.8688 18 1 1 1 1 5.8484 19 1 1 0 1 1.8291 20 1 1 -1 1 4.7680 21 1 1 1 0 4.7181 22 1 1 0 0 1.0693 23 1 1 -1 0 4.6091 24 1 1 1 -1 5.4926 25 1 1 0 -1 1.6696 26 1 1 -1 -1 6.1720 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3471 atoms have been selected out of 3545 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 471 157 157 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1524 508 508 0.00 6 C006 has 450 150 150 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1711 568 567 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1611 537 537 0.00 12 C012 has 99 33 33 0.00 13 C013 has 468 156 156 0.00 14 C014 has 111 37 37 0.91 Total of12675 atoms and 4216 groups and 4210 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3545 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1170 Number of atoms = 3545 Number of groups = 1175 Number of bonds = 3538 Number of angles = 1274 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1172 Number of HB donors = 2322 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1170 Number of atoms = 3545 Number of groups = 1175 Number of bonds = 3538 Number of angles = 1274 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1172 Number of HB donors = 2322 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.744" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1170" Evaluating: 1170-7 Parameter: NUMWAT <- "1163" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1163" Comparing "1081" and "1163". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.744" Parameter: BOX -> "32.744" Parameter: BOX -> "32.744" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.74400 B = 32.74400 C = 32.74400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8471 2 1 -1 0 -1 1.8265 3 1 -1 1 -1 4.7646 4 1 0 -1 -1 4.8669 5 1 0 0 -1 0.9159 6 1 0 1 -1 1.7651 7 1 -1 -1 0 4.7162 8 1 -1 0 0 1.0677 9 1 -1 1 0 4.6066 10 1 0 -1 0 0.7583 11 1 0 1 0 0.7583 12 1 -1 -1 1 5.4899 13 1 -1 0 1 1.6675 14 1 -1 1 1 6.1691 15 1 0 -1 1 1.7651 16 1 0 0 1 0.9159 17 1 0 1 1 4.8669 18 1 1 1 1 5.8471 19 1 1 0 1 1.8265 20 1 1 -1 1 4.7646 21 1 1 1 0 4.7162 22 1 1 0 0 1.0677 23 1 1 -1 0 4.6066 24 1 1 1 -1 5.4899 25 1 1 0 -1 1.6675 26 1 1 -1 -1 6.1691 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3471 atoms have been selected out of 3545 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 471 157 157 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1524 508 508 0.00 6 C006 has 450 150 150 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1711 568 567 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1611 537 537 0.00 12 C012 has 102 34 34 0.00 13 C013 has 468 156 156 0.00 14 C014 has 111 37 37 0.90 Total of12678 atoms and 4217 groups and 4211 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3545 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1170 Number of atoms = 3545 Number of groups = 1175 Number of bonds = 3538 Number of angles = 1274 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1172 Number of HB donors = 2322 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1170 Number of atoms = 3545 Number of groups = 1175 Number of bonds = 3538 Number of angles = 1274 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1172 Number of HB donors = 2322 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.742" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1170" Evaluating: 1170-7 Parameter: NUMWAT <- "1163" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1163" Comparing "1081" and "1163". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.742" Parameter: BOX -> "32.742" Parameter: BOX -> "32.742" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.74200 B = 32.74200 C = 32.74200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8458 2 1 -1 0 -1 1.8240 3 1 -1 1 -1 4.7611 4 1 0 -1 -1 4.8649 5 1 0 0 -1 0.9142 6 1 0 1 -1 1.7625 7 1 -1 -1 0 4.7144 8 1 -1 0 0 1.0661 9 1 -1 1 0 4.6041 10 1 0 -1 0 0.7565 11 1 0 1 0 0.7565 12 1 -1 -1 1 5.4871 13 1 -1 0 1 1.6654 14 1 -1 1 1 6.1661 15 1 0 -1 1 1.7625 16 1 0 0 1 0.9142 17 1 0 1 1 4.8649 18 1 1 1 1 5.8458 19 1 1 0 1 1.8240 20 1 1 -1 1 4.7611 21 1 1 1 0 4.7144 22 1 1 0 0 1.0661 23 1 1 -1 0 4.6041 24 1 1 1 -1 5.4871 25 1 1 0 -1 1.6654 26 1 1 -1 -1 6.1661 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3471 atoms have been selected out of 3545 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 992 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1524 508 508 0.00 6 C006 has 450 150 150 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1711 568 567 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1611 537 537 0.00 12 C012 has 102 34 34 0.00 13 C013 has 468 156 156 0.00 14 C014 has 111 37 37 0.90 Total of12678 atoms and 4217 groups and 4211 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3545 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1169 Number of atoms = 3542 Number of groups = 1174 Number of bonds = 3535 Number of angles = 1273 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1171 Number of HB donors = 2320 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1169 Number of atoms = 3542 Number of groups = 1174 Number of bonds = 3535 Number of angles = 1273 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1171 Number of HB donors = 2320 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.74" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1169" Evaluating: 1169-7 Parameter: NUMWAT <- "1162" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1162" Comparing "1081" and "1162". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.74" Parameter: BOX -> "32.74" Parameter: BOX -> "32.74" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.74000 B = 32.74000 C = 32.74000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8445 2 1 -1 0 -1 1.8214 3 1 -1 1 -1 4.7577 4 1 0 -1 -1 4.8630 5 1 0 0 -1 0.9125 6 1 0 1 -1 1.7600 7 1 -1 -1 0 4.7126 8 1 -1 0 0 1.0645 9 1 -1 1 0 4.6017 10 1 0 -1 0 0.7547 11 1 0 1 0 0.7547 12 1 -1 -1 1 5.4843 13 1 -1 0 1 1.6634 14 1 -1 1 1 6.1632 15 1 0 -1 1 1.7600 16 1 0 0 1 0.9125 17 1 0 1 1 4.8630 18 1 1 1 1 5.8445 19 1 1 0 1 1.8214 20 1 1 -1 1 4.7577 21 1 1 1 0 4.7126 22 1 1 0 0 1.0645 23 1 1 -1 0 4.6017 24 1 1 1 -1 5.4843 25 1 1 0 -1 1.6634 26 1 1 -1 -1 6.1632 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3468 atoms have been selected out of 3542 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 481 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1521 507 507 0.00 6 C006 has 450 150 150 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1714 569 568 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1608 536 536 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.90 Total of12663 atoms and 4212 groups and 4206 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3542 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1168 Number of atoms = 3539 Number of groups = 1173 Number of bonds = 3532 Number of angles = 1272 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1170 Number of HB donors = 2318 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1168 Number of atoms = 3539 Number of groups = 1173 Number of bonds = 3532 Number of angles = 1272 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1170 Number of HB donors = 2318 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.738" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1168" Evaluating: 1168-7 Parameter: NUMWAT <- "1161" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1161" Comparing "1081" and "1161". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.738" Parameter: BOX -> "32.738" Parameter: BOX -> "32.738" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.73800 B = 32.73800 C = 32.73800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8432 2 1 -1 0 -1 1.8188 3 1 -1 1 -1 4.7543 4 1 0 -1 -1 4.8611 5 1 0 0 -1 0.9109 6 1 0 1 -1 1.7574 7 1 -1 -1 0 4.7108 8 1 -1 0 0 1.0629 9 1 -1 1 0 4.5992 10 1 0 -1 0 0.7529 11 1 0 1 0 0.7529 12 1 -1 -1 1 5.4816 13 1 -1 0 1 1.6613 14 1 -1 1 1 6.1602 15 1 0 -1 1 1.7574 16 1 0 0 1 0.9109 17 1 0 1 1 4.8611 18 1 1 1 1 5.8432 19 1 1 0 1 1.8188 20 1 1 -1 1 4.7543 21 1 1 1 0 4.7108 22 1 1 0 0 1.0629 23 1 1 -1 0 4.5992 24 1 1 1 -1 5.4816 25 1 1 0 -1 1.6613 26 1 1 -1 -1 6.1602 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3465 atoms have been selected out of 3539 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 206 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1521 507 507 0.00 6 C006 has 450 150 150 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1705 566 565 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1605 535 535 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 108 36 36 0.90 Total of12642 atoms and 4205 groups and 4199 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3539 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1167 Number of atoms = 3536 Number of groups = 1172 Number of bonds = 3529 Number of angles = 1271 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2316 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1167 Number of atoms = 3536 Number of groups = 1172 Number of bonds = 3529 Number of angles = 1271 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2316 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.736" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1167" Evaluating: 1167-7 Parameter: NUMWAT <- "1160" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1160" Comparing "1081" and "1160". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.736" Parameter: BOX -> "32.736" Parameter: BOX -> "32.736" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.73600 B = 32.73600 C = 32.73600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8419 2 1 -1 0 -1 1.8163 3 1 -1 1 -1 4.7509 4 1 0 -1 -1 4.8591 5 1 0 0 -1 0.9092 6 1 0 1 -1 1.7548 7 1 -1 -1 0 4.7090 8 1 -1 0 0 1.0613 9 1 -1 1 0 4.5967 10 1 0 -1 0 0.7511 11 1 0 1 0 0.7511 12 1 -1 -1 1 5.4788 13 1 -1 0 1 1.6592 14 1 -1 1 1 6.1573 15 1 0 -1 1 1.7548 16 1 0 0 1 0.9092 17 1 0 1 1 4.8591 18 1 1 1 1 5.8419 19 1 1 0 1 1.8163 20 1 1 -1 1 4.7509 21 1 1 1 0 4.7090 22 1 1 0 0 1.0613 23 1 1 -1 0 4.5967 24 1 1 1 -1 5.4788 25 1 1 0 -1 1.6592 26 1 1 -1 -1 6.1573 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3462 atoms have been selected out of 3536 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 471 157 157 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1521 507 507 0.00 6 C006 has 450 150 150 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1705 566 565 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1605 535 535 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 108 36 36 0.90 Total of12639 atoms and 4204 groups and 4198 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3536 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1167 Number of atoms = 3536 Number of groups = 1172 Number of bonds = 3529 Number of angles = 1271 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2316 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1167 Number of atoms = 3536 Number of groups = 1172 Number of bonds = 3529 Number of angles = 1271 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2316 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.734" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1167" Evaluating: 1167-7 Parameter: NUMWAT <- "1160" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1160" Comparing "1081" and "1160". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.734" Parameter: BOX -> "32.734" Parameter: BOX -> "32.734" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.73400 B = 32.73400 C = 32.73400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8406 2 1 -1 0 -1 1.8137 3 1 -1 1 -1 4.7475 4 1 0 -1 -1 4.8572 5 1 0 0 -1 0.9075 6 1 0 1 -1 1.7522 7 1 -1 -1 0 4.7072 8 1 -1 0 0 1.0596 9 1 -1 1 0 4.5942 10 1 0 -1 0 0.7493 11 1 0 1 0 0.7493 12 1 -1 -1 1 5.4761 13 1 -1 0 1 1.6572 14 1 -1 1 1 6.1543 15 1 0 -1 1 1.7522 16 1 0 0 1 0.9075 17 1 0 1 1 4.8572 18 1 1 1 1 5.8406 19 1 1 0 1 1.8137 20 1 1 -1 1 4.7475 21 1 1 1 0 4.7072 22 1 1 0 0 1.0596 23 1 1 -1 0 4.5942 24 1 1 1 -1 5.4761 25 1 1 0 -1 1.6572 26 1 1 -1 -1 6.1543 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3462 atoms have been selected out of 3536 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 471 157 157 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1521 507 507 0.00 6 C006 has 450 150 150 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1705 566 565 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1605 535 535 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.89 Total of12642 atoms and 4205 groups and 4199 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3536 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1167 Number of atoms = 3536 Number of groups = 1172 Number of bonds = 3529 Number of angles = 1271 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2316 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1167 Number of atoms = 3536 Number of groups = 1172 Number of bonds = 3529 Number of angles = 1271 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2316 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.732" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1167" Evaluating: 1167-7 Parameter: NUMWAT <- "1160" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1160" Comparing "1081" and "1160". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.732" Parameter: BOX -> "32.732" Parameter: BOX -> "32.732" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.73200 B = 32.73200 C = 32.73200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8394 2 1 -1 0 -1 1.8111 3 1 -1 1 -1 4.7440 4 1 0 -1 -1 4.8553 5 1 0 0 -1 0.9059 6 1 0 1 -1 1.7497 7 1 -1 -1 0 4.7054 8 1 -1 0 0 1.0580 9 1 -1 1 0 4.5918 10 1 0 -1 0 0.7475 11 1 0 1 0 0.7475 12 1 -1 -1 1 5.4733 13 1 -1 0 1 1.6551 14 1 -1 1 1 6.1513 15 1 0 -1 1 1.7497 16 1 0 0 1 0.9059 17 1 0 1 1 4.8553 18 1 1 1 1 5.8394 19 1 1 0 1 1.8111 20 1 1 -1 1 4.7440 21 1 1 1 0 4.7054 22 1 1 0 0 1.0580 23 1 1 -1 0 4.5918 24 1 1 1 -1 5.4733 25 1 1 0 -1 1.6551 26 1 1 -1 -1 6.1513 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3462 atoms have been selected out of 3536 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 613 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1153 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1518 506 506 0.00 6 C006 has 450 150 150 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1711 568 567 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1608 536 536 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.89 Total of12651 atoms and 4208 groups and 4202 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3536 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1165 Number of atoms = 3530 Number of groups = 1170 Number of bonds = 3523 Number of angles = 1269 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1167 Number of HB donors = 2312 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1165 Number of atoms = 3530 Number of groups = 1170 Number of bonds = 3523 Number of angles = 1269 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1167 Number of HB donors = 2312 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.73" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1165" Evaluating: 1165-7 Parameter: NUMWAT <- "1158" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1158" Comparing "1081" and "1158". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.73" Parameter: BOX -> "32.73" Parameter: BOX -> "32.73" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.73000 B = 32.73000 C = 32.73000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8381 2 1 -1 0 -1 1.8086 3 1 -1 1 -1 4.7406 4 1 0 -1 -1 4.8533 5 1 0 0 -1 0.9042 6 1 0 1 -1 1.7471 7 1 -1 -1 0 4.7035 8 1 -1 0 0 1.0564 9 1 -1 1 0 4.5893 10 1 0 -1 0 0.7457 11 1 0 1 0 0.7457 12 1 -1 -1 1 5.4706 13 1 -1 0 1 1.6530 14 1 -1 1 1 6.1484 15 1 0 -1 1 1.7471 16 1 0 0 1 0.9042 17 1 0 1 1 4.8533 18 1 1 1 1 5.8381 19 1 1 0 1 1.8086 20 1 1 -1 1 4.7406 21 1 1 1 0 4.7035 22 1 1 0 0 1.0564 23 1 1 -1 0 4.5893 24 1 1 1 -1 5.4706 25 1 1 0 -1 1.6530 26 1 1 -1 -1 6.1484 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3456 atoms have been selected out of 3530 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1518 506 506 0.00 6 C006 has 450 150 150 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1705 566 565 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1602 534 534 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.89 Total of12624 atoms and 4199 groups and 4193 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3530 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1165 Number of atoms = 3530 Number of groups = 1170 Number of bonds = 3523 Number of angles = 1269 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1167 Number of HB donors = 2312 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1165 Number of atoms = 3530 Number of groups = 1170 Number of bonds = 3523 Number of angles = 1269 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1167 Number of HB donors = 2312 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.728" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1165" Evaluating: 1165-7 Parameter: NUMWAT <- "1158" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1158" Comparing "1081" and "1158". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.728" Parameter: BOX -> "32.728" Parameter: BOX -> "32.728" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.72800 B = 32.72800 C = 32.72800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8368 2 1 -1 0 -1 1.8060 3 1 -1 1 -1 4.7372 4 1 0 -1 -1 4.8514 5 1 0 0 -1 0.9026 6 1 0 1 -1 1.7445 7 1 -1 -1 0 4.7017 8 1 -1 0 0 1.0548 9 1 -1 1 0 4.5868 10 1 0 -1 0 0.7439 11 1 0 1 0 0.7439 12 1 -1 -1 1 5.4678 13 1 -1 0 1 1.6510 14 1 -1 1 1 6.1454 15 1 0 -1 1 1.7445 16 1 0 0 1 0.9026 17 1 0 1 1 4.8514 18 1 1 1 1 5.8368 19 1 1 0 1 1.8060 20 1 1 -1 1 4.7372 21 1 1 1 0 4.7017 22 1 1 0 0 1.0548 23 1 1 -1 0 4.5868 24 1 1 1 -1 5.4678 25 1 1 0 -1 1.6510 26 1 1 -1 -1 6.1454 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3456 atoms have been selected out of 3530 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1518 506 506 0.00 6 C006 has 450 150 150 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1705 566 565 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1602 534 534 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.89 Total of12624 atoms and 4199 groups and 4193 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3530 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1165 Number of atoms = 3530 Number of groups = 1170 Number of bonds = 3523 Number of angles = 1269 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1167 Number of HB donors = 2312 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1165 Number of atoms = 3530 Number of groups = 1170 Number of bonds = 3523 Number of angles = 1269 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1167 Number of HB donors = 2312 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.726" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1165" Evaluating: 1165-7 Parameter: NUMWAT <- "1158" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1158" Comparing "1081" and "1158". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.726" Parameter: BOX -> "32.726" Parameter: BOX -> "32.726" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.72600 B = 32.72600 C = 32.72600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8355 2 1 -1 0 -1 1.8035 3 1 -1 1 -1 4.7338 4 1 0 -1 -1 4.8495 5 1 0 0 -1 0.9009 6 1 0 1 -1 1.7419 7 1 -1 -1 0 4.6999 8 1 -1 0 0 1.0532 9 1 -1 1 0 4.5844 10 1 0 -1 0 0.7422 11 1 0 1 0 0.7422 12 1 -1 -1 1 5.4650 13 1 -1 0 1 1.6489 14 1 -1 1 1 6.1425 15 1 0 -1 1 1.7419 16 1 0 0 1 0.9009 17 1 0 1 1 4.8495 18 1 1 1 1 5.8355 19 1 1 0 1 1.8035 20 1 1 -1 1 4.7338 21 1 1 1 0 4.6999 22 1 1 0 0 1.0532 23 1 1 -1 0 4.5844 24 1 1 1 -1 5.4650 25 1 1 0 -1 1.6489 26 1 1 -1 -1 6.1425 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3456 atoms have been selected out of 3530 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1518 506 506 0.00 6 C006 has 450 150 150 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1705 566 565 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1602 534 534 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.89 Total of12624 atoms and 4199 groups and 4193 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3530 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1165 Number of atoms = 3530 Number of groups = 1170 Number of bonds = 3523 Number of angles = 1269 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1167 Number of HB donors = 2312 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1165 Number of atoms = 3530 Number of groups = 1170 Number of bonds = 3523 Number of angles = 1269 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1167 Number of HB donors = 2312 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.724" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1165" Evaluating: 1165-7 Parameter: NUMWAT <- "1158" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1158" Comparing "1081" and "1158". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.724" Parameter: BOX -> "32.724" Parameter: BOX -> "32.724" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.72400 B = 32.72400 C = 32.72400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8342 2 1 -1 0 -1 1.8009 3 1 -1 1 -1 4.7304 4 1 0 -1 -1 4.8476 5 1 0 0 -1 0.8993 6 1 0 1 -1 1.7394 7 1 -1 -1 0 4.6981 8 1 -1 0 0 1.0516 9 1 -1 1 0 4.5819 10 1 0 -1 0 0.7404 11 1 0 1 0 0.7404 12 1 -1 -1 1 5.4623 13 1 -1 0 1 1.6469 14 1 -1 1 1 6.1395 15 1 0 -1 1 1.7394 16 1 0 0 1 0.8993 17 1 0 1 1 4.8476 18 1 1 1 1 5.8342 19 1 1 0 1 1.8009 20 1 1 -1 1 4.7304 21 1 1 1 0 4.6981 22 1 1 0 0 1.0516 23 1 1 -1 0 4.5819 24 1 1 1 -1 5.4623 25 1 1 0 -1 1.6469 26 1 1 -1 -1 6.1395 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3456 atoms have been selected out of 3530 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1521 507 507 0.00 6 C006 has 450 150 150 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1705 566 565 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1602 534 534 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.88 Total of12627 atoms and 4200 groups and 4194 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3530 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1165 Number of atoms = 3530 Number of groups = 1170 Number of bonds = 3523 Number of angles = 1269 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1167 Number of HB donors = 2312 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1165 Number of atoms = 3530 Number of groups = 1170 Number of bonds = 3523 Number of angles = 1269 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1167 Number of HB donors = 2312 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.722" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1165" Evaluating: 1165-7 Parameter: NUMWAT <- "1158" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1158" Comparing "1081" and "1158". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.722" Parameter: BOX -> "32.722" Parameter: BOX -> "32.722" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.72200 B = 32.72200 C = 32.72200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8330 2 1 -1 0 -1 1.7983 3 1 -1 1 -1 4.7269 4 1 0 -1 -1 4.8456 5 1 0 0 -1 0.8976 6 1 0 1 -1 1.7368 7 1 -1 -1 0 4.6963 8 1 -1 0 0 1.0500 9 1 -1 1 0 4.5794 10 1 0 -1 0 0.7386 11 1 0 1 0 0.7386 12 1 -1 -1 1 5.4595 13 1 -1 0 1 1.6448 14 1 -1 1 1 6.1366 15 1 0 -1 1 1.7368 16 1 0 0 1 0.8976 17 1 0 1 1 4.8456 18 1 1 1 1 5.8330 19 1 1 0 1 1.7983 20 1 1 -1 1 4.7269 21 1 1 1 0 4.6963 22 1 1 0 0 1.0500 23 1 1 -1 0 4.5794 24 1 1 1 -1 5.4595 25 1 1 0 -1 1.6448 26 1 1 -1 -1 6.1366 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3456 atoms have been selected out of 3530 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1521 507 507 0.00 6 C006 has 450 150 150 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1705 566 565 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1602 534 534 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.88 Total of12627 atoms and 4200 groups and 4194 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3530 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1165 Number of atoms = 3530 Number of groups = 1170 Number of bonds = 3523 Number of angles = 1269 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1167 Number of HB donors = 2312 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1165 Number of atoms = 3530 Number of groups = 1170 Number of bonds = 3523 Number of angles = 1269 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1167 Number of HB donors = 2312 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.72" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1165" Evaluating: 1165-7 Parameter: NUMWAT <- "1158" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1158" Comparing "1081" and "1158". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.72" Parameter: BOX -> "32.72" Parameter: BOX -> "32.72" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.72000 B = 32.72000 C = 32.72000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8317 2 1 -1 0 -1 1.7958 3 1 -1 1 -1 4.7235 4 1 0 -1 -1 4.8437 5 1 0 0 -1 0.8960 6 1 0 1 -1 1.7342 7 1 -1 -1 0 4.6945 8 1 -1 0 0 1.0485 9 1 -1 1 0 4.5770 10 1 0 -1 0 0.7368 11 1 0 1 0 0.7368 12 1 -1 -1 1 5.4568 13 1 -1 0 1 1.6427 14 1 -1 1 1 6.1336 15 1 0 -1 1 1.7342 16 1 0 0 1 0.8960 17 1 0 1 1 4.8437 18 1 1 1 1 5.8317 19 1 1 0 1 1.7958 20 1 1 -1 1 4.7235 21 1 1 1 0 4.6945 22 1 1 0 0 1.0485 23 1 1 -1 0 4.5770 24 1 1 1 -1 5.4568 25 1 1 0 -1 1.6427 26 1 1 -1 -1 6.1336 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3456 atoms have been selected out of 3530 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1521 507 507 0.00 6 C006 has 450 150 150 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1705 566 565 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1602 534 534 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.88 Total of12627 atoms and 4200 groups and 4194 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3530 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1165 Number of atoms = 3530 Number of groups = 1170 Number of bonds = 3523 Number of angles = 1269 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1167 Number of HB donors = 2312 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1165 Number of atoms = 3530 Number of groups = 1170 Number of bonds = 3523 Number of angles = 1269 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1167 Number of HB donors = 2312 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.718" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1165" Evaluating: 1165-7 Parameter: NUMWAT <- "1158" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1158" Comparing "1081" and "1158". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.718" Parameter: BOX -> "32.718" Parameter: BOX -> "32.718" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.71800 B = 32.71800 C = 32.71800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8304 2 1 -1 0 -1 1.7932 3 1 -1 1 -1 4.7201 4 1 0 -1 -1 4.8418 5 1 0 0 -1 0.8943 6 1 0 1 -1 1.7317 7 1 -1 -1 0 4.6927 8 1 -1 0 0 1.0469 9 1 -1 1 0 4.5745 10 1 0 -1 0 0.7350 11 1 0 1 0 0.7350 12 1 -1 -1 1 5.4540 13 1 -1 0 1 1.6407 14 1 -1 1 1 6.1307 15 1 0 -1 1 1.7317 16 1 0 0 1 0.8943 17 1 0 1 1 4.8418 18 1 1 1 1 5.8304 19 1 1 0 1 1.7932 20 1 1 -1 1 4.7201 21 1 1 1 0 4.6927 22 1 1 0 0 1.0469 23 1 1 -1 0 4.5745 24 1 1 1 -1 5.4540 25 1 1 0 -1 1.6407 26 1 1 -1 -1 6.1307 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3456 atoms have been selected out of 3530 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1521 507 507 0.00 6 C006 has 450 150 150 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1705 566 565 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1602 534 534 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.88 Total of12630 atoms and 4201 groups and 4195 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3530 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1165 Number of atoms = 3530 Number of groups = 1170 Number of bonds = 3523 Number of angles = 1269 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1167 Number of HB donors = 2312 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1165 Number of atoms = 3530 Number of groups = 1170 Number of bonds = 3523 Number of angles = 1269 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1167 Number of HB donors = 2312 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.716" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1165" Evaluating: 1165-7 Parameter: NUMWAT <- "1158" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1158" Comparing "1081" and "1158". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.716" Parameter: BOX -> "32.716" Parameter: BOX -> "32.716" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.71600 B = 32.71600 C = 32.71600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8292 2 1 -1 0 -1 1.7907 3 1 -1 1 -1 4.7167 4 1 0 -1 -1 4.8399 5 1 0 0 -1 0.8927 6 1 0 1 -1 1.7291 7 1 -1 -1 0 4.6909 8 1 -1 0 0 1.0453 9 1 -1 1 0 4.5720 10 1 0 -1 0 0.7332 11 1 0 1 0 0.7332 12 1 -1 -1 1 5.4513 13 1 -1 0 1 1.6386 14 1 -1 1 1 6.1277 15 1 0 -1 1 1.7291 16 1 0 0 1 0.8927 17 1 0 1 1 4.8399 18 1 1 1 1 5.8292 19 1 1 0 1 1.7907 20 1 1 -1 1 4.7167 21 1 1 1 0 4.6909 22 1 1 0 0 1.0453 23 1 1 -1 0 4.5720 24 1 1 1 -1 5.4513 25 1 1 0 -1 1.6386 26 1 1 -1 -1 6.1277 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3456 atoms have been selected out of 3530 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1135 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1518 506 506 0.00 6 C006 has 450 150 150 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1705 566 565 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1602 534 534 0.00 12 C012 has 99 33 33 0.00 13 C013 has 468 156 156 0.00 14 C014 has 111 37 37 0.88 Total of12627 atoms and 4200 groups and 4194 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3530 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1164 Number of atoms = 3527 Number of groups = 1169 Number of bonds = 3520 Number of angles = 1268 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1166 Number of HB donors = 2310 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1164 Number of atoms = 3527 Number of groups = 1169 Number of bonds = 3520 Number of angles = 1268 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1166 Number of HB donors = 2310 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.714" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1164" Evaluating: 1164-7 Parameter: NUMWAT <- "1157" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1157" Comparing "1081" and "1157". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.714" Parameter: BOX -> "32.714" Parameter: BOX -> "32.714" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.71400 B = 32.71400 C = 32.71400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8279 2 1 -1 0 -1 1.7881 3 1 -1 1 -1 4.7133 4 1 0 -1 -1 4.8379 5 1 0 0 -1 0.8910 6 1 0 1 -1 1.7265 7 1 -1 -1 0 4.6891 8 1 -1 0 0 1.0437 9 1 -1 1 0 4.5696 10 1 0 -1 0 0.7315 11 1 0 1 0 0.7315 12 1 -1 -1 1 5.4485 13 1 -1 0 1 1.6366 14 1 -1 1 1 6.1248 15 1 0 -1 1 1.7265 16 1 0 0 1 0.8910 17 1 0 1 1 4.8379 18 1 1 1 1 5.8279 19 1 1 0 1 1.7881 20 1 1 -1 1 4.7133 21 1 1 1 0 4.6891 22 1 1 0 0 1.0437 23 1 1 -1 0 4.5696 24 1 1 1 -1 5.4485 25 1 1 0 -1 1.6366 26 1 1 -1 -1 6.1248 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3453 atoms have been selected out of 3527 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 180 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 756 252 252 0.00 3 C003 has 114 38 38 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1521 507 507 0.00 6 C006 has 456 152 152 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1702 565 564 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 108 36 36 0.87 Total of12621 atoms and 4198 groups and 4192 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3527 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1163 Number of atoms = 3524 Number of groups = 1168 Number of bonds = 3517 Number of angles = 1267 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1165 Number of HB donors = 2308 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1163 Number of atoms = 3524 Number of groups = 1168 Number of bonds = 3517 Number of angles = 1267 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1165 Number of HB donors = 2308 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.712" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1163" Evaluating: 1163-7 Parameter: NUMWAT <- "1156" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1156" Comparing "1081" and "1156". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.712" Parameter: BOX -> "32.712" Parameter: BOX -> "32.712" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.71200 B = 32.71200 C = 32.71200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8266 2 1 -1 0 -1 1.7856 3 1 -1 1 -1 4.7098 4 1 0 -1 -1 4.8360 5 1 0 0 -1 0.8894 6 1 0 1 -1 1.7240 7 1 -1 -1 0 4.6873 8 1 -1 0 0 1.0421 9 1 -1 1 0 4.5671 10 1 0 -1 0 0.7297 11 1 0 1 0 0.7297 12 1 -1 -1 1 5.4458 13 1 -1 0 1 1.6346 14 1 -1 1 1 6.1218 15 1 0 -1 1 1.7240 16 1 0 0 1 0.8894 17 1 0 1 1 4.8360 18 1 1 1 1 5.8266 19 1 1 0 1 1.7856 20 1 1 -1 1 4.7098 21 1 1 1 0 4.6873 22 1 1 0 0 1.0421 23 1 1 -1 0 4.5671 24 1 1 1 -1 5.4458 25 1 1 0 -1 1.6346 26 1 1 -1 -1 6.1218 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3450 atoms have been selected out of 3524 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1518 506 506 0.00 6 C006 has 453 151 151 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1699 564 563 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 108 36 36 0.87 Total of12600 atoms and 4191 groups and 4185 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3524 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1163 Number of atoms = 3524 Number of groups = 1168 Number of bonds = 3517 Number of angles = 1267 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1165 Number of HB donors = 2308 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1163 Number of atoms = 3524 Number of groups = 1168 Number of bonds = 3517 Number of angles = 1267 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1165 Number of HB donors = 2308 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.71" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1163" Evaluating: 1163-7 Parameter: NUMWAT <- "1156" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1156" Comparing "1081" and "1156". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.71" Parameter: BOX -> "32.71" Parameter: BOX -> "32.71" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.71000 B = 32.71000 C = 32.71000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8254 2 1 -1 0 -1 1.7830 3 1 -1 1 -1 4.7064 4 1 0 -1 -1 4.8341 5 1 0 0 -1 0.8877 6 1 0 1 -1 1.7214 7 1 -1 -1 0 4.6855 8 1 -1 0 0 1.0405 9 1 -1 1 0 4.5646 10 1 0 -1 0 0.7279 11 1 0 1 0 0.7279 12 1 -1 -1 1 5.4430 13 1 -1 0 1 1.6325 14 1 -1 1 1 6.1189 15 1 0 -1 1 1.7214 16 1 0 0 1 0.8877 17 1 0 1 1 4.8341 18 1 1 1 1 5.8254 19 1 1 0 1 1.7830 20 1 1 -1 1 4.7064 21 1 1 1 0 4.6855 22 1 1 0 0 1.0405 23 1 1 -1 0 4.5646 24 1 1 1 -1 5.4430 25 1 1 0 -1 1.6325 26 1 1 -1 -1 6.1189 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3450 atoms have been selected out of 3524 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1518 506 506 0.00 6 C006 has 453 151 151 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1699 564 563 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 108 36 36 0.87 Total of12603 atoms and 4192 groups and 4186 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3524 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1163 Number of atoms = 3524 Number of groups = 1168 Number of bonds = 3517 Number of angles = 1267 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1165 Number of HB donors = 2308 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1163 Number of atoms = 3524 Number of groups = 1168 Number of bonds = 3517 Number of angles = 1267 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1165 Number of HB donors = 2308 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.708" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1163" Evaluating: 1163-7 Parameter: NUMWAT <- "1156" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1156" Comparing "1081" and "1156". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.708" Parameter: BOX -> "32.708" Parameter: BOX -> "32.708" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.70800 B = 32.70800 C = 32.70800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8241 2 1 -1 0 -1 1.7804 3 1 -1 1 -1 4.7030 4 1 0 -1 -1 4.8322 5 1 0 0 -1 0.8861 6 1 0 1 -1 1.7188 7 1 -1 -1 0 4.6837 8 1 -1 0 0 1.0389 9 1 -1 1 0 4.5622 10 1 0 -1 0 0.7261 11 1 0 1 0 0.7261 12 1 -1 -1 1 5.4403 13 1 -1 0 1 1.6305 14 1 -1 1 1 6.1159 15 1 0 -1 1 1.7188 16 1 0 0 1 0.8861 17 1 0 1 1 4.8322 18 1 1 1 1 5.8241 19 1 1 0 1 1.7804 20 1 1 -1 1 4.7030 21 1 1 1 0 4.6837 22 1 1 0 0 1.0389 23 1 1 -1 0 4.5622 24 1 1 1 -1 5.4403 25 1 1 0 -1 1.6305 26 1 1 -1 -1 6.1159 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3450 atoms have been selected out of 3524 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1117 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 753 251 251 0.00 3 C003 has 114 38 38 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1518 506 506 0.00 6 C006 has 456 152 152 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1699 564 563 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 108 36 36 0.87 Total of12603 atoms and 4192 groups and 4186 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3524 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1162 Number of atoms = 3521 Number of groups = 1167 Number of bonds = 3514 Number of angles = 1266 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1164 Number of HB donors = 2306 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1162 Number of atoms = 3521 Number of groups = 1167 Number of bonds = 3514 Number of angles = 1266 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1164 Number of HB donors = 2306 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.706" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1162" Evaluating: 1162-7 Parameter: NUMWAT <- "1155" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1155" Comparing "1081" and "1155". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.706" Parameter: BOX -> "32.706" Parameter: BOX -> "32.706" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.70600 B = 32.70600 C = 32.70600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8229 2 1 -1 0 -1 1.7779 3 1 -1 1 -1 4.6996 4 1 0 -1 -1 4.8303 5 1 0 0 -1 0.8844 6 1 0 1 -1 1.7163 7 1 -1 -1 0 4.6819 8 1 -1 0 0 1.0373 9 1 -1 1 0 4.5597 10 1 0 -1 0 0.7243 11 1 0 1 0 0.7243 12 1 -1 -1 1 5.4375 13 1 -1 0 1 1.6284 14 1 -1 1 1 6.1130 15 1 0 -1 1 1.7163 16 1 0 0 1 0.8844 17 1 0 1 1 4.8303 18 1 1 1 1 5.8229 19 1 1 0 1 1.7779 20 1 1 -1 1 4.6996 21 1 1 1 0 4.6819 22 1 1 0 0 1.0373 23 1 1 -1 0 4.5597 24 1 1 1 -1 5.4375 25 1 1 0 -1 1.6284 26 1 1 -1 -1 6.1130 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3447 atoms have been selected out of 3521 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1515 505 505 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1696 563 562 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 108 36 36 0.87 Total of12582 atoms and 4185 groups and 4179 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3521 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1162 Number of atoms = 3521 Number of groups = 1167 Number of bonds = 3514 Number of angles = 1266 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1164 Number of HB donors = 2306 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1162 Number of atoms = 3521 Number of groups = 1167 Number of bonds = 3514 Number of angles = 1266 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1164 Number of HB donors = 2306 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.704" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1162" Evaluating: 1162-7 Parameter: NUMWAT <- "1155" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1155" Comparing "1081" and "1155". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.704" Parameter: BOX -> "32.704" Parameter: BOX -> "32.704" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.70400 B = 32.70400 C = 32.70400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8216 2 1 -1 0 -1 1.7753 3 1 -1 1 -1 4.6961 4 1 0 -1 -1 4.8283 5 1 0 0 -1 0.8828 6 1 0 1 -1 1.7137 7 1 -1 -1 0 4.6801 8 1 -1 0 0 1.0357 9 1 -1 1 0 4.5572 10 1 0 -1 0 0.7226 11 1 0 1 0 0.7226 12 1 -1 -1 1 5.4348 13 1 -1 0 1 1.6264 14 1 -1 1 1 6.1100 15 1 0 -1 1 1.7137 16 1 0 0 1 0.8828 17 1 0 1 1 4.8283 18 1 1 1 1 5.8216 19 1 1 0 1 1.7753 20 1 1 -1 1 4.6961 21 1 1 1 0 4.6801 22 1 1 0 0 1.0357 23 1 1 -1 0 4.5572 24 1 1 1 -1 5.4348 25 1 1 0 -1 1.6264 26 1 1 -1 -1 6.1100 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3447 atoms have been selected out of 3521 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 615 205 205 0.00 5 C005 has 1515 505 505 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1696 563 562 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 108 36 36 0.86 Total of12582 atoms and 4185 groups and 4179 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3521 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1162 Number of atoms = 3521 Number of groups = 1167 Number of bonds = 3514 Number of angles = 1266 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1164 Number of HB donors = 2306 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1162 Number of atoms = 3521 Number of groups = 1167 Number of bonds = 3514 Number of angles = 1266 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1164 Number of HB donors = 2306 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.702" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1162" Evaluating: 1162-7 Parameter: NUMWAT <- "1155" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1155" Comparing "1081" and "1155". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.702" Parameter: BOX -> "32.702" Parameter: BOX -> "32.702" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.70200 B = 32.70200 C = 32.70200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8203 2 1 -1 0 -1 1.7728 3 1 -1 1 -1 4.6927 4 1 0 -1 -1 4.8264 5 1 0 0 -1 0.8811 6 1 0 1 -1 1.7112 7 1 -1 -1 0 4.6783 8 1 -1 0 0 1.0342 9 1 -1 1 0 4.5548 10 1 0 -1 0 0.7208 11 1 0 1 0 0.7208 12 1 -1 -1 1 5.4321 13 1 -1 0 1 1.6244 14 1 -1 1 1 6.1071 15 1 0 -1 1 1.7112 16 1 0 0 1 0.8811 17 1 0 1 1 4.8264 18 1 1 1 1 5.8203 19 1 1 0 1 1.7728 20 1 1 -1 1 4.6927 21 1 1 1 0 4.6783 22 1 1 0 0 1.0342 23 1 1 -1 0 4.5548 24 1 1 1 -1 5.4321 25 1 1 0 -1 1.6244 26 1 1 -1 -1 6.1071 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3447 atoms have been selected out of 3521 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1515 505 505 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1696 563 562 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 108 36 36 0.86 Total of12585 atoms and 4186 groups and 4180 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3521 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1162 Number of atoms = 3521 Number of groups = 1167 Number of bonds = 3514 Number of angles = 1266 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1164 Number of HB donors = 2306 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1162 Number of atoms = 3521 Number of groups = 1167 Number of bonds = 3514 Number of angles = 1266 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1164 Number of HB donors = 2306 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.7" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1162" Evaluating: 1162-7 Parameter: NUMWAT <- "1155" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1155" Comparing "1081" and "1155". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.7" Parameter: BOX -> "32.7" Parameter: BOX -> "32.7" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.70000 B = 32.70000 C = 32.70000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8191 2 1 -1 0 -1 1.7702 3 1 -1 1 -1 4.6893 4 1 0 -1 -1 4.8245 5 1 0 0 -1 0.8795 6 1 0 1 -1 1.7086 7 1 -1 -1 0 4.6765 8 1 -1 0 0 1.0326 9 1 -1 1 0 4.5523 10 1 0 -1 0 0.7190 11 1 0 1 0 0.7190 12 1 -1 -1 1 5.4293 13 1 -1 0 1 1.6223 14 1 -1 1 1 6.1041 15 1 0 -1 1 1.7086 16 1 0 0 1 0.8795 17 1 0 1 1 4.8245 18 1 1 1 1 5.8191 19 1 1 0 1 1.7702 20 1 1 -1 1 4.6893 21 1 1 1 0 4.6765 22 1 1 0 0 1.0326 23 1 1 -1 0 4.5523 24 1 1 1 -1 5.4293 25 1 1 0 -1 1.6223 26 1 1 -1 -1 6.1041 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3447 atoms have been selected out of 3521 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1515 505 505 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1696 563 562 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 108 36 36 0.86 Total of12585 atoms and 4186 groups and 4180 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3521 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1162 Number of atoms = 3521 Number of groups = 1167 Number of bonds = 3514 Number of angles = 1266 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1164 Number of HB donors = 2306 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1162 Number of atoms = 3521 Number of groups = 1167 Number of bonds = 3514 Number of angles = 1266 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1164 Number of HB donors = 2306 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.698" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1162" Evaluating: 1162-7 Parameter: NUMWAT <- "1155" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1155" Comparing "1081" and "1155". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.698" Parameter: BOX -> "32.698" Parameter: BOX -> "32.698" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.69800 B = 32.69800 C = 32.69800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8178 2 1 -1 0 -1 1.7677 3 1 -1 1 -1 4.6859 4 1 0 -1 -1 4.8226 5 1 0 0 -1 0.8779 6 1 0 1 -1 1.7060 7 1 -1 -1 0 4.6747 8 1 -1 0 0 1.0310 9 1 -1 1 0 4.5499 10 1 0 -1 0 0.7173 11 1 0 1 0 0.7173 12 1 -1 -1 1 5.4266 13 1 -1 0 1 1.6203 14 1 -1 1 1 6.1012 15 1 0 -1 1 1.7060 16 1 0 0 1 0.8779 17 1 0 1 1 4.8226 18 1 1 1 1 5.8178 19 1 1 0 1 1.7677 20 1 1 -1 1 4.6859 21 1 1 1 0 4.6747 22 1 1 0 0 1.0310 23 1 1 -1 0 4.5499 24 1 1 1 -1 5.4266 25 1 1 0 -1 1.6203 26 1 1 -1 -1 6.1012 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3447 atoms have been selected out of 3521 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1515 505 505 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1696 563 562 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 108 36 36 0.86 Total of12588 atoms and 4187 groups and 4181 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3521 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1162 Number of atoms = 3521 Number of groups = 1167 Number of bonds = 3514 Number of angles = 1266 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1164 Number of HB donors = 2306 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1162 Number of atoms = 3521 Number of groups = 1167 Number of bonds = 3514 Number of angles = 1266 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1164 Number of HB donors = 2306 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.696" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1162" Evaluating: 1162-7 Parameter: NUMWAT <- "1155" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1155" Comparing "1081" and "1155". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.696" Parameter: BOX -> "32.696" Parameter: BOX -> "32.696" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.69600 B = 32.69600 C = 32.69600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8166 2 1 -1 0 -1 1.7651 3 1 -1 1 -1 4.6825 4 1 0 -1 -1 4.8207 5 1 0 0 -1 0.8762 6 1 0 1 -1 1.7035 7 1 -1 -1 0 4.6729 8 1 -1 0 0 1.0294 9 1 -1 1 0 4.5474 10 1 0 -1 0 0.7155 11 1 0 1 0 0.7155 12 1 -1 -1 1 5.4238 13 1 -1 0 1 1.6183 14 1 -1 1 1 6.0983 15 1 0 -1 1 1.7035 16 1 0 0 1 0.8762 17 1 0 1 1 4.8207 18 1 1 1 1 5.8166 19 1 1 0 1 1.7651 20 1 1 -1 1 4.6825 21 1 1 1 0 4.6729 22 1 1 0 0 1.0294 23 1 1 -1 0 4.5474 24 1 1 1 -1 5.4238 25 1 1 0 -1 1.6183 26 1 1 -1 -1 6.0983 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3447 atoms have been selected out of 3521 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1515 505 505 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1696 563 562 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 108 36 36 0.86 Total of12588 atoms and 4187 groups and 4181 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3521 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1162 Number of atoms = 3521 Number of groups = 1167 Number of bonds = 3514 Number of angles = 1266 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1164 Number of HB donors = 2306 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1162 Number of atoms = 3521 Number of groups = 1167 Number of bonds = 3514 Number of angles = 1266 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1164 Number of HB donors = 2306 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.694" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1162" Evaluating: 1162-7 Parameter: NUMWAT <- "1155" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1155" Comparing "1081" and "1155". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.694" Parameter: BOX -> "32.694" Parameter: BOX -> "32.694" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.69400 B = 32.69400 C = 32.69400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8153 2 1 -1 0 -1 1.7626 3 1 -1 1 -1 4.6790 4 1 0 -1 -1 4.8188 5 1 0 0 -1 0.8746 6 1 0 1 -1 1.7009 7 1 -1 -1 0 4.6711 8 1 -1 0 0 1.0278 9 1 -1 1 0 4.5449 10 1 0 -1 0 0.7137 11 1 0 1 0 0.7137 12 1 -1 -1 1 5.4211 13 1 -1 0 1 1.6163 14 1 -1 1 1 6.0953 15 1 0 -1 1 1.7009 16 1 0 0 1 0.8746 17 1 0 1 1 4.8188 18 1 1 1 1 5.8153 19 1 1 0 1 1.7626 20 1 1 -1 1 4.6790 21 1 1 1 0 4.6711 22 1 1 0 0 1.0278 23 1 1 -1 0 4.5449 24 1 1 1 -1 5.4211 25 1 1 0 -1 1.6163 26 1 1 -1 -1 6.0953 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3447 atoms have been selected out of 3521 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1515 505 505 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1696 563 562 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 108 36 36 0.85 Total of12588 atoms and 4187 groups and 4181 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3521 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1162 Number of atoms = 3521 Number of groups = 1167 Number of bonds = 3514 Number of angles = 1266 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1164 Number of HB donors = 2306 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1162 Number of atoms = 3521 Number of groups = 1167 Number of bonds = 3514 Number of angles = 1266 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1164 Number of HB donors = 2306 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.692" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1162" Evaluating: 1162-7 Parameter: NUMWAT <- "1155" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1155" Comparing "1081" and "1155". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.692" Parameter: BOX -> "32.692" Parameter: BOX -> "32.692" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.69200 B = 32.69200 C = 32.69200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8141 2 1 -1 0 -1 1.7600 3 1 -1 1 -1 4.6756 4 1 0 -1 -1 4.8168 5 1 0 0 -1 0.8730 6 1 0 1 -1 1.6984 7 1 -1 -1 0 4.6693 8 1 -1 0 0 1.0263 9 1 -1 1 0 4.5425 10 1 0 -1 0 0.7119 11 1 0 1 0 0.7119 12 1 -1 -1 1 5.4184 13 1 -1 0 1 1.6143 14 1 -1 1 1 6.0924 15 1 0 -1 1 1.6984 16 1 0 0 1 0.8730 17 1 0 1 1 4.8168 18 1 1 1 1 5.8141 19 1 1 0 1 1.7600 20 1 1 -1 1 4.6756 21 1 1 1 0 4.6693 22 1 1 0 0 1.0263 23 1 1 -1 0 4.5425 24 1 1 1 -1 5.4184 25 1 1 0 -1 1.6143 26 1 1 -1 -1 6.0924 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3447 atoms have been selected out of 3521 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1145 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 462 154 154 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1512 504 504 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1696 563 562 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 102 34 34 0.00 13 C013 has 468 156 156 0.00 14 C014 has 111 37 37 0.85 Total of12588 atoms and 4187 groups and 4181 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3521 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1161 Number of atoms = 3518 Number of groups = 1166 Number of bonds = 3511 Number of angles = 1265 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1163 Number of HB donors = 2304 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1161 Number of atoms = 3518 Number of groups = 1166 Number of bonds = 3511 Number of angles = 1265 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1163 Number of HB donors = 2304 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.69" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1161" Evaluating: 1161-7 Parameter: NUMWAT <- "1154" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1154" Comparing "1081" and "1154". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.69" Parameter: BOX -> "32.69" Parameter: BOX -> "32.69" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.69000 B = 32.69000 C = 32.69000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8129 2 1 -1 0 -1 1.7575 3 1 -1 1 -1 4.6722 4 1 0 -1 -1 4.8149 5 1 0 0 -1 0.8713 6 1 0 1 -1 1.6958 7 1 -1 -1 0 4.6675 8 1 -1 0 0 1.0247 9 1 -1 1 0 4.5400 10 1 0 -1 0 0.7102 11 1 0 1 0 0.7102 12 1 -1 -1 1 5.4156 13 1 -1 0 1 1.6122 14 1 -1 1 1 6.0894 15 1 0 -1 1 1.6958 16 1 0 0 1 0.8713 17 1 0 1 1 4.8149 18 1 1 1 1 5.8129 19 1 1 0 1 1.7575 20 1 1 -1 1 4.6722 21 1 1 1 0 4.6675 22 1 1 0 0 1.0247 23 1 1 -1 0 4.5400 24 1 1 1 -1 5.4156 25 1 1 0 -1 1.6122 26 1 1 -1 -1 6.0894 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3444 atoms have been selected out of 3518 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 462 154 154 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1512 504 504 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1693 562 561 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.85 Total of12570 atoms and 4181 groups and 4175 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3518 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1161 Number of atoms = 3518 Number of groups = 1166 Number of bonds = 3511 Number of angles = 1265 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1163 Number of HB donors = 2304 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1161 Number of atoms = 3518 Number of groups = 1166 Number of bonds = 3511 Number of angles = 1265 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1163 Number of HB donors = 2304 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.688" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1161" Evaluating: 1161-7 Parameter: NUMWAT <- "1154" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1154" Comparing "1081" and "1154". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.688" Parameter: BOX -> "32.688" Parameter: BOX -> "32.688" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.68800 B = 32.68800 C = 32.68800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8116 2 1 -1 0 -1 1.7550 3 1 -1 1 -1 4.6688 4 1 0 -1 -1 4.8130 5 1 0 0 -1 0.8697 6 1 0 1 -1 1.6933 7 1 -1 -1 0 4.6657 8 1 -1 0 0 1.0231 9 1 -1 1 0 4.5375 10 1 0 -1 0 0.7084 11 1 0 1 0 0.7084 12 1 -1 -1 1 5.4129 13 1 -1 0 1 1.6102 14 1 -1 1 1 6.0865 15 1 0 -1 1 1.6933 16 1 0 0 1 0.8697 17 1 0 1 1 4.8130 18 1 1 1 1 5.8116 19 1 1 0 1 1.7550 20 1 1 -1 1 4.6688 21 1 1 1 0 4.6657 22 1 1 0 0 1.0231 23 1 1 -1 0 4.5375 24 1 1 1 -1 5.4129 25 1 1 0 -1 1.6102 26 1 1 -1 -1 6.0865 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3444 atoms have been selected out of 3518 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 462 154 154 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1515 505 505 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1696 563 562 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.85 Total of12576 atoms and 4183 groups and 4177 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3518 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1161 Number of atoms = 3518 Number of groups = 1166 Number of bonds = 3511 Number of angles = 1265 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1163 Number of HB donors = 2304 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1161 Number of atoms = 3518 Number of groups = 1166 Number of bonds = 3511 Number of angles = 1265 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1163 Number of HB donors = 2304 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.686" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1161" Evaluating: 1161-7 Parameter: NUMWAT <- "1154" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1154" Comparing "1081" and "1154". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.686" Parameter: BOX -> "32.686" Parameter: BOX -> "32.686" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.68600 B = 32.68600 C = 32.68600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8104 2 1 -1 0 -1 1.7524 3 1 -1 1 -1 4.6654 4 1 0 -1 -1 4.8111 5 1 0 0 -1 0.8681 6 1 0 1 -1 1.6907 7 1 -1 -1 0 4.6639 8 1 -1 0 0 1.0215 9 1 -1 1 0 4.5351 10 1 0 -1 0 0.7067 11 1 0 1 0 0.7067 12 1 -1 -1 1 5.4101 13 1 -1 0 1 1.6082 14 1 -1 1 1 6.0835 15 1 0 -1 1 1.6907 16 1 0 0 1 0.8681 17 1 0 1 1 4.8111 18 1 1 1 1 5.8104 19 1 1 0 1 1.7524 20 1 1 -1 1 4.6654 21 1 1 1 0 4.6639 22 1 1 0 0 1.0215 23 1 1 -1 0 4.5351 24 1 1 1 -1 5.4101 25 1 1 0 -1 1.6082 26 1 1 -1 -1 6.0835 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3444 atoms have been selected out of 3518 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 462 154 154 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 618 206 206 0.00 5 C005 has 1515 505 505 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1696 563 562 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.85 Total of12576 atoms and 4183 groups and 4177 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3518 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1161 Number of atoms = 3518 Number of groups = 1166 Number of bonds = 3511 Number of angles = 1265 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1163 Number of HB donors = 2304 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1161 Number of atoms = 3518 Number of groups = 1166 Number of bonds = 3511 Number of angles = 1265 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1163 Number of HB donors = 2304 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.684" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1161" Evaluating: 1161-7 Parameter: NUMWAT <- "1154" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1154" Comparing "1081" and "1154". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.684" Parameter: BOX -> "32.684" Parameter: BOX -> "32.684" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.68400 B = 32.68400 C = 32.68400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8091 2 1 -1 0 -1 1.7499 3 1 -1 1 -1 4.6619 4 1 0 -1 -1 4.8092 5 1 0 0 -1 0.8665 6 1 0 1 -1 1.6881 7 1 -1 -1 0 4.6621 8 1 -1 0 0 1.0200 9 1 -1 1 0 4.5326 10 1 0 -1 0 0.7049 11 1 0 1 0 0.7049 12 1 -1 -1 1 5.4074 13 1 -1 0 1 1.6062 14 1 -1 1 1 6.0806 15 1 0 -1 1 1.6881 16 1 0 0 1 0.8665 17 1 0 1 1 4.8092 18 1 1 1 1 5.8091 19 1 1 0 1 1.7499 20 1 1 -1 1 4.6619 21 1 1 1 0 4.6621 22 1 1 0 0 1.0200 23 1 1 -1 0 4.5326 24 1 1 1 -1 5.4074 25 1 1 0 -1 1.6062 26 1 1 -1 -1 6.0806 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3444 atoms have been selected out of 3518 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 462 154 154 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1515 505 505 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1696 563 562 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 114 38 38 0.84 Total of12585 atoms and 4186 groups and 4180 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3518 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1161 Number of atoms = 3518 Number of groups = 1166 Number of bonds = 3511 Number of angles = 1265 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1163 Number of HB donors = 2304 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1161 Number of atoms = 3518 Number of groups = 1166 Number of bonds = 3511 Number of angles = 1265 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1163 Number of HB donors = 2304 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.682" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1161" Evaluating: 1161-7 Parameter: NUMWAT <- "1154" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1154" Comparing "1081" and "1154". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.682" Parameter: BOX -> "32.682" Parameter: BOX -> "32.682" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.68200 B = 32.68200 C = 32.68200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8079 2 1 -1 0 -1 1.7473 3 1 -1 1 -1 4.6585 4 1 0 -1 -1 4.8073 5 1 0 0 -1 0.8648 6 1 0 1 -1 1.6856 7 1 -1 -1 0 4.6604 8 1 -1 0 0 1.0184 9 1 -1 1 0 4.5302 10 1 0 -1 0 0.7031 11 1 0 1 0 0.7031 12 1 -1 -1 1 5.4047 13 1 -1 0 1 1.6042 14 1 -1 1 1 6.0777 15 1 0 -1 1 1.6856 16 1 0 0 1 0.8648 17 1 0 1 1 4.8073 18 1 1 1 1 5.8079 19 1 1 0 1 1.7473 20 1 1 -1 1 4.6585 21 1 1 1 0 4.6604 22 1 1 0 0 1.0184 23 1 1 -1 0 4.5302 24 1 1 1 -1 5.4047 25 1 1 0 -1 1.6042 26 1 1 -1 -1 6.0777 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3444 atoms have been selected out of 3518 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 462 154 154 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1515 505 505 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1696 563 562 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 114 38 38 0.84 Total of12585 atoms and 4186 groups and 4180 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3518 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1161 Number of atoms = 3518 Number of groups = 1166 Number of bonds = 3511 Number of angles = 1265 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1163 Number of HB donors = 2304 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1161 Number of atoms = 3518 Number of groups = 1166 Number of bonds = 3511 Number of angles = 1265 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1163 Number of HB donors = 2304 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.68" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1161" Evaluating: 1161-7 Parameter: NUMWAT <- "1154" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1154" Comparing "1081" and "1154". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.68" Parameter: BOX -> "32.68" Parameter: BOX -> "32.68" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.68000 B = 32.68000 C = 32.68000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8067 2 1 -1 0 -1 1.7448 3 1 -1 1 -1 4.6551 4 1 0 -1 -1 4.8054 5 1 0 0 -1 0.8632 6 1 0 1 -1 1.6830 7 1 -1 -1 0 4.6586 8 1 -1 0 0 1.0168 9 1 -1 1 0 4.5277 10 1 0 -1 0 0.7014 11 1 0 1 0 0.7014 12 1 -1 -1 1 5.4019 13 1 -1 0 1 1.6022 14 1 -1 1 1 6.0747 15 1 0 -1 1 1.6830 16 1 0 0 1 0.8632 17 1 0 1 1 4.8054 18 1 1 1 1 5.8067 19 1 1 0 1 1.7448 20 1 1 -1 1 4.6551 21 1 1 1 0 4.6586 22 1 1 0 0 1.0168 23 1 1 -1 0 4.5277 24 1 1 1 -1 5.4019 25 1 1 0 -1 1.6022 26 1 1 -1 -1 6.0747 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3444 atoms have been selected out of 3518 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 462 154 154 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1515 505 505 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1696 563 562 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 114 38 38 0.84 Total of12585 atoms and 4186 groups and 4180 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3518 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1161 Number of atoms = 3518 Number of groups = 1166 Number of bonds = 3511 Number of angles = 1265 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1163 Number of HB donors = 2304 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1161 Number of atoms = 3518 Number of groups = 1166 Number of bonds = 3511 Number of angles = 1265 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1163 Number of HB donors = 2304 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.678" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1161" Evaluating: 1161-7 Parameter: NUMWAT <- "1154" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1154" Comparing "1081" and "1154". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.678" Parameter: BOX -> "32.678" Parameter: BOX -> "32.678" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.67800 B = 32.67800 C = 32.67800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8054 2 1 -1 0 -1 1.7422 3 1 -1 1 -1 4.6517 4 1 0 -1 -1 4.8035 5 1 0 0 -1 0.8616 6 1 0 1 -1 1.6805 7 1 -1 -1 0 4.6568 8 1 -1 0 0 1.0153 9 1 -1 1 0 4.5252 10 1 0 -1 0 0.6996 11 1 0 1 0 0.6996 12 1 -1 -1 1 5.3992 13 1 -1 0 1 1.6002 14 1 -1 1 1 6.0718 15 1 0 -1 1 1.6805 16 1 0 0 1 0.8616 17 1 0 1 1 4.8035 18 1 1 1 1 5.8054 19 1 1 0 1 1.7422 20 1 1 -1 1 4.6517 21 1 1 1 0 4.6568 22 1 1 0 0 1.0153 23 1 1 -1 0 4.5252 24 1 1 1 -1 5.3992 25 1 1 0 -1 1.6002 26 1 1 -1 -1 6.0718 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3444 atoms have been selected out of 3518 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 462 154 154 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1515 505 505 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1696 563 562 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 114 38 38 0.84 Total of12585 atoms and 4186 groups and 4180 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3518 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1161 Number of atoms = 3518 Number of groups = 1166 Number of bonds = 3511 Number of angles = 1265 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1163 Number of HB donors = 2304 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1161 Number of atoms = 3518 Number of groups = 1166 Number of bonds = 3511 Number of angles = 1265 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1163 Number of HB donors = 2304 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.676" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1161" Evaluating: 1161-7 Parameter: NUMWAT <- "1154" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1154" Comparing "1081" and "1154". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.676" Parameter: BOX -> "32.676" Parameter: BOX -> "32.676" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.67600 B = 32.67600 C = 32.67600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8042 2 1 -1 0 -1 1.7397 3 1 -1 1 -1 4.6483 4 1 0 -1 -1 4.8016 5 1 0 0 -1 0.8600 6 1 0 1 -1 1.6779 7 1 -1 -1 0 4.6550 8 1 -1 0 0 1.0137 9 1 -1 1 0 4.5228 10 1 0 -1 0 0.6979 11 1 0 1 0 0.6979 12 1 -1 -1 1 5.3965 13 1 -1 0 1 1.5982 14 1 -1 1 1 6.0688 15 1 0 -1 1 1.6779 16 1 0 0 1 0.8600 17 1 0 1 1 4.8016 18 1 1 1 1 5.8042 19 1 1 0 1 1.7397 20 1 1 -1 1 4.6483 21 1 1 1 0 4.6550 22 1 1 0 0 1.0137 23 1 1 -1 0 4.5228 24 1 1 1 -1 5.3965 25 1 1 0 -1 1.5982 26 1 1 -1 -1 6.0688 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3444 atoms have been selected out of 3518 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 462 154 154 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1515 505 505 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1699 564 563 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 114 38 38 0.84 Total of12591 atoms and 4188 groups and 4182 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3518 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1161 Number of atoms = 3518 Number of groups = 1166 Number of bonds = 3511 Number of angles = 1265 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1163 Number of HB donors = 2304 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1161 Number of atoms = 3518 Number of groups = 1166 Number of bonds = 3511 Number of angles = 1265 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1163 Number of HB donors = 2304 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.674" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1161" Evaluating: 1161-7 Parameter: NUMWAT <- "1154" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1154" Comparing "1081" and "1154". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.674" Parameter: BOX -> "32.674" Parameter: BOX -> "32.674" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.67400 B = 32.67400 C = 32.67400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8030 2 1 -1 0 -1 1.7372 3 1 -1 1 -1 4.6448 4 1 0 -1 -1 4.7997 5 1 0 0 -1 0.8584 6 1 0 1 -1 1.6754 7 1 -1 -1 0 4.6532 8 1 -1 0 0 1.0122 9 1 -1 1 0 4.5203 10 1 0 -1 0 0.6961 11 1 0 1 0 0.6961 12 1 -1 -1 1 5.3937 13 1 -1 0 1 1.5962 14 1 -1 1 1 6.0659 15 1 0 -1 1 1.6754 16 1 0 0 1 0.8584 17 1 0 1 1 4.7997 18 1 1 1 1 5.8030 19 1 1 0 1 1.7372 20 1 1 -1 1 4.6448 21 1 1 1 0 4.6532 22 1 1 0 0 1.0122 23 1 1 -1 0 4.5203 24 1 1 1 -1 5.3937 25 1 1 0 -1 1.5962 26 1 1 -1 -1 6.0659 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3444 atoms have been selected out of 3518 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 275 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 462 154 154 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1515 505 505 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1696 563 562 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.83 Total of12579 atoms and 4184 groups and 4178 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3518 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1160 Number of atoms = 3515 Number of groups = 1165 Number of bonds = 3508 Number of angles = 1264 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1162 Number of HB donors = 2302 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1160 Number of atoms = 3515 Number of groups = 1165 Number of bonds = 3508 Number of angles = 1264 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1162 Number of HB donors = 2302 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.672" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1160" Evaluating: 1160-7 Parameter: NUMWAT <- "1153" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1153" Comparing "1081" and "1153". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.672" Parameter: BOX -> "32.672" Parameter: BOX -> "32.672" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.67200 B = 32.67200 C = 32.67200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8017 2 1 -1 0 -1 1.7346 3 1 -1 1 -1 4.6414 4 1 0 -1 -1 4.7978 5 1 0 0 -1 0.8567 6 1 0 1 -1 1.6728 7 1 -1 -1 0 4.6514 8 1 -1 0 0 1.0106 9 1 -1 1 0 4.5179 10 1 0 -1 0 0.6943 11 1 0 1 0 0.6943 12 1 -1 -1 1 5.3910 13 1 -1 0 1 1.5942 14 1 -1 1 1 6.0630 15 1 0 -1 1 1.6728 16 1 0 0 1 0.8567 17 1 0 1 1 4.7978 18 1 1 1 1 5.8017 19 1 1 0 1 1.7346 20 1 1 -1 1 4.6414 21 1 1 1 0 4.6514 22 1 1 0 0 1.0106 23 1 1 -1 0 4.5179 24 1 1 1 -1 5.3910 25 1 1 0 -1 1.5942 26 1 1 -1 -1 6.0630 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3441 atoms have been selected out of 3515 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 462 154 154 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1518 506 506 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1696 563 562 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.83 Total of12579 atoms and 4184 groups and 4178 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3515 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1160 Number of atoms = 3515 Number of groups = 1165 Number of bonds = 3508 Number of angles = 1264 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1162 Number of HB donors = 2302 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1160 Number of atoms = 3515 Number of groups = 1165 Number of bonds = 3508 Number of angles = 1264 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1162 Number of HB donors = 2302 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.67" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1160" Evaluating: 1160-7 Parameter: NUMWAT <- "1153" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1153" Comparing "1081" and "1153". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.67" Parameter: BOX -> "32.67" Parameter: BOX -> "32.67" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.67000 B = 32.67000 C = 32.67000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.8005 2 1 -1 0 -1 1.7321 3 1 -1 1 -1 4.6380 4 1 0 -1 -1 4.7959 5 1 0 0 -1 0.8551 6 1 0 1 -1 1.6703 7 1 -1 -1 0 4.6497 8 1 -1 0 0 1.0090 9 1 -1 1 0 4.5154 10 1 0 -1 0 0.6926 11 1 0 1 0 0.6926 12 1 -1 -1 1 5.3883 13 1 -1 0 1 1.5922 14 1 -1 1 1 6.0600 15 1 0 -1 1 1.6703 16 1 0 0 1 0.8551 17 1 0 1 1 4.7959 18 1 1 1 1 5.8005 19 1 1 0 1 1.7321 20 1 1 -1 1 4.6380 21 1 1 1 0 4.6497 22 1 1 0 0 1.0090 23 1 1 -1 0 4.5154 24 1 1 1 -1 5.3883 25 1 1 0 -1 1.5922 26 1 1 -1 -1 6.0600 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3441 atoms have been selected out of 3515 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 462 154 154 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1521 507 507 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1696 563 562 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.83 Total of12582 atoms and 4185 groups and 4179 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3515 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1160 Number of atoms = 3515 Number of groups = 1165 Number of bonds = 3508 Number of angles = 1264 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1162 Number of HB donors = 2302 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1160 Number of atoms = 3515 Number of groups = 1165 Number of bonds = 3508 Number of angles = 1264 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1162 Number of HB donors = 2302 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.668" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1160" Evaluating: 1160-7 Parameter: NUMWAT <- "1153" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1153" Comparing "1081" and "1153". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.668" Parameter: BOX -> "32.668" Parameter: BOX -> "32.668" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.66800 B = 32.66800 C = 32.66800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7993 2 1 -1 0 -1 1.7296 3 1 -1 1 -1 4.6346 4 1 0 -1 -1 4.7940 5 1 0 0 -1 0.8535 6 1 0 1 -1 1.6678 7 1 -1 -1 0 4.6479 8 1 -1 0 0 1.0075 9 1 -1 1 0 4.5130 10 1 0 -1 0 0.6908 11 1 0 1 0 0.6908 12 1 -1 -1 1 5.3855 13 1 -1 0 1 1.5902 14 1 -1 1 1 6.0571 15 1 0 -1 1 1.6678 16 1 0 0 1 0.8535 17 1 0 1 1 4.7940 18 1 1 1 1 5.7993 19 1 1 0 1 1.7296 20 1 1 -1 1 4.6346 21 1 1 1 0 4.6479 22 1 1 0 0 1.0075 23 1 1 -1 0 4.5130 24 1 1 1 -1 5.3855 25 1 1 0 -1 1.5902 26 1 1 -1 -1 6.0571 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3441 atoms have been selected out of 3515 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 462 154 154 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1521 507 507 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1696 563 562 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.83 Total of12582 atoms and 4185 groups and 4179 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3515 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1160 Number of atoms = 3515 Number of groups = 1165 Number of bonds = 3508 Number of angles = 1264 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1162 Number of HB donors = 2302 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1160 Number of atoms = 3515 Number of groups = 1165 Number of bonds = 3508 Number of angles = 1264 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1162 Number of HB donors = 2302 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.666" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1160" Evaluating: 1160-7 Parameter: NUMWAT <- "1153" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1153" Comparing "1081" and "1153". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.666" Parameter: BOX -> "32.666" Parameter: BOX -> "32.666" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.66600 B = 32.66600 C = 32.66600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7981 2 1 -1 0 -1 1.7270 3 1 -1 1 -1 4.6312 4 1 0 -1 -1 4.7921 5 1 0 0 -1 0.8519 6 1 0 1 -1 1.6652 7 1 -1 -1 0 4.6461 8 1 -1 0 0 1.0059 9 1 -1 1 0 4.5105 10 1 0 -1 0 0.6891 11 1 0 1 0 0.6891 12 1 -1 -1 1 5.3828 13 1 -1 0 1 1.5882 14 1 -1 1 1 6.0541 15 1 0 -1 1 1.6652 16 1 0 0 1 0.8519 17 1 0 1 1 4.7921 18 1 1 1 1 5.7981 19 1 1 0 1 1.7270 20 1 1 -1 1 4.6312 21 1 1 1 0 4.6461 22 1 1 0 0 1.0059 23 1 1 -1 0 4.5105 24 1 1 1 -1 5.3828 25 1 1 0 -1 1.5882 26 1 1 -1 -1 6.0541 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3441 atoms have been selected out of 3515 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 462 154 154 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1521 507 507 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1696 563 562 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.83 Total of12582 atoms and 4185 groups and 4179 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3515 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1160 Number of atoms = 3515 Number of groups = 1165 Number of bonds = 3508 Number of angles = 1264 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1162 Number of HB donors = 2302 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1160 Number of atoms = 3515 Number of groups = 1165 Number of bonds = 3508 Number of angles = 1264 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1162 Number of HB donors = 2302 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.664" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1160" Evaluating: 1160-7 Parameter: NUMWAT <- "1153" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1153" Comparing "1081" and "1153". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.664" Parameter: BOX -> "32.664" Parameter: BOX -> "32.664" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.66400 B = 32.66400 C = 32.66400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7968 2 1 -1 0 -1 1.7245 3 1 -1 1 -1 4.6277 4 1 0 -1 -1 4.7902 5 1 0 0 -1 0.8503 6 1 0 1 -1 1.6627 7 1 -1 -1 0 4.6443 8 1 -1 0 0 1.0044 9 1 -1 1 0 4.5081 10 1 0 -1 0 0.6873 11 1 0 1 0 0.6873 12 1 -1 -1 1 5.3801 13 1 -1 0 1 1.5862 14 1 -1 1 1 6.0512 15 1 0 -1 1 1.6627 16 1 0 0 1 0.8503 17 1 0 1 1 4.7902 18 1 1 1 1 5.7968 19 1 1 0 1 1.7245 20 1 1 -1 1 4.6277 21 1 1 1 0 4.6443 22 1 1 0 0 1.0044 23 1 1 -1 0 4.5081 24 1 1 1 -1 5.3801 25 1 1 0 -1 1.5862 26 1 1 -1 -1 6.0512 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3441 atoms have been selected out of 3515 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 462 154 154 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1521 507 507 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1696 563 562 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.82 Total of12582 atoms and 4185 groups and 4179 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3515 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1160 Number of atoms = 3515 Number of groups = 1165 Number of bonds = 3508 Number of angles = 1264 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1162 Number of HB donors = 2302 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1160 Number of atoms = 3515 Number of groups = 1165 Number of bonds = 3508 Number of angles = 1264 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1162 Number of HB donors = 2302 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.662" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1160" Evaluating: 1160-7 Parameter: NUMWAT <- "1153" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1153" Comparing "1081" and "1153". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.662" Parameter: BOX -> "32.662" Parameter: BOX -> "32.662" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.66200 B = 32.66200 C = 32.66200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7956 2 1 -1 0 -1 1.7220 3 1 -1 1 -1 4.6243 4 1 0 -1 -1 4.7883 5 1 0 0 -1 0.8487 6 1 0 1 -1 1.6601 7 1 -1 -1 0 4.6425 8 1 -1 0 0 1.0028 9 1 -1 1 0 4.5056 10 1 0 -1 0 0.6856 11 1 0 1 0 0.6856 12 1 -1 -1 1 5.3773 13 1 -1 0 1 1.5843 14 1 -1 1 1 6.0483 15 1 0 -1 1 1.6601 16 1 0 0 1 0.8487 17 1 0 1 1 4.7883 18 1 1 1 1 5.7956 19 1 1 0 1 1.7220 20 1 1 -1 1 4.6243 21 1 1 1 0 4.6425 22 1 1 0 0 1.0028 23 1 1 -1 0 4.5056 24 1 1 1 -1 5.3773 25 1 1 0 -1 1.5843 26 1 1 -1 -1 6.0483 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3441 atoms have been selected out of 3515 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1521 507 507 0.00 6 C006 has 456 152 152 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1696 563 562 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.82 Total of12588 atoms and 4187 groups and 4181 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3515 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1160 Number of atoms = 3515 Number of groups = 1165 Number of bonds = 3508 Number of angles = 1264 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1162 Number of HB donors = 2302 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1160 Number of atoms = 3515 Number of groups = 1165 Number of bonds = 3508 Number of angles = 1264 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1162 Number of HB donors = 2302 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.66" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1160" Evaluating: 1160-7 Parameter: NUMWAT <- "1153" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1153" Comparing "1081" and "1153". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.66" Parameter: BOX -> "32.66" Parameter: BOX -> "32.66" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.66000 B = 32.66000 C = 32.66000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7944 2 1 -1 0 -1 1.7194 3 1 -1 1 -1 4.6209 4 1 0 -1 -1 4.7864 5 1 0 0 -1 0.8471 6 1 0 1 -1 1.6576 7 1 -1 -1 0 4.6408 8 1 -1 0 0 1.0013 9 1 -1 1 0 4.5031 10 1 0 -1 0 0.6838 11 1 0 1 0 0.6838 12 1 -1 -1 1 5.3746 13 1 -1 0 1 1.5823 14 1 -1 1 1 6.0453 15 1 0 -1 1 1.6576 16 1 0 0 1 0.8471 17 1 0 1 1 4.7864 18 1 1 1 1 5.7944 19 1 1 0 1 1.7194 20 1 1 -1 1 4.6209 21 1 1 1 0 4.6408 22 1 1 0 0 1.0013 23 1 1 -1 0 4.5031 24 1 1 1 -1 5.3746 25 1 1 0 -1 1.5823 26 1 1 -1 -1 6.0453 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3441 atoms have been selected out of 3515 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1521 507 507 0.00 6 C006 has 456 152 152 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1702 565 564 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.82 Total of12594 atoms and 4189 groups and 4183 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3515 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1160 Number of atoms = 3515 Number of groups = 1165 Number of bonds = 3508 Number of angles = 1264 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1162 Number of HB donors = 2302 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1160 Number of atoms = 3515 Number of groups = 1165 Number of bonds = 3508 Number of angles = 1264 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1162 Number of HB donors = 2302 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.658" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1160" Evaluating: 1160-7 Parameter: NUMWAT <- "1153" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1153" Comparing "1081" and "1153". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.658" Parameter: BOX -> "32.658" Parameter: BOX -> "32.658" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.65800 B = 32.65800 C = 32.65800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7932 2 1 -1 0 -1 1.7169 3 1 -1 1 -1 4.6175 4 1 0 -1 -1 4.7845 5 1 0 0 -1 0.8455 6 1 0 1 -1 1.6550 7 1 -1 -1 0 4.6390 8 1 -1 0 0 0.9997 9 1 -1 1 0 4.5007 10 1 0 -1 0 0.6821 11 1 0 1 0 0.6821 12 1 -1 -1 1 5.3719 13 1 -1 0 1 1.5803 14 1 -1 1 1 6.0424 15 1 0 -1 1 1.6550 16 1 0 0 1 0.8455 17 1 0 1 1 4.7845 18 1 1 1 1 5.7932 19 1 1 0 1 1.7169 20 1 1 -1 1 4.6175 21 1 1 1 0 4.6390 22 1 1 0 0 0.9997 23 1 1 -1 0 4.5007 24 1 1 1 -1 5.3719 25 1 1 0 -1 1.5803 26 1 1 -1 -1 6.0424 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3441 atoms have been selected out of 3515 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1521 507 507 0.00 6 C006 has 459 153 153 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1705 566 565 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.82 Total of12600 atoms and 4191 groups and 4185 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3515 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1160 Number of atoms = 3515 Number of groups = 1165 Number of bonds = 3508 Number of angles = 1264 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1162 Number of HB donors = 2302 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1160 Number of atoms = 3515 Number of groups = 1165 Number of bonds = 3508 Number of angles = 1264 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1162 Number of HB donors = 2302 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.656" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1160" Evaluating: 1160-7 Parameter: NUMWAT <- "1153" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1153" Comparing "1081" and "1153". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.656" Parameter: BOX -> "32.656" Parameter: BOX -> "32.656" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.65600 B = 32.65600 C = 32.65600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7920 2 1 -1 0 -1 1.7144 3 1 -1 1 -1 4.6141 4 1 0 -1 -1 4.7826 5 1 0 0 -1 0.8439 6 1 0 1 -1 1.6525 7 1 -1 -1 0 4.6372 8 1 -1 0 0 0.9982 9 1 -1 1 0 4.4982 10 1 0 -1 0 0.6804 11 1 0 1 0 0.6804 12 1 -1 -1 1 5.3692 13 1 -1 0 1 1.5783 14 1 -1 1 1 6.0395 15 1 0 -1 1 1.6525 16 1 0 0 1 0.8439 17 1 0 1 1 4.7826 18 1 1 1 1 5.7920 19 1 1 0 1 1.7144 20 1 1 -1 1 4.6141 21 1 1 1 0 4.6372 22 1 1 0 0 0.9982 23 1 1 -1 0 4.4982 24 1 1 1 -1 5.3692 25 1 1 0 -1 1.5783 26 1 1 -1 -1 6.0395 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3441 atoms have been selected out of 3515 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1521 507 507 0.00 6 C006 has 459 153 153 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1705 566 565 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.82 Total of12603 atoms and 4192 groups and 4186 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3515 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1160 Number of atoms = 3515 Number of groups = 1165 Number of bonds = 3508 Number of angles = 1264 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1162 Number of HB donors = 2302 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1160 Number of atoms = 3515 Number of groups = 1165 Number of bonds = 3508 Number of angles = 1264 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1162 Number of HB donors = 2302 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.654" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1160" Evaluating: 1160-7 Parameter: NUMWAT <- "1153" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1153" Comparing "1081" and "1153". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.654" Parameter: BOX -> "32.654" Parameter: BOX -> "32.654" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.65400 B = 32.65400 C = 32.65400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7908 2 1 -1 0 -1 1.7118 3 1 -1 1 -1 4.6107 4 1 0 -1 -1 4.7807 5 1 0 0 -1 0.8423 6 1 0 1 -1 1.6500 7 1 -1 -1 0 4.6354 8 1 -1 0 0 0.9966 9 1 -1 1 0 4.4958 10 1 0 -1 0 0.6786 11 1 0 1 0 0.6786 12 1 -1 -1 1 5.3664 13 1 -1 0 1 1.5764 14 1 -1 1 1 6.0365 15 1 0 -1 1 1.6500 16 1 0 0 1 0.8423 17 1 0 1 1 4.7807 18 1 1 1 1 5.7908 19 1 1 0 1 1.7118 20 1 1 -1 1 4.6107 21 1 1 1 0 4.6354 22 1 1 0 0 0.9966 23 1 1 -1 0 4.4958 24 1 1 1 -1 5.3664 25 1 1 0 -1 1.5764 26 1 1 -1 -1 6.0365 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3441 atoms have been selected out of 3515 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 350 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1524 508 508 0.00 6 C006 has 459 153 153 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1708 567 566 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.81 Total of12603 atoms and 4192 groups and 4186 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3515 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1159 Number of atoms = 3512 Number of groups = 1164 Number of bonds = 3505 Number of angles = 1263 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1161 Number of HB donors = 2300 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1159 Number of atoms = 3512 Number of groups = 1164 Number of bonds = 3505 Number of angles = 1263 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1161 Number of HB donors = 2300 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.652" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1159" Evaluating: 1159-7 Parameter: NUMWAT <- "1152" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1152" Comparing "1081" and "1152". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.652" Parameter: BOX -> "32.652" Parameter: BOX -> "32.652" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.65200 B = 32.65200 C = 32.65200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7896 2 1 -1 0 -1 1.7093 3 1 -1 1 -1 4.6072 4 1 0 -1 -1 4.7788 5 1 0 0 -1 0.8407 6 1 0 1 -1 1.6474 7 1 -1 -1 0 4.6337 8 1 -1 0 0 0.9951 9 1 -1 1 0 4.4933 10 1 0 -1 0 0.6769 11 1 0 1 0 0.6769 12 1 -1 -1 1 5.3637 13 1 -1 0 1 1.5744 14 1 -1 1 1 6.0336 15 1 0 -1 1 1.6474 16 1 0 0 1 0.8407 17 1 0 1 1 4.7788 18 1 1 1 1 5.7896 19 1 1 0 1 1.7093 20 1 1 -1 1 4.6072 21 1 1 1 0 4.6337 22 1 1 0 0 0.9951 23 1 1 -1 0 4.4933 24 1 1 1 -1 5.3637 25 1 1 0 -1 1.5744 26 1 1 -1 -1 6.0336 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3438 atoms have been selected out of 3512 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1524 508 508 0.00 6 C006 has 459 153 153 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1705 566 565 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.81 Total of12597 atoms and 4190 groups and 4184 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3512 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1159 Number of atoms = 3512 Number of groups = 1164 Number of bonds = 3505 Number of angles = 1263 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1161 Number of HB donors = 2300 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1159 Number of atoms = 3512 Number of groups = 1164 Number of bonds = 3505 Number of angles = 1263 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1161 Number of HB donors = 2300 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.65" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1159" Evaluating: 1159-7 Parameter: NUMWAT <- "1152" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1152" Comparing "1081" and "1152". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.65" Parameter: BOX -> "32.65" Parameter: BOX -> "32.65" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.65000 B = 32.65000 C = 32.65000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7884 2 1 -1 0 -1 1.7068 3 1 -1 1 -1 4.6038 4 1 0 -1 -1 4.7769 5 1 0 0 -1 0.8391 6 1 0 1 -1 1.6449 7 1 -1 -1 0 4.6319 8 1 -1 0 0 0.9935 9 1 -1 1 0 4.4909 10 1 0 -1 0 0.6751 11 1 0 1 0 0.6751 12 1 -1 -1 1 5.3610 13 1 -1 0 1 1.5724 14 1 -1 1 1 6.0307 15 1 0 -1 1 1.6449 16 1 0 0 1 0.8391 17 1 0 1 1 4.7769 18 1 1 1 1 5.7884 19 1 1 0 1 1.7068 20 1 1 -1 1 4.6038 21 1 1 1 0 4.6319 22 1 1 0 0 0.9935 23 1 1 -1 0 4.4909 24 1 1 1 -1 5.3610 25 1 1 0 -1 1.5724 26 1 1 -1 -1 6.0307 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3438 atoms have been selected out of 3512 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1524 508 508 0.00 6 C006 has 459 153 153 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1705 566 565 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.81 Total of12597 atoms and 4190 groups and 4184 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3512 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1159 Number of atoms = 3512 Number of groups = 1164 Number of bonds = 3505 Number of angles = 1263 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1161 Number of HB donors = 2300 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1159 Number of atoms = 3512 Number of groups = 1164 Number of bonds = 3505 Number of angles = 1263 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1161 Number of HB donors = 2300 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.648" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1159" Evaluating: 1159-7 Parameter: NUMWAT <- "1152" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1152" Comparing "1081" and "1152". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.648" Parameter: BOX -> "32.648" Parameter: BOX -> "32.648" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.64800 B = 32.64800 C = 32.64800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7872 2 1 -1 0 -1 1.7042 3 1 -1 1 -1 4.6004 4 1 0 -1 -1 4.7750 5 1 0 0 -1 0.8375 6 1 0 1 -1 1.6423 7 1 -1 -1 0 4.6301 8 1 -1 0 0 0.9920 9 1 -1 1 0 4.4884 10 1 0 -1 0 0.6734 11 1 0 1 0 0.6734 12 1 -1 -1 1 5.3583 13 1 -1 0 1 1.5705 14 1 -1 1 1 6.0277 15 1 0 -1 1 1.6423 16 1 0 0 1 0.8375 17 1 0 1 1 4.7750 18 1 1 1 1 5.7872 19 1 1 0 1 1.7042 20 1 1 -1 1 4.6004 21 1 1 1 0 4.6301 22 1 1 0 0 0.9920 23 1 1 -1 0 4.4884 24 1 1 1 -1 5.3583 25 1 1 0 -1 1.5705 26 1 1 -1 -1 6.0277 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3438 atoms have been selected out of 3512 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1524 508 508 0.00 6 C006 has 459 153 153 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1705 566 565 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.81 Total of12600 atoms and 4191 groups and 4185 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3512 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1159 Number of atoms = 3512 Number of groups = 1164 Number of bonds = 3505 Number of angles = 1263 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1161 Number of HB donors = 2300 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1159 Number of atoms = 3512 Number of groups = 1164 Number of bonds = 3505 Number of angles = 1263 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1161 Number of HB donors = 2300 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.646" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1159" Evaluating: 1159-7 Parameter: NUMWAT <- "1152" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1152" Comparing "1081" and "1152". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.646" Parameter: BOX -> "32.646" Parameter: BOX -> "32.646" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.64600 B = 32.64600 C = 32.64600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7859 2 1 -1 0 -1 1.7017 3 1 -1 1 -1 4.5970 4 1 0 -1 -1 4.7731 5 1 0 0 -1 0.8359 6 1 0 1 -1 1.6398 7 1 -1 -1 0 4.6284 8 1 -1 0 0 0.9905 9 1 -1 1 0 4.4860 10 1 0 -1 0 0.6717 11 1 0 1 0 0.6717 12 1 -1 -1 1 5.3556 13 1 -1 0 1 1.5685 14 1 -1 1 1 6.0248 15 1 0 -1 1 1.6398 16 1 0 0 1 0.8359 17 1 0 1 1 4.7731 18 1 1 1 1 5.7859 19 1 1 0 1 1.7017 20 1 1 -1 1 4.5970 21 1 1 1 0 4.6284 22 1 1 0 0 0.9905 23 1 1 -1 0 4.4860 24 1 1 1 -1 5.3556 25 1 1 0 -1 1.5685 26 1 1 -1 -1 6.0248 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3438 atoms have been selected out of 3512 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1524 508 508 0.00 6 C006 has 459 153 153 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1708 567 566 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.81 Total of12603 atoms and 4192 groups and 4186 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3512 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1159 Number of atoms = 3512 Number of groups = 1164 Number of bonds = 3505 Number of angles = 1263 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1161 Number of HB donors = 2300 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1159 Number of atoms = 3512 Number of groups = 1164 Number of bonds = 3505 Number of angles = 1263 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1161 Number of HB donors = 2300 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.644" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1159" Evaluating: 1159-7 Parameter: NUMWAT <- "1152" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1152" Comparing "1081" and "1152". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.644" Parameter: BOX -> "32.644" Parameter: BOX -> "32.644" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.64400 B = 32.64400 C = 32.64400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7847 2 1 -1 0 -1 1.6992 3 1 -1 1 -1 4.5936 4 1 0 -1 -1 4.7712 5 1 0 0 -1 0.8343 6 1 0 1 -1 1.6373 7 1 -1 -1 0 4.6266 8 1 -1 0 0 0.9889 9 1 -1 1 0 4.4835 10 1 0 -1 0 0.6699 11 1 0 1 0 0.6699 12 1 -1 -1 1 5.3528 13 1 -1 0 1 1.5665 14 1 -1 1 1 6.0219 15 1 0 -1 1 1.6373 16 1 0 0 1 0.8343 17 1 0 1 1 4.7712 18 1 1 1 1 5.7847 19 1 1 0 1 1.6992 20 1 1 -1 1 4.5936 21 1 1 1 0 4.6266 22 1 1 0 0 0.9889 23 1 1 -1 0 4.4835 24 1 1 1 -1 5.3528 25 1 1 0 -1 1.5665 26 1 1 -1 -1 6.0219 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3438 atoms have been selected out of 3512 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1524 508 508 0.00 6 C006 has 459 153 153 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1708 567 566 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.80 Total of12606 atoms and 4193 groups and 4187 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3512 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1159 Number of atoms = 3512 Number of groups = 1164 Number of bonds = 3505 Number of angles = 1263 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1161 Number of HB donors = 2300 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1159 Number of atoms = 3512 Number of groups = 1164 Number of bonds = 3505 Number of angles = 1263 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1161 Number of HB donors = 2300 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.642" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1159" Evaluating: 1159-7 Parameter: NUMWAT <- "1152" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1152" Comparing "1081" and "1152". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.642" Parameter: BOX -> "32.642" Parameter: BOX -> "32.642" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.64200 B = 32.64200 C = 32.64200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7835 2 1 -1 0 -1 1.6967 3 1 -1 1 -1 4.5901 4 1 0 -1 -1 4.7693 5 1 0 0 -1 0.8327 6 1 0 1 -1 1.6347 7 1 -1 -1 0 4.6248 8 1 -1 0 0 0.9874 9 1 -1 1 0 4.4811 10 1 0 -1 0 0.6682 11 1 0 1 0 0.6682 12 1 -1 -1 1 5.3501 13 1 -1 0 1 1.5646 14 1 -1 1 1 6.0189 15 1 0 -1 1 1.6347 16 1 0 0 1 0.8327 17 1 0 1 1 4.7693 18 1 1 1 1 5.7835 19 1 1 0 1 1.6967 20 1 1 -1 1 4.5901 21 1 1 1 0 4.6248 22 1 1 0 0 0.9874 23 1 1 -1 0 4.4811 24 1 1 1 -1 5.3501 25 1 1 0 -1 1.5646 26 1 1 -1 -1 6.0189 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3438 atoms have been selected out of 3512 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1524 508 508 0.00 6 C006 has 459 153 153 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1708 567 566 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.80 Total of12606 atoms and 4193 groups and 4187 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3512 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1159 Number of atoms = 3512 Number of groups = 1164 Number of bonds = 3505 Number of angles = 1263 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1161 Number of HB donors = 2300 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1159 Number of atoms = 3512 Number of groups = 1164 Number of bonds = 3505 Number of angles = 1263 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1161 Number of HB donors = 2300 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.64" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1159" Evaluating: 1159-7 Parameter: NUMWAT <- "1152" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1152" Comparing "1081" and "1152". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.64" Parameter: BOX -> "32.64" Parameter: BOX -> "32.64" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.64000 B = 32.64000 C = 32.64000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7823 2 1 -1 0 -1 1.6941 3 1 -1 1 -1 4.5867 4 1 0 -1 -1 4.7674 5 1 0 0 -1 0.8311 6 1 0 1 -1 1.6322 7 1 -1 -1 0 4.6231 8 1 -1 0 0 0.9859 9 1 -1 1 0 4.4786 10 1 0 -1 0 0.6665 11 1 0 1 0 0.6665 12 1 -1 -1 1 5.3474 13 1 -1 0 1 1.5626 14 1 -1 1 1 6.0160 15 1 0 -1 1 1.6322 16 1 0 0 1 0.8311 17 1 0 1 1 4.7674 18 1 1 1 1 5.7823 19 1 1 0 1 1.6941 20 1 1 -1 1 4.5867 21 1 1 1 0 4.6231 22 1 1 0 0 0.9859 23 1 1 -1 0 4.4786 24 1 1 1 -1 5.3474 25 1 1 0 -1 1.5626 26 1 1 -1 -1 6.0160 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3438 atoms have been selected out of 3512 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1527 509 509 0.00 6 C006 has 459 153 153 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1708 567 566 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.80 Total of12612 atoms and 4195 groups and 4189 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3512 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1159 Number of atoms = 3512 Number of groups = 1164 Number of bonds = 3505 Number of angles = 1263 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1161 Number of HB donors = 2300 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1159 Number of atoms = 3512 Number of groups = 1164 Number of bonds = 3505 Number of angles = 1263 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1161 Number of HB donors = 2300 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.638" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1159" Evaluating: 1159-7 Parameter: NUMWAT <- "1152" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1152" Comparing "1081" and "1152". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.638" Parameter: BOX -> "32.638" Parameter: BOX -> "32.638" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.63800 B = 32.63800 C = 32.63800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7811 2 1 -1 0 -1 1.6916 3 1 -1 1 -1 4.5833 4 1 0 -1 -1 4.7656 5 1 0 0 -1 0.8295 6 1 0 1 -1 1.6297 7 1 -1 -1 0 4.6213 8 1 -1 0 0 0.9843 9 1 -1 1 0 4.4762 10 1 0 -1 0 0.6647 11 1 0 1 0 0.6647 12 1 -1 -1 1 5.3447 13 1 -1 0 1 1.5607 14 1 -1 1 1 6.0131 15 1 0 -1 1 1.6297 16 1 0 0 1 0.8295 17 1 0 1 1 4.7656 18 1 1 1 1 5.7811 19 1 1 0 1 1.6916 20 1 1 -1 1 4.5833 21 1 1 1 0 4.6213 22 1 1 0 0 0.9843 23 1 1 -1 0 4.4762 24 1 1 1 -1 5.3447 25 1 1 0 -1 1.5607 26 1 1 -1 -1 6.0131 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3438 atoms have been selected out of 3512 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1527 509 509 0.00 6 C006 has 459 153 153 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1708 567 566 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.80 Total of12615 atoms and 4196 groups and 4190 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3512 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1159 Number of atoms = 3512 Number of groups = 1164 Number of bonds = 3505 Number of angles = 1263 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1161 Number of HB donors = 2300 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1159 Number of atoms = 3512 Number of groups = 1164 Number of bonds = 3505 Number of angles = 1263 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1161 Number of HB donors = 2300 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.636" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1159" Evaluating: 1159-7 Parameter: NUMWAT <- "1152" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1152" Comparing "1081" and "1152". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.636" Parameter: BOX -> "32.636" Parameter: BOX -> "32.636" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.63600 B = 32.63600 C = 32.63600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7800 2 1 -1 0 -1 1.6891 3 1 -1 1 -1 4.5799 4 1 0 -1 -1 4.7637 5 1 0 0 -1 0.8279 6 1 0 1 -1 1.6271 7 1 -1 -1 0 4.6195 8 1 -1 0 0 0.9828 9 1 -1 1 0 4.4737 10 1 0 -1 0 0.6630 11 1 0 1 0 0.6630 12 1 -1 -1 1 5.3420 13 1 -1 0 1 1.5587 14 1 -1 1 1 6.0102 15 1 0 -1 1 1.6271 16 1 0 0 1 0.8279 17 1 0 1 1 4.7637 18 1 1 1 1 5.7800 19 1 1 0 1 1.6891 20 1 1 -1 1 4.5799 21 1 1 1 0 4.6195 22 1 1 0 0 0.9828 23 1 1 -1 0 4.4737 24 1 1 1 -1 5.3420 25 1 1 0 -1 1.5587 26 1 1 -1 -1 6.0102 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3438 atoms have been selected out of 3512 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 143 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1527 509 509 0.00 6 C006 has 459 153 153 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1708 567 566 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.63 Total of12615 atoms and 4196 groups and 4190 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3512 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1158 Number of atoms = 3509 Number of groups = 1163 Number of bonds = 3502 Number of angles = 1262 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1160 Number of HB donors = 2298 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1158 Number of atoms = 3509 Number of groups = 1163 Number of bonds = 3502 Number of angles = 1262 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1160 Number of HB donors = 2298 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.634" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1158" Evaluating: 1158-7 Parameter: NUMWAT <- "1151" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1151" Comparing "1081" and "1151". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.634" Parameter: BOX -> "32.634" Parameter: BOX -> "32.634" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.63400 B = 32.63400 C = 32.63400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7788 2 1 -1 0 -1 1.6866 3 1 -1 1 -1 4.5765 4 1 0 -1 -1 4.7618 5 1 0 0 -1 0.8264 6 1 0 1 -1 1.6246 7 1 -1 -1 0 4.6178 8 1 -1 0 0 0.9813 9 1 -1 1 0 4.4713 10 1 0 -1 0 0.6613 11 1 0 1 0 0.6613 12 1 -1 -1 1 5.3392 13 1 -1 0 1 1.5568 14 1 -1 1 1 6.0072 15 1 0 -1 1 1.6246 16 1 0 0 1 0.8264 17 1 0 1 1 4.7618 18 1 1 1 1 5.7788 19 1 1 0 1 1.6866 20 1 1 -1 1 4.5765 21 1 1 1 0 4.6178 22 1 1 0 0 0.9813 23 1 1 -1 0 4.4713 24 1 1 1 -1 5.3392 25 1 1 0 -1 1.5568 26 1 1 -1 -1 6.0072 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3435 atoms have been selected out of 3509 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1527 509 509 0.00 6 C006 has 459 153 153 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1708 567 566 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.79 Total of12612 atoms and 4195 groups and 4189 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3509 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1158 Number of atoms = 3509 Number of groups = 1163 Number of bonds = 3502 Number of angles = 1262 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1160 Number of HB donors = 2298 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1158 Number of atoms = 3509 Number of groups = 1163 Number of bonds = 3502 Number of angles = 1262 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1160 Number of HB donors = 2298 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.632" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1158" Evaluating: 1158-7 Parameter: NUMWAT <- "1151" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1151" Comparing "1081" and "1151". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.632" Parameter: BOX -> "32.632" Parameter: BOX -> "32.632" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.63200 B = 32.63200 C = 32.63200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7776 2 1 -1 0 -1 1.6841 3 1 -1 1 -1 4.5731 4 1 0 -1 -1 4.7599 5 1 0 0 -1 0.8248 6 1 0 1 -1 1.6221 7 1 -1 -1 0 4.6160 8 1 -1 0 0 0.9797 9 1 -1 1 0 4.4688 10 1 0 -1 0 0.6595 11 1 0 1 0 0.6595 12 1 -1 -1 1 5.3365 13 1 -1 0 1 1.5549 14 1 -1 1 1 6.0043 15 1 0 -1 1 1.6221 16 1 0 0 1 0.8248 17 1 0 1 1 4.7599 18 1 1 1 1 5.7776 19 1 1 0 1 1.6841 20 1 1 -1 1 4.5731 21 1 1 1 0 4.6160 22 1 1 0 0 0.9797 23 1 1 -1 0 4.4688 24 1 1 1 -1 5.3365 25 1 1 0 -1 1.5549 26 1 1 -1 -1 6.0043 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3435 atoms have been selected out of 3509 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 406 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1527 509 509 0.00 6 C006 has 459 153 153 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1708 567 566 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.79 Total of12609 atoms and 4194 groups and 4188 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3509 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1157 Number of atoms = 3506 Number of groups = 1162 Number of bonds = 3499 Number of angles = 1261 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1159 Number of HB donors = 2296 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1157 Number of atoms = 3506 Number of groups = 1162 Number of bonds = 3499 Number of angles = 1261 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1159 Number of HB donors = 2296 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.63" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1157" Evaluating: 1157-7 Parameter: NUMWAT <- "1150" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1150" Comparing "1081" and "1150". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.63" Parameter: BOX -> "32.63" Parameter: BOX -> "32.63" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.63000 B = 32.63000 C = 32.63000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7764 2 1 -1 0 -1 1.6815 3 1 -1 1 -1 4.5696 4 1 0 -1 -1 4.7580 5 1 0 0 -1 0.8232 6 1 0 1 -1 1.6196 7 1 -1 -1 0 4.6143 8 1 -1 0 0 0.9782 9 1 -1 1 0 4.4664 10 1 0 -1 0 0.6578 11 1 0 1 0 0.6578 12 1 -1 -1 1 5.3338 13 1 -1 0 1 1.5529 14 1 -1 1 1 6.0014 15 1 0 -1 1 1.6196 16 1 0 0 1 0.8232 17 1 0 1 1 4.7580 18 1 1 1 1 5.7764 19 1 1 0 1 1.6815 20 1 1 -1 1 4.5696 21 1 1 1 0 4.6143 22 1 1 0 0 0.9782 23 1 1 -1 0 4.4664 24 1 1 1 -1 5.3338 25 1 1 0 -1 1.5529 26 1 1 -1 -1 6.0014 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3432 atoms have been selected out of 3506 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 747 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1527 509 509 0.00 6 C006 has 459 153 153 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1717 570 569 0.00 9 C009 has 411 137 137 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 99 33 33 0.00 13 C013 has 474 158 158 0.00 14 C014 has 111 37 37 0.79 Total of12618 atoms and 4197 groups and 4191 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3506 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1156 Number of atoms = 3503 Number of groups = 1161 Number of bonds = 3496 Number of angles = 1260 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1158 Number of HB donors = 2294 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1156 Number of atoms = 3503 Number of groups = 1161 Number of bonds = 3496 Number of angles = 1260 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1158 Number of HB donors = 2294 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.628" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1156" Evaluating: 1156-7 Parameter: NUMWAT <- "1149" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1149" Comparing "1081" and "1149". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.628" Parameter: BOX -> "32.628" Parameter: BOX -> "32.628" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.62800 B = 32.62800 C = 32.62800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7752 2 1 -1 0 -1 1.6790 3 1 -1 1 -1 4.5662 4 1 0 -1 -1 4.7561 5 1 0 0 -1 0.8216 6 1 0 1 -1 1.6170 7 1 -1 -1 0 4.6125 8 1 -1 0 0 0.9767 9 1 -1 1 0 4.4639 10 1 0 -1 0 0.6561 11 1 0 1 0 0.6561 12 1 -1 -1 1 5.3311 13 1 -1 0 1 1.5510 14 1 -1 1 1 5.9985 15 1 0 -1 1 1.6170 16 1 0 0 1 0.8216 17 1 0 1 1 4.7561 18 1 1 1 1 5.7752 19 1 1 0 1 1.6790 20 1 1 -1 1 4.5662 21 1 1 1 0 4.6125 22 1 1 0 0 0.9767 23 1 1 -1 0 4.4639 24 1 1 1 -1 5.3311 25 1 1 0 -1 1.5510 26 1 1 -1 -1 5.9985 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3429 atoms have been selected out of 3503 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1524 508 508 0.00 6 C006 has 456 152 152 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1705 566 565 0.00 9 C009 has 411 137 137 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.79 Total of12591 atoms and 4188 groups and 4182 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3503 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1156 Number of atoms = 3503 Number of groups = 1161 Number of bonds = 3496 Number of angles = 1260 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1158 Number of HB donors = 2294 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1156 Number of atoms = 3503 Number of groups = 1161 Number of bonds = 3496 Number of angles = 1260 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1158 Number of HB donors = 2294 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.626" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1156" Evaluating: 1156-7 Parameter: NUMWAT <- "1149" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1149" Comparing "1081" and "1149". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.626" Parameter: BOX -> "32.626" Parameter: BOX -> "32.626" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.62600 B = 32.62600 C = 32.62600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7740 2 1 -1 0 -1 1.6765 3 1 -1 1 -1 4.5628 4 1 0 -1 -1 4.7543 5 1 0 0 -1 0.8200 6 1 0 1 -1 1.6145 7 1 -1 -1 0 4.6107 8 1 -1 0 0 0.9752 9 1 -1 1 0 4.4615 10 1 0 -1 0 0.6544 11 1 0 1 0 0.6544 12 1 -1 -1 1 5.3284 13 1 -1 0 1 1.5490 14 1 -1 1 1 5.9955 15 1 0 -1 1 1.6145 16 1 0 0 1 0.8200 17 1 0 1 1 4.7543 18 1 1 1 1 5.7740 19 1 1 0 1 1.6765 20 1 1 -1 1 4.5628 21 1 1 1 0 4.6107 22 1 1 0 0 0.9752 23 1 1 -1 0 4.4615 24 1 1 1 -1 5.3284 25 1 1 0 -1 1.5490 26 1 1 -1 -1 5.9955 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3429 atoms have been selected out of 3503 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1524 508 508 0.00 6 C006 has 456 152 152 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1705 566 565 0.00 9 C009 has 411 137 137 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.79 Total of12594 atoms and 4189 groups and 4183 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3503 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1156 Number of atoms = 3503 Number of groups = 1161 Number of bonds = 3496 Number of angles = 1260 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1158 Number of HB donors = 2294 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1156 Number of atoms = 3503 Number of groups = 1161 Number of bonds = 3496 Number of angles = 1260 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1158 Number of HB donors = 2294 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.624" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1156" Evaluating: 1156-7 Parameter: NUMWAT <- "1149" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1149" Comparing "1081" and "1149". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.624" Parameter: BOX -> "32.624" Parameter: BOX -> "32.624" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.62400 B = 32.62400 C = 32.62400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7728 2 1 -1 0 -1 1.6740 3 1 -1 1 -1 4.5594 4 1 0 -1 -1 4.7524 5 1 0 0 -1 0.8185 6 1 0 1 -1 1.6120 7 1 -1 -1 0 4.6090 8 1 -1 0 0 0.9736 9 1 -1 1 0 4.4590 10 1 0 -1 0 0.6527 11 1 0 1 0 0.6527 12 1 -1 -1 1 5.3257 13 1 -1 0 1 1.5471 14 1 -1 1 1 5.9926 15 1 0 -1 1 1.6120 16 1 0 0 1 0.8185 17 1 0 1 1 4.7524 18 1 1 1 1 5.7728 19 1 1 0 1 1.6740 20 1 1 -1 1 4.5594 21 1 1 1 0 4.6090 22 1 1 0 0 0.9736 23 1 1 -1 0 4.4590 24 1 1 1 -1 5.3257 25 1 1 0 -1 1.5471 26 1 1 -1 -1 5.9926 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3429 atoms have been selected out of 3503 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1524 508 508 0.00 6 C006 has 456 152 152 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1705 566 565 0.00 9 C009 has 411 137 137 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.78 Total of12600 atoms and 4191 groups and 4185 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3503 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1156 Number of atoms = 3503 Number of groups = 1161 Number of bonds = 3496 Number of angles = 1260 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1158 Number of HB donors = 2294 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1156 Number of atoms = 3503 Number of groups = 1161 Number of bonds = 3496 Number of angles = 1260 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1158 Number of HB donors = 2294 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.622" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1156" Evaluating: 1156-7 Parameter: NUMWAT <- "1149" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1149" Comparing "1081" and "1149". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.622" Parameter: BOX -> "32.622" Parameter: BOX -> "32.622" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.62200 B = 32.62200 C = 32.62200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7716 2 1 -1 0 -1 1.6715 3 1 -1 1 -1 4.5560 4 1 0 -1 -1 4.7505 5 1 0 0 -1 0.8169 6 1 0 1 -1 1.6094 7 1 -1 -1 0 4.6072 8 1 -1 0 0 0.9721 9 1 -1 1 0 4.4566 10 1 0 -1 0 0.6509 11 1 0 1 0 0.6509 12 1 -1 -1 1 5.3230 13 1 -1 0 1 1.5452 14 1 -1 1 1 5.9897 15 1 0 -1 1 1.6094 16 1 0 0 1 0.8169 17 1 0 1 1 4.7505 18 1 1 1 1 5.7716 19 1 1 0 1 1.6715 20 1 1 -1 1 4.5560 21 1 1 1 0 4.6072 22 1 1 0 0 0.9721 23 1 1 -1 0 4.4566 24 1 1 1 -1 5.3230 25 1 1 0 -1 1.5452 26 1 1 -1 -1 5.9897 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3429 atoms have been selected out of 3503 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1524 508 508 0.00 6 C006 has 459 153 153 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1705 566 565 0.00 9 C009 has 411 137 137 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.78 Total of12603 atoms and 4192 groups and 4186 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3503 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1156 Number of atoms = 3503 Number of groups = 1161 Number of bonds = 3496 Number of angles = 1260 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1158 Number of HB donors = 2294 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1156 Number of atoms = 3503 Number of groups = 1161 Number of bonds = 3496 Number of angles = 1260 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1158 Number of HB donors = 2294 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.62" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1156" Evaluating: 1156-7 Parameter: NUMWAT <- "1149" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1149" Comparing "1081" and "1149". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.62" Parameter: BOX -> "32.62" Parameter: BOX -> "32.62" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.62000 B = 32.62000 C = 32.62000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7705 2 1 -1 0 -1 1.6690 3 1 -1 1 -1 4.5525 4 1 0 -1 -1 4.7486 5 1 0 0 -1 0.8153 6 1 0 1 -1 1.6069 7 1 -1 -1 0 4.6055 8 1 -1 0 0 0.9706 9 1 -1 1 0 4.4541 10 1 0 -1 0 0.6492 11 1 0 1 0 0.6492 12 1 -1 -1 1 5.3203 13 1 -1 0 1 1.5433 14 1 -1 1 1 5.9868 15 1 0 -1 1 1.6069 16 1 0 0 1 0.8153 17 1 0 1 1 4.7486 18 1 1 1 1 5.7705 19 1 1 0 1 1.6690 20 1 1 -1 1 4.5525 21 1 1 1 0 4.6055 22 1 1 0 0 0.9706 23 1 1 -1 0 4.4541 24 1 1 1 -1 5.3203 25 1 1 0 -1 1.5433 26 1 1 -1 -1 5.9868 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3429 atoms have been selected out of 3503 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1132 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1524 508 508 0.00 6 C006 has 462 154 154 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1708 567 566 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1605 535 535 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.78 Total of12612 atoms and 4195 groups and 4189 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3503 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1155 Number of atoms = 3500 Number of groups = 1160 Number of bonds = 3493 Number of angles = 1259 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1157 Number of HB donors = 2292 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1155 Number of atoms = 3500 Number of groups = 1160 Number of bonds = 3493 Number of angles = 1259 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1157 Number of HB donors = 2292 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.618" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1155" Evaluating: 1155-7 Parameter: NUMWAT <- "1148" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1148" Comparing "1081" and "1148". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.618" Parameter: BOX -> "32.618" Parameter: BOX -> "32.618" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.61800 B = 32.61800 C = 32.61800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7693 2 1 -1 0 -1 1.6665 3 1 -1 1 -1 4.5491 4 1 0 -1 -1 4.7467 5 1 0 0 -1 0.8138 6 1 0 1 -1 1.6044 7 1 -1 -1 0 4.6037 8 1 -1 0 0 0.9691 9 1 -1 1 0 4.4517 10 1 0 -1 0 0.6475 11 1 0 1 0 0.6475 12 1 -1 -1 1 5.3176 13 1 -1 0 1 1.5413 14 1 -1 1 1 5.9838 15 1 0 -1 1 1.6044 16 1 0 0 1 0.8138 17 1 0 1 1 4.7467 18 1 1 1 1 5.7693 19 1 1 0 1 1.6665 20 1 1 -1 1 4.5491 21 1 1 1 0 4.6037 22 1 1 0 0 0.9691 23 1 1 -1 0 4.4517 24 1 1 1 -1 5.3176 25 1 1 0 -1 1.5413 26 1 1 -1 -1 5.9838 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3426 atoms have been selected out of 3500 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1521 507 507 0.00 6 C006 has 459 153 153 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1705 566 565 0.00 9 C009 has 411 137 137 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.78 Total of12585 atoms and 4186 groups and 4180 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3500 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1155 Number of atoms = 3500 Number of groups = 1160 Number of bonds = 3493 Number of angles = 1259 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1157 Number of HB donors = 2292 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1155 Number of atoms = 3500 Number of groups = 1160 Number of bonds = 3493 Number of angles = 1259 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1157 Number of HB donors = 2292 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.616" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1155" Evaluating: 1155-7 Parameter: NUMWAT <- "1148" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1148" Comparing "1081" and "1148". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.616" Parameter: BOX -> "32.616" Parameter: BOX -> "32.616" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.61600 B = 32.61600 C = 32.61600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7681 2 1 -1 0 -1 1.6639 3 1 -1 1 -1 4.5457 4 1 0 -1 -1 4.7449 5 1 0 0 -1 0.8122 6 1 0 1 -1 1.6019 7 1 -1 -1 0 4.6020 8 1 -1 0 0 0.9676 9 1 -1 1 0 4.4493 10 1 0 -1 0 0.6458 11 1 0 1 0 0.6458 12 1 -1 -1 1 5.3148 13 1 -1 0 1 1.5394 14 1 -1 1 1 5.9809 15 1 0 -1 1 1.6019 16 1 0 0 1 0.8122 17 1 0 1 1 4.7449 18 1 1 1 1 5.7681 19 1 1 0 1 1.6639 20 1 1 -1 1 4.5457 21 1 1 1 0 4.6020 22 1 1 0 0 0.9676 23 1 1 -1 0 4.4493 24 1 1 1 -1 5.3148 25 1 1 0 -1 1.5394 26 1 1 -1 -1 5.9809 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3426 atoms have been selected out of 3500 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 465 155 155 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1521 507 507 0.00 6 C006 has 459 153 153 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1705 566 565 0.00 9 C009 has 411 137 137 0.00 10 C010 has 1602 534 534 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.78 Total of12588 atoms and 4187 groups and 4181 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3500 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1155 Number of atoms = 3500 Number of groups = 1160 Number of bonds = 3493 Number of angles = 1259 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1157 Number of HB donors = 2292 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1155 Number of atoms = 3500 Number of groups = 1160 Number of bonds = 3493 Number of angles = 1259 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1157 Number of HB donors = 2292 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.614" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1155" Evaluating: 1155-7 Parameter: NUMWAT <- "1148" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1148" Comparing "1081" and "1148". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.614" Parameter: BOX -> "32.614" Parameter: BOX -> "32.614" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.61400 B = 32.61400 C = 32.61400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7669 2 1 -1 0 -1 1.6614 3 1 -1 1 -1 4.5423 4 1 0 -1 -1 4.7430 5 1 0 0 -1 0.8106 6 1 0 1 -1 1.5994 7 1 -1 -1 0 4.6002 8 1 -1 0 0 0.9661 9 1 -1 1 0 4.4468 10 1 0 -1 0 0.6441 11 1 0 1 0 0.6441 12 1 -1 -1 1 5.3121 13 1 -1 0 1 1.5375 14 1 -1 1 1 5.9780 15 1 0 -1 1 1.5994 16 1 0 0 1 0.8106 17 1 0 1 1 4.7430 18 1 1 1 1 5.7669 19 1 1 0 1 1.6614 20 1 1 -1 1 4.5423 21 1 1 1 0 4.6002 22 1 1 0 0 0.9661 23 1 1 -1 0 4.4468 24 1 1 1 -1 5.3121 25 1 1 0 -1 1.5375 26 1 1 -1 -1 5.9780 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3426 atoms have been selected out of 3500 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1521 507 507 0.00 6 C006 has 459 153 153 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1705 566 565 0.00 9 C009 has 411 137 137 0.00 10 C010 has 1602 534 534 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.77 Total of12591 atoms and 4188 groups and 4182 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3500 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1155 Number of atoms = 3500 Number of groups = 1160 Number of bonds = 3493 Number of angles = 1259 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1157 Number of HB donors = 2292 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1155 Number of atoms = 3500 Number of groups = 1160 Number of bonds = 3493 Number of angles = 1259 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1157 Number of HB donors = 2292 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.612" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1155" Evaluating: 1155-7 Parameter: NUMWAT <- "1148" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1148" Comparing "1081" and "1148". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.612" Parameter: BOX -> "32.612" Parameter: BOX -> "32.612" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.61200 B = 32.61200 C = 32.61200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7658 2 1 -1 0 -1 1.6589 3 1 -1 1 -1 4.5389 4 1 0 -1 -1 4.7411 5 1 0 0 -1 0.8091 6 1 0 1 -1 1.5968 7 1 -1 -1 0 4.5985 8 1 -1 0 0 0.9646 9 1 -1 1 0 4.4444 10 1 0 -1 0 0.6424 11 1 0 1 0 0.6424 12 1 -1 -1 1 5.3094 13 1 -1 0 1 1.5356 14 1 -1 1 1 5.9751 15 1 0 -1 1 1.5968 16 1 0 0 1 0.8091 17 1 0 1 1 4.7411 18 1 1 1 1 5.7658 19 1 1 0 1 1.6589 20 1 1 -1 1 4.5389 21 1 1 1 0 4.5985 22 1 1 0 0 0.9646 23 1 1 -1 0 4.4444 24 1 1 1 -1 5.3094 25 1 1 0 -1 1.5356 26 1 1 -1 -1 5.9751 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3426 atoms have been selected out of 3500 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 471 157 157 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1521 507 507 0.00 6 C006 has 459 153 153 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1705 566 565 0.00 9 C009 has 411 137 137 0.00 10 C010 has 1602 534 534 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.77 Total of12594 atoms and 4189 groups and 4183 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3500 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1155 Number of atoms = 3500 Number of groups = 1160 Number of bonds = 3493 Number of angles = 1259 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1157 Number of HB donors = 2292 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1155 Number of atoms = 3500 Number of groups = 1160 Number of bonds = 3493 Number of angles = 1259 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1157 Number of HB donors = 2292 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.61" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1155" Evaluating: 1155-7 Parameter: NUMWAT <- "1148" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1148" Comparing "1081" and "1148". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.61" Parameter: BOX -> "32.61" Parameter: BOX -> "32.61" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.61000 B = 32.61000 C = 32.61000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7646 2 1 -1 0 -1 1.6564 3 1 -1 1 -1 4.5355 4 1 0 -1 -1 4.7392 5 1 0 0 -1 0.8075 6 1 0 1 -1 1.5943 7 1 -1 -1 0 4.5967 8 1 -1 0 0 0.9630 9 1 -1 1 0 4.4419 10 1 0 -1 0 0.6407 11 1 0 1 0 0.6407 12 1 -1 -1 1 5.3067 13 1 -1 0 1 1.5337 14 1 -1 1 1 5.9721 15 1 0 -1 1 1.5943 16 1 0 0 1 0.8075 17 1 0 1 1 4.7392 18 1 1 1 1 5.7646 19 1 1 0 1 1.6564 20 1 1 -1 1 4.5355 21 1 1 1 0 4.5967 22 1 1 0 0 0.9630 23 1 1 -1 0 4.4419 24 1 1 1 -1 5.3067 25 1 1 0 -1 1.5337 26 1 1 -1 -1 5.9721 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3426 atoms have been selected out of 3500 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 471 157 157 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1521 507 507 0.00 6 C006 has 459 153 153 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1705 566 565 0.00 9 C009 has 411 137 137 0.00 10 C010 has 1602 534 534 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.77 Total of12597 atoms and 4190 groups and 4184 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3500 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1155 Number of atoms = 3500 Number of groups = 1160 Number of bonds = 3493 Number of angles = 1259 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1157 Number of HB donors = 2292 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1155 Number of atoms = 3500 Number of groups = 1160 Number of bonds = 3493 Number of angles = 1259 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1157 Number of HB donors = 2292 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.608" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1155" Evaluating: 1155-7 Parameter: NUMWAT <- "1148" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1148" Comparing "1081" and "1148". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.608" Parameter: BOX -> "32.608" Parameter: BOX -> "32.608" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.60800 B = 32.60800 C = 32.60800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7634 2 1 -1 0 -1 1.6539 3 1 -1 1 -1 4.5320 4 1 0 -1 -1 4.7374 5 1 0 0 -1 0.8059 6 1 0 1 -1 1.5918 7 1 -1 -1 0 4.5950 8 1 -1 0 0 0.9615 9 1 -1 1 0 4.4395 10 1 0 -1 0 0.6390 11 1 0 1 0 0.6390 12 1 -1 -1 1 5.3040 13 1 -1 0 1 1.5318 14 1 -1 1 1 5.9692 15 1 0 -1 1 1.5918 16 1 0 0 1 0.8059 17 1 0 1 1 4.7374 18 1 1 1 1 5.7634 19 1 1 0 1 1.6539 20 1 1 -1 1 4.5320 21 1 1 1 0 4.5950 22 1 1 0 0 0.9615 23 1 1 -1 0 4.4395 24 1 1 1 -1 5.3040 25 1 1 0 -1 1.5318 26 1 1 -1 -1 5.9692 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3426 atoms have been selected out of 3500 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1046 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1521 507 507 0.00 6 C006 has 459 153 153 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1705 566 565 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1602 534 534 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 114 38 38 0.77 Total of12606 atoms and 4193 groups and 4187 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3500 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1154 Number of atoms = 3497 Number of groups = 1159 Number of bonds = 3490 Number of angles = 1258 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1156 Number of HB donors = 2290 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1154 Number of atoms = 3497 Number of groups = 1159 Number of bonds = 3490 Number of angles = 1258 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1156 Number of HB donors = 2290 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.606" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1154" Evaluating: 1154-7 Parameter: NUMWAT <- "1147" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1147" Comparing "1081" and "1147". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.606" Parameter: BOX -> "32.606" Parameter: BOX -> "32.606" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.60600 B = 32.60600 C = 32.60600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7623 2 1 -1 0 -1 1.6514 3 1 -1 1 -1 4.5286 4 1 0 -1 -1 4.7355 5 1 0 0 -1 0.8044 6 1 0 1 -1 1.5893 7 1 -1 -1 0 4.5932 8 1 -1 0 0 0.9600 9 1 -1 1 0 4.4370 10 1 0 -1 0 0.6373 11 1 0 1 0 0.6373 12 1 -1 -1 1 5.3013 13 1 -1 0 1 1.5299 14 1 -1 1 1 5.9663 15 1 0 -1 1 1.5893 16 1 0 0 1 0.8044 17 1 0 1 1 4.7355 18 1 1 1 1 5.7623 19 1 1 0 1 1.6514 20 1 1 -1 1 4.5286 21 1 1 1 0 4.5932 22 1 1 0 0 0.9600 23 1 1 -1 0 4.4370 24 1 1 1 -1 5.3013 25 1 1 0 -1 1.5299 26 1 1 -1 -1 5.9663 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3423 atoms have been selected out of 3497 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1521 507 507 0.00 6 C006 has 459 153 153 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1702 565 564 0.00 9 C009 has 411 137 137 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 114 38 38 0.77 Total of12585 atoms and 4186 groups and 4180 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3497 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1154 Number of atoms = 3497 Number of groups = 1159 Number of bonds = 3490 Number of angles = 1258 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1156 Number of HB donors = 2290 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1154 Number of atoms = 3497 Number of groups = 1159 Number of bonds = 3490 Number of angles = 1258 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1156 Number of HB donors = 2290 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.604" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1154" Evaluating: 1154-7 Parameter: NUMWAT <- "1147" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1147" Comparing "1081" and "1147". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.604" Parameter: BOX -> "32.604" Parameter: BOX -> "32.604" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.60400 B = 32.60400 C = 32.60400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7611 2 1 -1 0 -1 1.6489 3 1 -1 1 -1 4.5252 4 1 0 -1 -1 4.7336 5 1 0 0 -1 0.8028 6 1 0 1 -1 1.5868 7 1 -1 -1 0 4.5915 8 1 -1 0 0 0.9585 9 1 -1 1 0 4.4346 10 1 0 -1 0 0.6356 11 1 0 1 0 0.6356 12 1 -1 -1 1 5.2986 13 1 -1 0 1 1.5280 14 1 -1 1 1 5.9634 15 1 0 -1 1 1.5868 16 1 0 0 1 0.8028 17 1 0 1 1 4.7336 18 1 1 1 1 5.7611 19 1 1 0 1 1.6489 20 1 1 -1 1 4.5252 21 1 1 1 0 4.5915 22 1 1 0 0 0.9585 23 1 1 -1 0 4.4346 24 1 1 1 -1 5.2986 25 1 1 0 -1 1.5280 26 1 1 -1 -1 5.9634 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3423 atoms have been selected out of 3497 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 746 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 744 248 248 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1518 506 506 0.00 6 C006 has 456 152 152 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1705 566 565 0.00 9 C009 has 411 137 137 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 114 38 38 0.76 Total of12579 atoms and 4184 groups and 4178 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3497 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1153 Number of atoms = 3494 Number of groups = 1158 Number of bonds = 3487 Number of angles = 1257 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1155 Number of HB donors = 2288 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1153 Number of atoms = 3494 Number of groups = 1158 Number of bonds = 3487 Number of angles = 1257 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1155 Number of HB donors = 2288 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.602" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1153" Evaluating: 1153-7 Parameter: NUMWAT <- "1146" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1146" Comparing "1081" and "1146". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.602" Parameter: BOX -> "32.602" Parameter: BOX -> "32.602" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.60200 B = 32.60200 C = 32.60200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7599 2 1 -1 0 -1 1.6464 3 1 -1 1 -1 4.5218 4 1 0 -1 -1 4.7317 5 1 0 0 -1 0.8013 6 1 0 1 -1 1.5843 7 1 -1 -1 0 4.5897 8 1 -1 0 0 0.9570 9 1 -1 1 0 4.4322 10 1 0 -1 0 0.6339 11 1 0 1 0 0.6339 12 1 -1 -1 1 5.2959 13 1 -1 0 1 1.5261 14 1 -1 1 1 5.9605 15 1 0 -1 1 1.5843 16 1 0 0 1 0.8013 17 1 0 1 1 4.7317 18 1 1 1 1 5.7599 19 1 1 0 1 1.6464 20 1 1 -1 1 4.5218 21 1 1 1 0 4.5897 22 1 1 0 0 0.9570 23 1 1 -1 0 4.4322 24 1 1 1 -1 5.2959 25 1 1 0 -1 1.5261 26 1 1 -1 -1 5.9605 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3420 atoms have been selected out of 3494 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 744 248 248 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1521 507 507 0.00 6 C006 has 456 152 152 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1702 565 564 0.00 9 C009 has 411 137 137 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 114 38 38 0.76 Total of12576 atoms and 4183 groups and 4177 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3494 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1153 Number of atoms = 3494 Number of groups = 1158 Number of bonds = 3487 Number of angles = 1257 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1155 Number of HB donors = 2288 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1153 Number of atoms = 3494 Number of groups = 1158 Number of bonds = 3487 Number of angles = 1257 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1155 Number of HB donors = 2288 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.6" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1153" Evaluating: 1153-7 Parameter: NUMWAT <- "1146" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1146" Comparing "1081" and "1146". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.6" Parameter: BOX -> "32.6" Parameter: BOX -> "32.6" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.60000 B = 32.60000 C = 32.60000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7588 2 1 -1 0 -1 1.6439 3 1 -1 1 -1 4.5184 4 1 0 -1 -1 4.7299 5 1 0 0 -1 0.7997 6 1 0 1 -1 1.5818 7 1 -1 -1 0 4.5880 8 1 -1 0 0 0.9555 9 1 -1 1 0 4.4297 10 1 0 -1 0 0.6322 11 1 0 1 0 0.6322 12 1 -1 -1 1 5.2932 13 1 -1 0 1 1.5242 14 1 -1 1 1 5.9576 15 1 0 -1 1 1.5818 16 1 0 0 1 0.7997 17 1 0 1 1 4.7299 18 1 1 1 1 5.7588 19 1 1 0 1 1.6439 20 1 1 -1 1 4.5184 21 1 1 1 0 4.5880 22 1 1 0 0 0.9555 23 1 1 -1 0 4.4297 24 1 1 1 -1 5.2932 25 1 1 0 -1 1.5242 26 1 1 -1 -1 5.9576 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3420 atoms have been selected out of 3494 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 744 248 248 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1521 507 507 0.00 6 C006 has 456 152 152 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1702 565 564 0.00 9 C009 has 411 137 137 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 114 38 38 0.76 Total of12576 atoms and 4183 groups and 4177 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3494 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1153 Number of atoms = 3494 Number of groups = 1158 Number of bonds = 3487 Number of angles = 1257 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1155 Number of HB donors = 2288 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1153 Number of atoms = 3494 Number of groups = 1158 Number of bonds = 3487 Number of angles = 1257 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1155 Number of HB donors = 2288 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.598" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1153" Evaluating: 1153-7 Parameter: NUMWAT <- "1146" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1146" Comparing "1081" and "1146". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.598" Parameter: BOX -> "32.598" Parameter: BOX -> "32.598" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.59800 B = 32.59800 C = 32.59800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7576 2 1 -1 0 -1 1.6414 3 1 -1 1 -1 4.5150 4 1 0 -1 -1 4.7280 5 1 0 0 -1 0.7982 6 1 0 1 -1 1.5792 7 1 -1 -1 0 4.5862 8 1 -1 0 0 0.9540 9 1 -1 1 0 4.4273 10 1 0 -1 0 0.6305 11 1 0 1 0 0.6305 12 1 -1 -1 1 5.2905 13 1 -1 0 1 1.5223 14 1 -1 1 1 5.9546 15 1 0 -1 1 1.5792 16 1 0 0 1 0.7982 17 1 0 1 1 4.7280 18 1 1 1 1 5.7576 19 1 1 0 1 1.6414 20 1 1 -1 1 4.5150 21 1 1 1 0 4.5862 22 1 1 0 0 0.9540 23 1 1 -1 0 4.4273 24 1 1 1 -1 5.2905 25 1 1 0 -1 1.5223 26 1 1 -1 -1 5.9546 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3420 atoms have been selected out of 3494 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 744 248 248 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1521 507 507 0.00 6 C006 has 456 152 152 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1702 565 564 0.00 9 C009 has 411 137 137 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 114 38 38 0.76 Total of12576 atoms and 4183 groups and 4177 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3494 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1153 Number of atoms = 3494 Number of groups = 1158 Number of bonds = 3487 Number of angles = 1257 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1155 Number of HB donors = 2288 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1153 Number of atoms = 3494 Number of groups = 1158 Number of bonds = 3487 Number of angles = 1257 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1155 Number of HB donors = 2288 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.596" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1153" Evaluating: 1153-7 Parameter: NUMWAT <- "1146" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1146" Comparing "1081" and "1146". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.596" Parameter: BOX -> "32.596" Parameter: BOX -> "32.596" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.59600 B = 32.59600 C = 32.59600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7564 2 1 -1 0 -1 1.6389 3 1 -1 1 -1 4.5115 4 1 0 -1 -1 4.7261 5 1 0 0 -1 0.7966 6 1 0 1 -1 1.5767 7 1 -1 -1 0 4.5845 8 1 -1 0 0 0.9525 9 1 -1 1 0 4.4248 10 1 0 -1 0 0.6288 11 1 0 1 0 0.6288 12 1 -1 -1 1 5.2878 13 1 -1 0 1 1.5204 14 1 -1 1 1 5.9517 15 1 0 -1 1 1.5767 16 1 0 0 1 0.7966 17 1 0 1 1 4.7261 18 1 1 1 1 5.7564 19 1 1 0 1 1.6389 20 1 1 -1 1 4.5115 21 1 1 1 0 4.5845 22 1 1 0 0 0.9525 23 1 1 -1 0 4.4248 24 1 1 1 -1 5.2878 25 1 1 0 -1 1.5204 26 1 1 -1 -1 5.9517 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3420 atoms have been selected out of 3494 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 246 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 111 37 37 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1518 506 506 0.00 6 C006 has 459 153 153 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1702 565 564 0.00 9 C009 has 411 137 137 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.76 Total of12576 atoms and 4183 groups and 4177 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3494 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1152 Number of atoms = 3491 Number of groups = 1157 Number of bonds = 3484 Number of angles = 1256 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1154 Number of HB donors = 2286 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1152 Number of atoms = 3491 Number of groups = 1157 Number of bonds = 3484 Number of angles = 1256 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1154 Number of HB donors = 2286 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.594" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1152" Evaluating: 1152-7 Parameter: NUMWAT <- "1145" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1145" Comparing "1081" and "1145". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.594" Parameter: BOX -> "32.594" Parameter: BOX -> "32.594" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.59400 B = 32.59400 C = 32.59400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7553 2 1 -1 0 -1 1.6364 3 1 -1 1 -1 4.5081 4 1 0 -1 -1 4.7243 5 1 0 0 -1 0.7951 6 1 0 1 -1 1.5742 7 1 -1 -1 0 4.5828 8 1 -1 0 0 0.9510 9 1 -1 1 0 4.4224 10 1 0 -1 0 0.6271 11 1 0 1 0 0.6271 12 1 -1 -1 1 5.2851 13 1 -1 0 1 1.5185 14 1 -1 1 1 5.9488 15 1 0 -1 1 1.5742 16 1 0 0 1 0.7951 17 1 0 1 1 4.7243 18 1 1 1 1 5.7553 19 1 1 0 1 1.6364 20 1 1 -1 1 4.5081 21 1 1 1 0 4.5828 22 1 1 0 0 0.9510 23 1 1 -1 0 4.4224 24 1 1 1 -1 5.2851 25 1 1 0 -1 1.5185 26 1 1 -1 -1 5.9488 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3417 atoms have been selected out of 3491 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 948 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1515 505 505 0.00 6 C006 has 456 152 152 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1699 564 563 0.00 9 C009 has 408 136 136 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.75 Total of12558 atoms and 4177 groups and 4171 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3491 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1151 Number of atoms = 3488 Number of groups = 1156 Number of bonds = 3481 Number of angles = 1255 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1153 Number of HB donors = 2284 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1151 Number of atoms = 3488 Number of groups = 1156 Number of bonds = 3481 Number of angles = 1255 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1153 Number of HB donors = 2284 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.592" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1151" Evaluating: 1151-7 Parameter: NUMWAT <- "1144" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1144" Comparing "1081" and "1144". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.592" Parameter: BOX -> "32.592" Parameter: BOX -> "32.592" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.59200 B = 32.59200 C = 32.59200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7541 2 1 -1 0 -1 1.6339 3 1 -1 1 -1 4.5047 4 1 0 -1 -1 4.7224 5 1 0 0 -1 0.7935 6 1 0 1 -1 1.5717 7 1 -1 -1 0 4.5810 8 1 -1 0 0 0.9495 9 1 -1 1 0 4.4200 10 1 0 -1 0 0.6254 11 1 0 1 0 0.6254 12 1 -1 -1 1 5.2824 13 1 -1 0 1 1.5166 14 1 -1 1 1 5.9459 15 1 0 -1 1 1.5717 16 1 0 0 1 0.7935 17 1 0 1 1 4.7224 18 1 1 1 1 5.7541 19 1 1 0 1 1.6339 20 1 1 -1 1 4.5047 21 1 1 1 0 4.5810 22 1 1 0 0 0.9495 23 1 1 -1 0 4.4200 24 1 1 1 -1 5.2824 25 1 1 0 -1 1.5166 26 1 1 -1 -1 5.9459 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3414 atoms have been selected out of 3488 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 744 248 248 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1512 504 504 0.00 6 C006 has 456 152 152 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1696 563 562 0.00 9 C009 has 408 136 136 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.75 Total of12546 atoms and 4173 groups and 4167 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3488 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1151 Number of atoms = 3488 Number of groups = 1156 Number of bonds = 3481 Number of angles = 1255 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1153 Number of HB donors = 2284 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1151 Number of atoms = 3488 Number of groups = 1156 Number of bonds = 3481 Number of angles = 1255 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1153 Number of HB donors = 2284 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.59" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1151" Evaluating: 1151-7 Parameter: NUMWAT <- "1144" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1144" Comparing "1081" and "1144". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.59" Parameter: BOX -> "32.59" Parameter: BOX -> "32.59" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.59000 B = 32.59000 C = 32.59000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7530 2 1 -1 0 -1 1.6314 3 1 -1 1 -1 4.5013 4 1 0 -1 -1 4.7205 5 1 0 0 -1 0.7920 6 1 0 1 -1 1.5692 7 1 -1 -1 0 4.5793 8 1 -1 0 0 0.9481 9 1 -1 1 0 4.4175 10 1 0 -1 0 0.6237 11 1 0 1 0 0.6237 12 1 -1 -1 1 5.2797 13 1 -1 0 1 1.5147 14 1 -1 1 1 5.9430 15 1 0 -1 1 1.5692 16 1 0 0 1 0.7920 17 1 0 1 1 4.7205 18 1 1 1 1 5.7530 19 1 1 0 1 1.6314 20 1 1 -1 1 4.5013 21 1 1 1 0 4.5793 22 1 1 0 0 0.9481 23 1 1 -1 0 4.4175 24 1 1 1 -1 5.2797 25 1 1 0 -1 1.5147 26 1 1 -1 -1 5.9430 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3414 atoms have been selected out of 3488 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1512 504 504 0.00 6 C006 has 456 152 152 0.00 7 C007 has 768 256 256 0.00 8 C008 has 1696 563 562 0.00 9 C009 has 408 136 136 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 99 33 33 0.00 13 C013 has 462 154 154 0.00 14 C014 has 111 37 37 0.75 Total of12549 atoms and 4174 groups and 4168 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3488 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1151 Number of atoms = 3488 Number of groups = 1156 Number of bonds = 3481 Number of angles = 1255 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1153 Number of HB donors = 2284 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1151 Number of atoms = 3488 Number of groups = 1156 Number of bonds = 3481 Number of angles = 1255 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1153 Number of HB donors = 2284 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.588" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1151" Evaluating: 1151-7 Parameter: NUMWAT <- "1144" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1144" Comparing "1081" and "1144". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.588" Parameter: BOX -> "32.588" Parameter: BOX -> "32.588" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.58800 B = 32.58800 C = 32.58800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7518 2 1 -1 0 -1 1.6289 3 1 -1 1 -1 4.4979 4 1 0 -1 -1 4.7187 5 1 0 0 -1 0.7905 6 1 0 1 -1 1.5667 7 1 -1 -1 0 4.5775 8 1 -1 0 0 0.9466 9 1 -1 1 0 4.4151 10 1 0 -1 0 0.6220 11 1 0 1 0 0.6220 12 1 -1 -1 1 5.2770 13 1 -1 0 1 1.5128 14 1 -1 1 1 5.9401 15 1 0 -1 1 1.5667 16 1 0 0 1 0.7905 17 1 0 1 1 4.7187 18 1 1 1 1 5.7518 19 1 1 0 1 1.6289 20 1 1 -1 1 4.4979 21 1 1 1 0 4.5775 22 1 1 0 0 0.9466 23 1 1 -1 0 4.4151 24 1 1 1 -1 5.2770 25 1 1 0 -1 1.5128 26 1 1 -1 -1 5.9401 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3414 atoms have been selected out of 3488 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1512 504 504 0.00 6 C006 has 456 152 152 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1696 563 562 0.00 9 C009 has 408 136 136 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.75 Total of12555 atoms and 4176 groups and 4170 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3488 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1151 Number of atoms = 3488 Number of groups = 1156 Number of bonds = 3481 Number of angles = 1255 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1153 Number of HB donors = 2284 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1151 Number of atoms = 3488 Number of groups = 1156 Number of bonds = 3481 Number of angles = 1255 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1153 Number of HB donors = 2284 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.586" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1151" Evaluating: 1151-7 Parameter: NUMWAT <- "1144" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1144" Comparing "1081" and "1144". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.586" Parameter: BOX -> "32.586" Parameter: BOX -> "32.586" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.58600 B = 32.58600 C = 32.58600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7507 2 1 -1 0 -1 1.6264 3 1 -1 1 -1 4.4945 4 1 0 -1 -1 4.7168 5 1 0 0 -1 0.7889 6 1 0 1 -1 1.5642 7 1 -1 -1 0 4.5758 8 1 -1 0 0 0.9451 9 1 -1 1 0 4.4126 10 1 0 -1 0 0.6203 11 1 0 1 0 0.6203 12 1 -1 -1 1 5.2743 13 1 -1 0 1 1.5110 14 1 -1 1 1 5.9371 15 1 0 -1 1 1.5642 16 1 0 0 1 0.7889 17 1 0 1 1 4.7168 18 1 1 1 1 5.7507 19 1 1 0 1 1.6264 20 1 1 -1 1 4.4945 21 1 1 1 0 4.5758 22 1 1 0 0 0.9451 23 1 1 -1 0 4.4126 24 1 1 1 -1 5.2743 25 1 1 0 -1 1.5110 26 1 1 -1 -1 5.9371 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3414 atoms have been selected out of 3488 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1512 504 504 0.00 6 C006 has 456 152 152 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1699 564 563 0.00 9 C009 has 408 136 136 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.75 Total of12558 atoms and 4177 groups and 4171 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3488 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1151 Number of atoms = 3488 Number of groups = 1156 Number of bonds = 3481 Number of angles = 1255 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1153 Number of HB donors = 2284 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1151 Number of atoms = 3488 Number of groups = 1156 Number of bonds = 3481 Number of angles = 1255 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1153 Number of HB donors = 2284 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.584" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1151" Evaluating: 1151-7 Parameter: NUMWAT <- "1144" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1144" Comparing "1081" and "1144". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.584" Parameter: BOX -> "32.584" Parameter: BOX -> "32.584" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.58400 B = 32.58400 C = 32.58400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7495 2 1 -1 0 -1 1.6239 3 1 -1 1 -1 4.4910 4 1 0 -1 -1 4.7149 5 1 0 0 -1 0.7874 6 1 0 1 -1 1.5617 7 1 -1 -1 0 4.5741 8 1 -1 0 0 0.9436 9 1 -1 1 0 4.4102 10 1 0 -1 0 0.6186 11 1 0 1 0 0.6186 12 1 -1 -1 1 5.2716 13 1 -1 0 1 1.5091 14 1 -1 1 1 5.9342 15 1 0 -1 1 1.5617 16 1 0 0 1 0.7874 17 1 0 1 1 4.7149 18 1 1 1 1 5.7495 19 1 1 0 1 1.6239 20 1 1 -1 1 4.4910 21 1 1 1 0 4.5741 22 1 1 0 0 0.9436 23 1 1 -1 0 4.4102 24 1 1 1 -1 5.2716 25 1 1 0 -1 1.5091 26 1 1 -1 -1 5.9342 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3414 atoms have been selected out of 3488 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1512 504 504 0.00 6 C006 has 456 152 152 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1699 564 563 0.00 9 C009 has 408 136 136 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.74 Total of12558 atoms and 4177 groups and 4171 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3488 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1151 Number of atoms = 3488 Number of groups = 1156 Number of bonds = 3481 Number of angles = 1255 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1153 Number of HB donors = 2284 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1151 Number of atoms = 3488 Number of groups = 1156 Number of bonds = 3481 Number of angles = 1255 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1153 Number of HB donors = 2284 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.582" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1151" Evaluating: 1151-7 Parameter: NUMWAT <- "1144" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1144" Comparing "1081" and "1144". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.582" Parameter: BOX -> "32.582" Parameter: BOX -> "32.582" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.58200 B = 32.58200 C = 32.58200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7484 2 1 -1 0 -1 1.6214 3 1 -1 1 -1 4.4876 4 1 0 -1 -1 4.7131 5 1 0 0 -1 0.7859 6 1 0 1 -1 1.5592 7 1 -1 -1 0 4.5723 8 1 -1 0 0 0.9421 9 1 -1 1 0 4.4078 10 1 0 -1 0 0.6169 11 1 0 1 0 0.6169 12 1 -1 -1 1 5.2689 13 1 -1 0 1 1.5072 14 1 -1 1 1 5.9313 15 1 0 -1 1 1.5592 16 1 0 0 1 0.7859 17 1 0 1 1 4.7131 18 1 1 1 1 5.7484 19 1 1 0 1 1.6214 20 1 1 -1 1 4.4876 21 1 1 1 0 4.5723 22 1 1 0 0 0.9421 23 1 1 -1 0 4.4078 24 1 1 1 -1 5.2689 25 1 1 0 -1 1.5072 26 1 1 -1 -1 5.9313 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3414 atoms have been selected out of 3488 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1512 504 504 0.00 6 C006 has 456 152 152 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1702 565 564 0.00 9 C009 has 408 136 136 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.74 Total of12561 atoms and 4178 groups and 4172 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3488 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1151 Number of atoms = 3488 Number of groups = 1156 Number of bonds = 3481 Number of angles = 1255 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1153 Number of HB donors = 2284 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1151 Number of atoms = 3488 Number of groups = 1156 Number of bonds = 3481 Number of angles = 1255 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1153 Number of HB donors = 2284 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.58" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1151" Evaluating: 1151-7 Parameter: NUMWAT <- "1144" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1144" Comparing "1081" and "1144". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.58" Parameter: BOX -> "32.58" Parameter: BOX -> "32.58" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.58000 B = 32.58000 C = 32.58000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7472 2 1 -1 0 -1 1.6189 3 1 -1 1 -1 4.4842 4 1 0 -1 -1 4.7112 5 1 0 0 -1 0.7843 6 1 0 1 -1 1.5567 7 1 -1 -1 0 4.5706 8 1 -1 0 0 0.9406 9 1 -1 1 0 4.4053 10 1 0 -1 0 0.6153 11 1 0 1 0 0.6153 12 1 -1 -1 1 5.2663 13 1 -1 0 1 1.5053 14 1 -1 1 1 5.9284 15 1 0 -1 1 1.5567 16 1 0 0 1 0.7843 17 1 0 1 1 4.7112 18 1 1 1 1 5.7472 19 1 1 0 1 1.6189 20 1 1 -1 1 4.4842 21 1 1 1 0 4.5706 22 1 1 0 0 0.9406 23 1 1 -1 0 4.4053 24 1 1 1 -1 5.2663 25 1 1 0 -1 1.5053 26 1 1 -1 -1 5.9284 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3414 atoms have been selected out of 3488 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1512 504 504 0.00 6 C006 has 456 152 152 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1714 566 564 0.00 9 C009 has 408 136 136 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.74 Total of12573 atoms and 4179 groups and 4172 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3488 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1151 Number of atoms = 3488 Number of groups = 1156 Number of bonds = 3481 Number of angles = 1255 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1153 Number of HB donors = 2284 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1151 Number of atoms = 3488 Number of groups = 1156 Number of bonds = 3481 Number of angles = 1255 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1153 Number of HB donors = 2284 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.578" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1151" Evaluating: 1151-7 Parameter: NUMWAT <- "1144" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1144" Comparing "1081" and "1144". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.578" Parameter: BOX -> "32.578" Parameter: BOX -> "32.578" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.57800 B = 32.57800 C = 32.57800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7461 2 1 -1 0 -1 1.6164 3 1 -1 1 -1 4.4808 4 1 0 -1 -1 4.7094 5 1 0 0 -1 0.7828 6 1 0 1 -1 1.5542 7 1 -1 -1 0 4.5689 8 1 -1 0 0 0.9392 9 1 -1 1 0 4.4029 10 1 0 -1 0 0.6136 11 1 0 1 0 0.6136 12 1 -1 -1 1 5.2636 13 1 -1 0 1 1.5035 14 1 -1 1 1 5.9255 15 1 0 -1 1 1.5542 16 1 0 0 1 0.7828 17 1 0 1 1 4.7094 18 1 1 1 1 5.7461 19 1 1 0 1 1.6164 20 1 1 -1 1 4.4808 21 1 1 1 0 4.5689 22 1 1 0 0 0.9392 23 1 1 -1 0 4.4029 24 1 1 1 -1 5.2636 25 1 1 0 -1 1.5035 26 1 1 -1 -1 5.9255 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3414 atoms have been selected out of 3488 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 698 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1512 504 504 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1714 566 564 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.74 Total of12576 atoms and 4180 groups and 4173 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3488 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1150 Number of atoms = 3485 Number of groups = 1155 Number of bonds = 3478 Number of angles = 1254 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1152 Number of HB donors = 2282 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1150 Number of atoms = 3485 Number of groups = 1155 Number of bonds = 3478 Number of angles = 1254 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1152 Number of HB donors = 2282 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.576" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1150" Evaluating: 1150-7 Parameter: NUMWAT <- "1143" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1143" Comparing "1081" and "1143". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.576" Parameter: BOX -> "32.576" Parameter: BOX -> "32.576" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.57600 B = 32.57600 C = 32.57600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7450 2 1 -1 0 -1 1.6139 3 1 -1 1 -1 4.4774 4 1 0 -1 -1 4.7075 5 1 0 0 -1 0.7813 6 1 0 1 -1 1.5517 7 1 -1 -1 0 4.5671 8 1 -1 0 0 0.9377 9 1 -1 1 0 4.4005 10 1 0 -1 0 0.6119 11 1 0 1 0 0.6119 12 1 -1 -1 1 5.2609 13 1 -1 0 1 1.5016 14 1 -1 1 1 5.9226 15 1 0 -1 1 1.5517 16 1 0 0 1 0.7813 17 1 0 1 1 4.7075 18 1 1 1 1 5.7450 19 1 1 0 1 1.6139 20 1 1 -1 1 4.4774 21 1 1 1 0 4.5671 22 1 1 0 0 0.9377 23 1 1 -1 0 4.4005 24 1 1 1 -1 5.2609 25 1 1 0 -1 1.5016 26 1 1 -1 -1 5.9226 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3411 atoms have been selected out of 3485 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1714 566 564 0.00 9 C009 has 408 136 136 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.74 Total of12558 atoms and 4174 groups and 4167 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3485 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1150 Number of atoms = 3485 Number of groups = 1155 Number of bonds = 3478 Number of angles = 1254 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1152 Number of HB donors = 2282 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1150 Number of atoms = 3485 Number of groups = 1155 Number of bonds = 3478 Number of angles = 1254 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1152 Number of HB donors = 2282 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.574" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1150" Evaluating: 1150-7 Parameter: NUMWAT <- "1143" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1143" Comparing "1081" and "1143". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.574" Parameter: BOX -> "32.574" Parameter: BOX -> "32.574" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.57400 B = 32.57400 C = 32.57400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7438 2 1 -1 0 -1 1.6115 3 1 -1 1 -1 4.4740 4 1 0 -1 -1 4.7056 5 1 0 0 -1 0.7797 6 1 0 1 -1 1.5492 7 1 -1 -1 0 4.5654 8 1 -1 0 0 0.9362 9 1 -1 1 0 4.3980 10 1 0 -1 0 0.6102 11 1 0 1 0 0.6102 12 1 -1 -1 1 5.2582 13 1 -1 0 1 1.4998 14 1 -1 1 1 5.9197 15 1 0 -1 1 1.5492 16 1 0 0 1 0.7797 17 1 0 1 1 4.7056 18 1 1 1 1 5.7438 19 1 1 0 1 1.6115 20 1 1 -1 1 4.4740 21 1 1 1 0 4.5654 22 1 1 0 0 0.9362 23 1 1 -1 0 4.3980 24 1 1 1 -1 5.2582 25 1 1 0 -1 1.4998 26 1 1 -1 -1 5.9197 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3411 atoms have been selected out of 3485 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1714 566 564 0.00 9 C009 has 411 137 137 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.73 Total of12561 atoms and 4175 groups and 4168 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3485 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1150 Number of atoms = 3485 Number of groups = 1155 Number of bonds = 3478 Number of angles = 1254 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1152 Number of HB donors = 2282 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1150 Number of atoms = 3485 Number of groups = 1155 Number of bonds = 3478 Number of angles = 1254 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1152 Number of HB donors = 2282 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.572" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1150" Evaluating: 1150-7 Parameter: NUMWAT <- "1143" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1143" Comparing "1081" and "1143". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.572" Parameter: BOX -> "32.572" Parameter: BOX -> "32.572" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.57200 B = 32.57200 C = 32.57200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7427 2 1 -1 0 -1 1.6090 3 1 -1 1 -1 4.4705 4 1 0 -1 -1 4.7038 5 1 0 0 -1 0.7782 6 1 0 1 -1 1.5467 7 1 -1 -1 0 4.5637 8 1 -1 0 0 0.9347 9 1 -1 1 0 4.3956 10 1 0 -1 0 0.6086 11 1 0 1 0 0.6086 12 1 -1 -1 1 5.2555 13 1 -1 0 1 1.4979 14 1 -1 1 1 5.9168 15 1 0 -1 1 1.5467 16 1 0 0 1 0.7782 17 1 0 1 1 4.7038 18 1 1 1 1 5.7427 19 1 1 0 1 1.6090 20 1 1 -1 1 4.4705 21 1 1 1 0 4.5637 22 1 1 0 0 0.9347 23 1 1 -1 0 4.3956 24 1 1 1 -1 5.2555 25 1 1 0 -1 1.4979 26 1 1 -1 -1 5.9168 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3411 atoms have been selected out of 3485 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1714 566 564 0.00 9 C009 has 411 137 137 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.73 Total of12564 atoms and 4176 groups and 4169 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3485 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1150 Number of atoms = 3485 Number of groups = 1155 Number of bonds = 3478 Number of angles = 1254 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1152 Number of HB donors = 2282 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1150 Number of atoms = 3485 Number of groups = 1155 Number of bonds = 3478 Number of angles = 1254 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1152 Number of HB donors = 2282 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.57" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1150" Evaluating: 1150-7 Parameter: NUMWAT <- "1143" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1143" Comparing "1081" and "1143". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.57" Parameter: BOX -> "32.57" Parameter: BOX -> "32.57" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.57000 B = 32.57000 C = 32.57000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7416 2 1 -1 0 -1 1.6065 3 1 -1 1 -1 4.4671 4 1 0 -1 -1 4.7019 5 1 0 0 -1 0.7767 6 1 0 1 -1 1.5442 7 1 -1 -1 0 4.5619 8 1 -1 0 0 0.9333 9 1 -1 1 0 4.3932 10 1 0 -1 0 0.6069 11 1 0 1 0 0.6069 12 1 -1 -1 1 5.2528 13 1 -1 0 1 1.4961 14 1 -1 1 1 5.9139 15 1 0 -1 1 1.5442 16 1 0 0 1 0.7767 17 1 0 1 1 4.7019 18 1 1 1 1 5.7416 19 1 1 0 1 1.6065 20 1 1 -1 1 4.4671 21 1 1 1 0 4.5619 22 1 1 0 0 0.9333 23 1 1 -1 0 4.3932 24 1 1 1 -1 5.2528 25 1 1 0 -1 1.4961 26 1 1 -1 -1 5.9139 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3411 atoms have been selected out of 3485 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1512 504 504 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1714 566 564 0.00 9 C009 has 411 137 137 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 99 33 33 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.73 Total of12567 atoms and 4177 groups and 4170 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3485 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1150 Number of atoms = 3485 Number of groups = 1155 Number of bonds = 3478 Number of angles = 1254 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1152 Number of HB donors = 2282 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1150 Number of atoms = 3485 Number of groups = 1155 Number of bonds = 3478 Number of angles = 1254 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1152 Number of HB donors = 2282 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.568" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1150" Evaluating: 1150-7 Parameter: NUMWAT <- "1143" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1143" Comparing "1081" and "1143". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.568" Parameter: BOX -> "32.568" Parameter: BOX -> "32.568" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.56800 B = 32.56800 C = 32.56800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7404 2 1 -1 0 -1 1.6040 3 1 -1 1 -1 4.4637 4 1 0 -1 -1 4.7001 5 1 0 0 -1 0.7752 6 1 0 1 -1 1.5417 7 1 -1 -1 0 4.5602 8 1 -1 0 0 0.9318 9 1 -1 1 0 4.3907 10 1 0 -1 0 0.6052 11 1 0 1 0 0.6052 12 1 -1 -1 1 5.2501 13 1 -1 0 1 1.4942 14 1 -1 1 1 5.9109 15 1 0 -1 1 1.5417 16 1 0 0 1 0.7752 17 1 0 1 1 4.7001 18 1 1 1 1 5.7404 19 1 1 0 1 1.6040 20 1 1 -1 1 4.4637 21 1 1 1 0 4.5602 22 1 1 0 0 0.9318 23 1 1 -1 0 4.3907 24 1 1 1 -1 5.2501 25 1 1 0 -1 1.4942 26 1 1 -1 -1 5.9109 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3411 atoms have been selected out of 3485 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1512 504 504 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1714 566 564 0.00 9 C009 has 411 137 137 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 102 34 34 0.00 13 C013 has 465 155 155 0.00 14 C014 has 111 37 37 0.73 Total of12570 atoms and 4178 groups and 4171 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3485 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1150 Number of atoms = 3485 Number of groups = 1155 Number of bonds = 3478 Number of angles = 1254 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1152 Number of HB donors = 2282 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1150 Number of atoms = 3485 Number of groups = 1155 Number of bonds = 3478 Number of angles = 1254 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1152 Number of HB donors = 2282 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.566" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1150" Evaluating: 1150-7 Parameter: NUMWAT <- "1143" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1143" Comparing "1081" and "1143". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.566" Parameter: BOX -> "32.566" Parameter: BOX -> "32.566" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.56600 B = 32.56600 C = 32.56600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7393 2 1 -1 0 -1 1.6015 3 1 -1 1 -1 4.4603 4 1 0 -1 -1 4.6982 5 1 0 0 -1 0.7737 6 1 0 1 -1 1.5392 7 1 -1 -1 0 4.5585 8 1 -1 0 0 0.9303 9 1 -1 1 0 4.3883 10 1 0 -1 0 0.6035 11 1 0 1 0 0.6035 12 1 -1 -1 1 5.2474 13 1 -1 0 1 1.4924 14 1 -1 1 1 5.9080 15 1 0 -1 1 1.5392 16 1 0 0 1 0.7737 17 1 0 1 1 4.6982 18 1 1 1 1 5.7393 19 1 1 0 1 1.6015 20 1 1 -1 1 4.4603 21 1 1 1 0 4.5585 22 1 1 0 0 0.9303 23 1 1 -1 0 4.3883 24 1 1 1 -1 5.2474 25 1 1 0 -1 1.4924 26 1 1 -1 -1 5.9080 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3411 atoms have been selected out of 3485 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1512 504 504 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1714 566 564 0.00 9 C009 has 411 137 137 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 105 35 35 0.00 13 C013 has 468 156 156 0.00 14 C014 has 111 37 37 0.73 Total of12576 atoms and 4180 groups and 4173 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3485 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1150 Number of atoms = 3485 Number of groups = 1155 Number of bonds = 3478 Number of angles = 1254 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1152 Number of HB donors = 2282 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1150 Number of atoms = 3485 Number of groups = 1155 Number of bonds = 3478 Number of angles = 1254 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1152 Number of HB donors = 2282 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.564" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1150" Evaluating: 1150-7 Parameter: NUMWAT <- "1143" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1143" Comparing "1081" and "1143". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.564" Parameter: BOX -> "32.564" Parameter: BOX -> "32.564" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.56400 B = 32.56400 C = 32.56400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7382 2 1 -1 0 -1 1.5990 3 1 -1 1 -1 4.4569 4 1 0 -1 -1 4.6964 5 1 0 0 -1 0.7722 6 1 0 1 -1 1.5367 7 1 -1 -1 0 4.5568 8 1 -1 0 0 0.9289 9 1 -1 1 0 4.3859 10 1 0 -1 0 0.6019 11 1 0 1 0 0.6019 12 1 -1 -1 1 5.2448 13 1 -1 0 1 1.4905 14 1 -1 1 1 5.9051 15 1 0 -1 1 1.5367 16 1 0 0 1 0.7722 17 1 0 1 1 4.6964 18 1 1 1 1 5.7382 19 1 1 0 1 1.5990 20 1 1 -1 1 4.4569 21 1 1 1 0 4.5568 22 1 1 0 0 0.9289 23 1 1 -1 0 4.3859 24 1 1 1 -1 5.2448 25 1 1 0 -1 1.4905 26 1 1 -1 -1 5.9051 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3411 atoms have been selected out of 3485 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 171 OPERATED ON BY TRANSFORMATION C011 RESIDUE 596 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 450 150 150 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 411 137 137 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 105 35 35 0.00 13 C013 has 468 156 156 0.00 14 C014 has 111 37 37 0.72 Total of12564 atoms and 4176 groups and 4169 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3485 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.562" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1148" Evaluating: 1148-7 Parameter: NUMWAT <- "1141" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1141" Comparing "1081" and "1141". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.562" Parameter: BOX -> "32.562" Parameter: BOX -> "32.562" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.56200 B = 32.56200 C = 32.56200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7370 2 1 -1 0 -1 1.5965 3 1 -1 1 -1 4.4535 4 1 0 -1 -1 4.6945 5 1 0 0 -1 0.7706 6 1 0 1 -1 1.5342 7 1 -1 -1 0 4.5550 8 1 -1 0 0 0.9274 9 1 -1 1 0 4.3834 10 1 0 -1 0 0.6002 11 1 0 1 0 0.6002 12 1 -1 -1 1 5.2421 13 1 -1 0 1 1.4887 14 1 -1 1 1 5.9022 15 1 0 -1 1 1.5342 16 1 0 0 1 0.7706 17 1 0 1 1 4.6945 18 1 1 1 1 5.7370 19 1 1 0 1 1.5965 20 1 1 -1 1 4.4535 21 1 1 1 0 4.5550 22 1 1 0 0 0.9274 23 1 1 -1 0 4.3834 24 1 1 1 -1 5.2421 25 1 1 0 -1 1.4887 26 1 1 -1 -1 5.9022 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3405 atoms have been selected out of 3479 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 450 150 150 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1714 566 564 0.00 9 C009 has 411 137 137 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 105 35 35 0.00 13 C013 has 468 156 156 0.00 14 C014 has 114 38 38 0.72 Total of12555 atoms and 4173 groups and 4166 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3479 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.56" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1148" Evaluating: 1148-7 Parameter: NUMWAT <- "1141" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1141" Comparing "1081" and "1141". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.56" Parameter: BOX -> "32.56" Parameter: BOX -> "32.56" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.56000 B = 32.56000 C = 32.56000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7359 2 1 -1 0 -1 1.5941 3 1 -1 1 -1 4.4500 4 1 0 -1 -1 4.6927 5 1 0 0 -1 0.7691 6 1 0 1 -1 1.5317 7 1 -1 -1 0 4.5533 8 1 -1 0 0 0.9259 9 1 -1 1 0 4.3810 10 1 0 -1 0 0.5986 11 1 0 1 0 0.5986 12 1 -1 -1 1 5.2394 13 1 -1 0 1 1.4868 14 1 -1 1 1 5.8993 15 1 0 -1 1 1.5317 16 1 0 0 1 0.7691 17 1 0 1 1 4.6927 18 1 1 1 1 5.7359 19 1 1 0 1 1.5941 20 1 1 -1 1 4.4500 21 1 1 1 0 4.5533 22 1 1 0 0 0.9259 23 1 1 -1 0 4.3810 24 1 1 1 -1 5.2394 25 1 1 0 -1 1.4868 26 1 1 -1 -1 5.8993 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3405 atoms have been selected out of 3479 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 453 151 151 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1714 566 564 0.00 9 C009 has 411 137 137 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 105 35 35 0.00 13 C013 has 468 156 156 0.00 14 C014 has 114 38 38 0.72 Total of12558 atoms and 4174 groups and 4167 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3479 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.558" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1148" Evaluating: 1148-7 Parameter: NUMWAT <- "1141" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1141" Comparing "1081" and "1141". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.558" Parameter: BOX -> "32.558" Parameter: BOX -> "32.558" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.55800 B = 32.55800 C = 32.55800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7348 2 1 -1 0 -1 1.5916 3 1 -1 1 -1 4.4466 4 1 0 -1 -1 4.6908 5 1 0 0 -1 0.7676 6 1 0 1 -1 1.5292 7 1 -1 -1 0 4.5516 8 1 -1 0 0 0.9245 9 1 -1 1 0 4.3786 10 1 0 -1 0 0.5969 11 1 0 1 0 0.5969 12 1 -1 -1 1 5.2367 13 1 -1 0 1 1.4850 14 1 -1 1 1 5.8964 15 1 0 -1 1 1.5292 16 1 0 0 1 0.7676 17 1 0 1 1 4.6908 18 1 1 1 1 5.7348 19 1 1 0 1 1.5916 20 1 1 -1 1 4.4466 21 1 1 1 0 4.5516 22 1 1 0 0 0.9245 23 1 1 -1 0 4.3786 24 1 1 1 -1 5.2367 25 1 1 0 -1 1.4850 26 1 1 -1 -1 5.8964 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3405 atoms have been selected out of 3479 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1714 566 564 0.00 9 C009 has 411 137 137 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 105 35 35 0.00 13 C013 has 468 156 156 0.00 14 C014 has 114 38 38 0.72 Total of12561 atoms and 4175 groups and 4168 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3479 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.556" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1148" Evaluating: 1148-7 Parameter: NUMWAT <- "1141" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1141" Comparing "1081" and "1141". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.556" Parameter: BOX -> "32.556" Parameter: BOX -> "32.556" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.55600 B = 32.55600 C = 32.55600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7337 2 1 -1 0 -1 1.5891 3 1 -1 1 -1 4.4432 4 1 0 -1 -1 4.6890 5 1 0 0 -1 0.7661 6 1 0 1 -1 1.5268 7 1 -1 -1 0 4.5499 8 1 -1 0 0 0.9230 9 1 -1 1 0 4.3761 10 1 0 -1 0 0.5952 11 1 0 1 0 0.5952 12 1 -1 -1 1 5.2340 13 1 -1 0 1 1.4832 14 1 -1 1 1 5.8935 15 1 0 -1 1 1.5268 16 1 0 0 1 0.7661 17 1 0 1 1 4.6890 18 1 1 1 1 5.7337 19 1 1 0 1 1.5891 20 1 1 -1 1 4.4432 21 1 1 1 0 4.5499 22 1 1 0 0 0.9230 23 1 1 -1 0 4.3761 24 1 1 1 -1 5.2340 25 1 1 0 -1 1.4832 26 1 1 -1 -1 5.8935 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3405 atoms have been selected out of 3479 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1714 566 564 0.00 9 C009 has 411 137 137 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 105 35 35 0.00 13 C013 has 468 156 156 0.00 14 C014 has 114 38 38 0.72 Total of12561 atoms and 4175 groups and 4168 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3479 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.554" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1148" Evaluating: 1148-7 Parameter: NUMWAT <- "1141" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1141" Comparing "1081" and "1141". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.554" Parameter: BOX -> "32.554" Parameter: BOX -> "32.554" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.55400 B = 32.55400 C = 32.55400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7326 2 1 -1 0 -1 1.5866 3 1 -1 1 -1 4.4398 4 1 0 -1 -1 4.6871 5 1 0 0 -1 0.7646 6 1 0 1 -1 1.5243 7 1 -1 -1 0 4.5482 8 1 -1 0 0 0.9216 9 1 -1 1 0 4.3737 10 1 0 -1 0 0.5936 11 1 0 1 0 0.5936 12 1 -1 -1 1 5.2313 13 1 -1 0 1 1.4813 14 1 -1 1 1 5.8906 15 1 0 -1 1 1.5243 16 1 0 0 1 0.7646 17 1 0 1 1 4.6871 18 1 1 1 1 5.7326 19 1 1 0 1 1.5866 20 1 1 -1 1 4.4398 21 1 1 1 0 4.5482 22 1 1 0 0 0.9216 23 1 1 -1 0 4.3737 24 1 1 1 -1 5.2313 25 1 1 0 -1 1.4813 26 1 1 -1 -1 5.8906 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3405 atoms have been selected out of 3479 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1714 566 564 0.00 9 C009 has 411 137 137 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 105 35 35 0.00 13 C013 has 468 156 156 0.00 14 C014 has 117 39 39 0.71 Total of12564 atoms and 4176 groups and 4169 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3479 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.552" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1148" Evaluating: 1148-7 Parameter: NUMWAT <- "1141" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1141" Comparing "1081" and "1141". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.552" Parameter: BOX -> "32.552" Parameter: BOX -> "32.552" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.55200 B = 32.55200 C = 32.55200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7314 2 1 -1 0 -1 1.5842 3 1 -1 1 -1 4.4364 4 1 0 -1 -1 4.6853 5 1 0 0 -1 0.7631 6 1 0 1 -1 1.5218 7 1 -1 -1 0 4.5464 8 1 -1 0 0 0.9201 9 1 -1 1 0 4.3713 10 1 0 -1 0 0.5919 11 1 0 1 0 0.5919 12 1 -1 -1 1 5.2287 13 1 -1 0 1 1.4795 14 1 -1 1 1 5.8877 15 1 0 -1 1 1.5218 16 1 0 0 1 0.7631 17 1 0 1 1 4.6853 18 1 1 1 1 5.7314 19 1 1 0 1 1.5842 20 1 1 -1 1 4.4364 21 1 1 1 0 4.5464 22 1 1 0 0 0.9201 23 1 1 -1 0 4.3713 24 1 1 1 -1 5.2287 25 1 1 0 -1 1.4795 26 1 1 -1 -1 5.8877 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3405 atoms have been selected out of 3479 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1714 566 564 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 105 35 35 0.00 13 C013 has 468 156 156 0.00 14 C014 has 117 39 39 0.71 Total of12570 atoms and 4178 groups and 4171 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3479 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.55" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1148" Evaluating: 1148-7 Parameter: NUMWAT <- "1141" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1141" Comparing "1081" and "1141". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.55" Parameter: BOX -> "32.55" Parameter: BOX -> "32.55" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.55000 B = 32.55000 C = 32.55000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7303 2 1 -1 0 -1 1.5817 3 1 -1 1 -1 4.4330 4 1 0 -1 -1 4.6834 5 1 0 0 -1 0.7616 6 1 0 1 -1 1.5193 7 1 -1 -1 0 4.5447 8 1 -1 0 0 0.9187 9 1 -1 1 0 4.3688 10 1 0 -1 0 0.5903 11 1 0 1 0 0.5903 12 1 -1 -1 1 5.2260 13 1 -1 0 1 1.4777 14 1 -1 1 1 5.8848 15 1 0 -1 1 1.5193 16 1 0 0 1 0.7616 17 1 0 1 1 4.6834 18 1 1 1 1 5.7303 19 1 1 0 1 1.5817 20 1 1 -1 1 4.4330 21 1 1 1 0 4.5447 22 1 1 0 0 0.9187 23 1 1 -1 0 4.3688 24 1 1 1 -1 5.2260 25 1 1 0 -1 1.4777 26 1 1 -1 -1 5.8848 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3405 atoms have been selected out of 3479 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1512 504 504 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1714 566 564 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 105 35 35 0.00 13 C013 has 468 156 156 0.00 14 C014 has 117 39 39 0.71 Total of12573 atoms and 4179 groups and 4172 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3479 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.548" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1148" Evaluating: 1148-7 Parameter: NUMWAT <- "1141" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1141" Comparing "1081" and "1141". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.548" Parameter: BOX -> "32.548" Parameter: BOX -> "32.548" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.54800 B = 32.54800 C = 32.54800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7292 2 1 -1 0 -1 1.5792 3 1 -1 1 -1 4.4296 4 1 0 -1 -1 4.6816 5 1 0 0 -1 0.7601 6 1 0 1 -1 1.5168 7 1 -1 -1 0 4.5430 8 1 -1 0 0 0.9172 9 1 -1 1 0 4.3664 10 1 0 -1 0 0.5886 11 1 0 1 0 0.5886 12 1 -1 -1 1 5.2233 13 1 -1 0 1 1.4759 14 1 -1 1 1 5.8819 15 1 0 -1 1 1.5168 16 1 0 0 1 0.7601 17 1 0 1 1 4.6816 18 1 1 1 1 5.7292 19 1 1 0 1 1.5792 20 1 1 -1 1 4.4296 21 1 1 1 0 4.5430 22 1 1 0 0 0.9172 23 1 1 -1 0 4.3664 24 1 1 1 -1 5.2233 25 1 1 0 -1 1.4759 26 1 1 -1 -1 5.8819 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3405 atoms have been selected out of 3479 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1512 504 504 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1714 566 564 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 105 35 35 0.00 13 C013 has 468 156 156 0.00 14 C014 has 117 39 39 0.71 Total of12573 atoms and 4179 groups and 4172 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3479 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.546" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1148" Evaluating: 1148-7 Parameter: NUMWAT <- "1141" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1141" Comparing "1081" and "1141". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.546" Parameter: BOX -> "32.546" Parameter: BOX -> "32.546" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.54600 B = 32.54600 C = 32.54600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7281 2 1 -1 0 -1 1.5767 3 1 -1 1 -1 4.4261 4 1 0 -1 -1 4.6797 5 1 0 0 -1 0.7586 6 1 0 1 -1 1.5143 7 1 -1 -1 0 4.5413 8 1 -1 0 0 0.9158 9 1 -1 1 0 4.3640 10 1 0 -1 0 0.5870 11 1 0 1 0 0.5870 12 1 -1 -1 1 5.2206 13 1 -1 0 1 1.4741 14 1 -1 1 1 5.8790 15 1 0 -1 1 1.5143 16 1 0 0 1 0.7586 17 1 0 1 1 4.6797 18 1 1 1 1 5.7281 19 1 1 0 1 1.5767 20 1 1 -1 1 4.4261 21 1 1 1 0 4.5413 22 1 1 0 0 0.9158 23 1 1 -1 0 4.3640 24 1 1 1 -1 5.2206 25 1 1 0 -1 1.4741 26 1 1 -1 -1 5.8790 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3405 atoms have been selected out of 3479 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1512 504 504 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1714 566 564 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 105 35 35 0.00 13 C013 has 468 156 156 0.00 14 C014 has 117 39 39 0.71 Total of12573 atoms and 4179 groups and 4172 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3479 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.544" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1148" Evaluating: 1148-7 Parameter: NUMWAT <- "1141" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1141" Comparing "1081" and "1141". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.544" Parameter: BOX -> "32.544" Parameter: BOX -> "32.544" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.54400 B = 32.54400 C = 32.54400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7270 2 1 -1 0 -1 1.5743 3 1 -1 1 -1 4.4227 4 1 0 -1 -1 4.6779 5 1 0 0 -1 0.7571 6 1 0 1 -1 1.5119 7 1 -1 -1 0 4.5396 8 1 -1 0 0 0.9143 9 1 -1 1 0 4.3616 10 1 0 -1 0 0.5853 11 1 0 1 0 0.5853 12 1 -1 -1 1 5.2180 13 1 -1 0 1 1.4722 14 1 -1 1 1 5.8761 15 1 0 -1 1 1.5119 16 1 0 0 1 0.7571 17 1 0 1 1 4.6779 18 1 1 1 1 5.7270 19 1 1 0 1 1.5743 20 1 1 -1 1 4.4227 21 1 1 1 0 4.5396 22 1 1 0 0 0.9143 23 1 1 -1 0 4.3616 24 1 1 1 -1 5.2180 25 1 1 0 -1 1.4722 26 1 1 -1 -1 5.8761 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3405 atoms have been selected out of 3479 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1512 504 504 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1714 566 564 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 105 35 35 0.00 13 C013 has 468 156 156 0.00 14 C014 has 117 39 39 0.70 Total of12573 atoms and 4179 groups and 4172 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3479 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.542" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1148" Evaluating: 1148-7 Parameter: NUMWAT <- "1141" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1141" Comparing "1081" and "1141". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.542" Parameter: BOX -> "32.542" Parameter: BOX -> "32.542" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.54200 B = 32.54200 C = 32.54200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7259 2 1 -1 0 -1 1.5718 3 1 -1 1 -1 4.4193 4 1 0 -1 -1 4.6761 5 1 0 0 -1 0.7557 6 1 0 1 -1 1.5094 7 1 -1 -1 0 4.5379 8 1 -1 0 0 0.9129 9 1 -1 1 0 4.3591 10 1 0 -1 0 0.5837 11 1 0 1 0 0.5837 12 1 -1 -1 1 5.2153 13 1 -1 0 1 1.4704 14 1 -1 1 1 5.8732 15 1 0 -1 1 1.5094 16 1 0 0 1 0.7557 17 1 0 1 1 4.6761 18 1 1 1 1 5.7259 19 1 1 0 1 1.5718 20 1 1 -1 1 4.4193 21 1 1 1 0 4.5379 22 1 1 0 0 0.9129 23 1 1 -1 0 4.3591 24 1 1 1 -1 5.2153 25 1 1 0 -1 1.4704 26 1 1 -1 -1 5.8732 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3405 atoms have been selected out of 3479 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1512 504 504 0.00 6 C006 has 453 151 151 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 105 35 35 0.00 13 C013 has 471 157 157 0.00 14 C014 has 117 39 39 0.70 Total of12579 atoms and 4181 groups and 4174 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3479 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.54" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1148" Evaluating: 1148-7 Parameter: NUMWAT <- "1141" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1141" Comparing "1081" and "1141". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.54" Parameter: BOX -> "32.54" Parameter: BOX -> "32.54" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.54000 B = 32.54000 C = 32.54000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7248 2 1 -1 0 -1 1.5693 3 1 -1 1 -1 4.4159 4 1 0 -1 -1 4.6742 5 1 0 0 -1 0.7542 6 1 0 1 -1 1.5069 7 1 -1 -1 0 4.5362 8 1 -1 0 0 0.9114 9 1 -1 1 0 4.3567 10 1 0 -1 0 0.5821 11 1 0 1 0 0.5821 12 1 -1 -1 1 5.2126 13 1 -1 0 1 1.4686 14 1 -1 1 1 5.8703 15 1 0 -1 1 1.5069 16 1 0 0 1 0.7542 17 1 0 1 1 4.6742 18 1 1 1 1 5.7248 19 1 1 0 1 1.5693 20 1 1 -1 1 4.4159 21 1 1 1 0 4.5362 22 1 1 0 0 0.9114 23 1 1 -1 0 4.3567 24 1 1 1 -1 5.2126 25 1 1 0 -1 1.4686 26 1 1 -1 -1 5.8703 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3405 atoms have been selected out of 3479 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1512 504 504 0.00 6 C006 has 453 151 151 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 105 35 35 0.00 13 C013 has 471 157 157 0.00 14 C014 has 117 39 39 0.70 Total of12582 atoms and 4182 groups and 4175 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3479 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.538" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1148" Evaluating: 1148-7 Parameter: NUMWAT <- "1141" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1141" Comparing "1081" and "1141". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.538" Parameter: BOX -> "32.538" Parameter: BOX -> "32.538" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.53800 B = 32.53800 C = 32.53800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7237 2 1 -1 0 -1 1.5669 3 1 -1 1 -1 4.4125 4 1 0 -1 -1 4.6724 5 1 0 0 -1 0.7527 6 1 0 1 -1 1.5044 7 1 -1 -1 0 4.5345 8 1 -1 0 0 0.9100 9 1 -1 1 0 4.3543 10 1 0 -1 0 0.5804 11 1 0 1 0 0.5804 12 1 -1 -1 1 5.2099 13 1 -1 0 1 1.4668 14 1 -1 1 1 5.8674 15 1 0 -1 1 1.5044 16 1 0 0 1 0.7527 17 1 0 1 1 4.6724 18 1 1 1 1 5.7237 19 1 1 0 1 1.5669 20 1 1 -1 1 4.4125 21 1 1 1 0 4.5345 22 1 1 0 0 0.9100 23 1 1 -1 0 4.3543 24 1 1 1 -1 5.2099 25 1 1 0 -1 1.4668 26 1 1 -1 -1 5.8674 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3405 atoms have been selected out of 3479 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1512 504 504 0.00 6 C006 has 453 151 151 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 105 35 35 0.00 13 C013 has 471 157 157 0.00 14 C014 has 117 39 39 0.70 Total of12585 atoms and 4183 groups and 4176 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3479 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1148 Number of atoms = 3479 Number of groups = 1153 Number of bonds = 3472 Number of angles = 1252 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1150 Number of HB donors = 2278 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.536" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1148" Evaluating: 1148-7 Parameter: NUMWAT <- "1141" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1141" Comparing "1081" and "1141". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.536" Parameter: BOX -> "32.536" Parameter: BOX -> "32.536" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.53600 B = 32.53600 C = 32.53600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7226 2 1 -1 0 -1 1.5644 3 1 -1 1 -1 4.4091 4 1 0 -1 -1 4.6705 5 1 0 0 -1 0.7512 6 1 0 1 -1 1.5019 7 1 -1 -1 0 4.5327 8 1 -1 0 0 0.9086 9 1 -1 1 0 4.3519 10 1 0 -1 0 0.5788 11 1 0 1 0 0.5788 12 1 -1 -1 1 5.2073 13 1 -1 0 1 1.4650 14 1 -1 1 1 5.8645 15 1 0 -1 1 1.5019 16 1 0 0 1 0.7512 17 1 0 1 1 4.6705 18 1 1 1 1 5.7226 19 1 1 0 1 1.5644 20 1 1 -1 1 4.4091 21 1 1 1 0 4.5327 22 1 1 0 0 0.9086 23 1 1 -1 0 4.3519 24 1 1 1 -1 5.2073 25 1 1 0 -1 1.4650 26 1 1 -1 -1 5.8645 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3405 atoms have been selected out of 3479 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 704 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 450 150 150 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 105 35 35 0.00 13 C013 has 471 157 157 0.00 14 C014 has 117 39 39 0.70 Total of12582 atoms and 4182 groups and 4175 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3479 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1147 Number of atoms = 3476 Number of groups = 1152 Number of bonds = 3469 Number of angles = 1251 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1149 Number of HB donors = 2276 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1147 Number of atoms = 3476 Number of groups = 1152 Number of bonds = 3469 Number of angles = 1251 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1149 Number of HB donors = 2276 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.534" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1147" Evaluating: 1147-7 Parameter: NUMWAT <- "1140" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1140" Comparing "1081" and "1140". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.534" Parameter: BOX -> "32.534" Parameter: BOX -> "32.534" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.53400 B = 32.53400 C = 32.53400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7215 2 1 -1 0 -1 1.5619 3 1 -1 1 -1 4.4056 4 1 0 -1 -1 4.6687 5 1 0 0 -1 0.7497 6 1 0 1 -1 1.4995 7 1 -1 -1 0 4.5310 8 1 -1 0 0 0.9071 9 1 -1 1 0 4.3494 10 1 0 -1 0 0.5772 11 1 0 1 0 0.5772 12 1 -1 -1 1 5.2046 13 1 -1 0 1 1.4632 14 1 -1 1 1 5.8616 15 1 0 -1 1 1.4995 16 1 0 0 1 0.7497 17 1 0 1 1 4.6687 18 1 1 1 1 5.7215 19 1 1 0 1 1.5619 20 1 1 -1 1 4.4056 21 1 1 1 0 4.5310 22 1 1 0 0 0.9071 23 1 1 -1 0 4.3494 24 1 1 1 -1 5.2046 25 1 1 0 -1 1.4632 26 1 1 -1 -1 5.8616 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3402 atoms have been selected out of 3476 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 450 150 150 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 105 35 35 0.00 13 C013 has 471 157 157 0.00 14 C014 has 117 39 39 0.69 Total of12582 atoms and 4182 groups and 4175 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3476 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1147 Number of atoms = 3476 Number of groups = 1152 Number of bonds = 3469 Number of angles = 1251 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1149 Number of HB donors = 2276 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1147 Number of atoms = 3476 Number of groups = 1152 Number of bonds = 3469 Number of angles = 1251 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1149 Number of HB donors = 2276 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.532" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1147" Evaluating: 1147-7 Parameter: NUMWAT <- "1140" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1140" Comparing "1081" and "1140". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.532" Parameter: BOX -> "32.532" Parameter: BOX -> "32.532" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.53200 B = 32.53200 C = 32.53200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7204 2 1 -1 0 -1 1.5595 3 1 -1 1 -1 4.4022 4 1 0 -1 -1 4.6669 5 1 0 0 -1 0.7482 6 1 0 1 -1 1.4970 7 1 -1 -1 0 4.5293 8 1 -1 0 0 0.9057 9 1 -1 1 0 4.3470 10 1 0 -1 0 0.5755 11 1 0 1 0 0.5755 12 1 -1 -1 1 5.2019 13 1 -1 0 1 1.4614 14 1 -1 1 1 5.8587 15 1 0 -1 1 1.4970 16 1 0 0 1 0.7482 17 1 0 1 1 4.6669 18 1 1 1 1 5.7204 19 1 1 0 1 1.5595 20 1 1 -1 1 4.4022 21 1 1 1 0 4.5293 22 1 1 0 0 0.9057 23 1 1 -1 0 4.3470 24 1 1 1 -1 5.2019 25 1 1 0 -1 1.4614 26 1 1 -1 -1 5.8587 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3402 atoms have been selected out of 3476 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 450 150 150 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 414 138 138 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 105 35 35 0.00 13 C013 has 471 157 157 0.00 14 C014 has 117 39 39 0.69 Total of12582 atoms and 4182 groups and 4175 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3476 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1147 Number of atoms = 3476 Number of groups = 1152 Number of bonds = 3469 Number of angles = 1251 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1149 Number of HB donors = 2276 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1147 Number of atoms = 3476 Number of groups = 1152 Number of bonds = 3469 Number of angles = 1251 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1149 Number of HB donors = 2276 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.53" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1147" Evaluating: 1147-7 Parameter: NUMWAT <- "1140" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1140" Comparing "1081" and "1140". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.53" Parameter: BOX -> "32.53" Parameter: BOX -> "32.53" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.53000 B = 32.53000 C = 32.53000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7193 2 1 -1 0 -1 1.5570 3 1 -1 1 -1 4.3988 4 1 0 -1 -1 4.6650 5 1 0 0 -1 0.7468 6 1 0 1 -1 1.4945 7 1 -1 -1 0 4.5276 8 1 -1 0 0 0.9043 9 1 -1 1 0 4.3446 10 1 0 -1 0 0.5739 11 1 0 1 0 0.5739 12 1 -1 -1 1 5.1993 13 1 -1 0 1 1.4597 14 1 -1 1 1 5.8558 15 1 0 -1 1 1.4945 16 1 0 0 1 0.7468 17 1 0 1 1 4.6650 18 1 1 1 1 5.7193 19 1 1 0 1 1.5570 20 1 1 -1 1 4.3988 21 1 1 1 0 4.5276 22 1 1 0 0 0.9043 23 1 1 -1 0 4.3446 24 1 1 1 -1 5.1993 25 1 1 0 -1 1.4597 26 1 1 -1 -1 5.8558 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3402 atoms have been selected out of 3476 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 450 150 150 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 105 35 35 0.00 13 C013 has 471 157 157 0.00 14 C014 has 117 39 39 0.69 Total of12588 atoms and 4184 groups and 4177 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3476 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1147 Number of atoms = 3476 Number of groups = 1152 Number of bonds = 3469 Number of angles = 1251 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1149 Number of HB donors = 2276 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1147 Number of atoms = 3476 Number of groups = 1152 Number of bonds = 3469 Number of angles = 1251 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1149 Number of HB donors = 2276 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.528" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1147" Evaluating: 1147-7 Parameter: NUMWAT <- "1140" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1140" Comparing "1081" and "1140". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.528" Parameter: BOX -> "32.528" Parameter: BOX -> "32.528" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.52800 B = 32.52800 C = 32.52800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7182 2 1 -1 0 -1 1.5545 3 1 -1 1 -1 4.3954 4 1 0 -1 -1 4.6632 5 1 0 0 -1 0.7453 6 1 0 1 -1 1.4920 7 1 -1 -1 0 4.5259 8 1 -1 0 0 0.9028 9 1 -1 1 0 4.3422 10 1 0 -1 0 0.5723 11 1 0 1 0 0.5723 12 1 -1 -1 1 5.1966 13 1 -1 0 1 1.4579 14 1 -1 1 1 5.8529 15 1 0 -1 1 1.4920 16 1 0 0 1 0.7453 17 1 0 1 1 4.6632 18 1 1 1 1 5.7182 19 1 1 0 1 1.5545 20 1 1 -1 1 4.3954 21 1 1 1 0 4.5259 22 1 1 0 0 0.9028 23 1 1 -1 0 4.3422 24 1 1 1 -1 5.1966 25 1 1 0 -1 1.4579 26 1 1 -1 -1 5.8529 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3402 atoms have been selected out of 3476 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 384 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 450 150 150 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 105 35 35 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.69 Total of12591 atoms and 4185 groups and 4178 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3476 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1146 Number of atoms = 3473 Number of groups = 1151 Number of bonds = 3466 Number of angles = 1250 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1148 Number of HB donors = 2274 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1146 Number of atoms = 3473 Number of groups = 1151 Number of bonds = 3466 Number of angles = 1250 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1148 Number of HB donors = 2274 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.526" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1146" Evaluating: 1146-7 Parameter: NUMWAT <- "1139" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1139" Comparing "1081" and "1139". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.526" Parameter: BOX -> "32.526" Parameter: BOX -> "32.526" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.52600 B = 32.52600 C = 32.52600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7171 2 1 -1 0 -1 1.5521 3 1 -1 1 -1 4.3920 4 1 0 -1 -1 4.6614 5 1 0 0 -1 0.7438 6 1 0 1 -1 1.4896 7 1 -1 -1 0 4.5242 8 1 -1 0 0 0.9014 9 1 -1 1 0 4.3397 10 1 0 -1 0 0.5706 11 1 0 1 0 0.5706 12 1 -1 -1 1 5.1939 13 1 -1 0 1 1.4561 14 1 -1 1 1 5.8500 15 1 0 -1 1 1.4896 16 1 0 0 1 0.7438 17 1 0 1 1 4.6614 18 1 1 1 1 5.7171 19 1 1 0 1 1.5521 20 1 1 -1 1 4.3920 21 1 1 1 0 4.5242 22 1 1 0 0 0.9014 23 1 1 -1 0 4.3397 24 1 1 1 -1 5.1939 25 1 1 0 -1 1.4561 26 1 1 -1 -1 5.8500 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3399 atoms have been selected out of 3473 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 450 150 150 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 105 35 35 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.69 Total of12585 atoms and 4183 groups and 4176 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3473 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1146 Number of atoms = 3473 Number of groups = 1151 Number of bonds = 3466 Number of angles = 1250 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1148 Number of HB donors = 2274 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1146 Number of atoms = 3473 Number of groups = 1151 Number of bonds = 3466 Number of angles = 1250 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1148 Number of HB donors = 2274 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.524" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1146" Evaluating: 1146-7 Parameter: NUMWAT <- "1139" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1139" Comparing "1081" and "1139". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.524" Parameter: BOX -> "32.524" Parameter: BOX -> "32.524" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.52400 B = 32.52400 C = 32.52400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7160 2 1 -1 0 -1 1.5496 3 1 -1 1 -1 4.3886 4 1 0 -1 -1 4.6595 5 1 0 0 -1 0.7424 6 1 0 1 -1 1.4871 7 1 -1 -1 0 4.5225 8 1 -1 0 0 0.9000 9 1 -1 1 0 4.3373 10 1 0 -1 0 0.5690 11 1 0 1 0 0.5690 12 1 -1 -1 1 5.1913 13 1 -1 0 1 1.4543 14 1 -1 1 1 5.8471 15 1 0 -1 1 1.4871 16 1 0 0 1 0.7424 17 1 0 1 1 4.6595 18 1 1 1 1 5.7160 19 1 1 0 1 1.5496 20 1 1 -1 1 4.3886 21 1 1 1 0 4.5225 22 1 1 0 0 0.9000 23 1 1 -1 0 4.3373 24 1 1 1 -1 5.1913 25 1 1 0 -1 1.4543 26 1 1 -1 -1 5.8471 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3399 atoms have been selected out of 3473 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 750 250 250 0.00 3 C003 has 108 36 36 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 450 150 150 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 105 35 35 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.68 Total of12588 atoms and 4184 groups and 4177 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3473 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1146 Number of atoms = 3473 Number of groups = 1151 Number of bonds = 3466 Number of angles = 1250 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1148 Number of HB donors = 2274 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1146 Number of atoms = 3473 Number of groups = 1151 Number of bonds = 3466 Number of angles = 1250 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1148 Number of HB donors = 2274 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.522" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1146" Evaluating: 1146-7 Parameter: NUMWAT <- "1139" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1139" Comparing "1081" and "1139". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.522" Parameter: BOX -> "32.522" Parameter: BOX -> "32.522" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.52200 B = 32.52200 C = 32.52200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7149 2 1 -1 0 -1 1.5472 3 1 -1 1 -1 4.3852 4 1 0 -1 -1 4.6577 5 1 0 0 -1 0.7409 6 1 0 1 -1 1.4846 7 1 -1 -1 0 4.5208 8 1 -1 0 0 0.8986 9 1 -1 1 0 4.3349 10 1 0 -1 0 0.5674 11 1 0 1 0 0.5674 12 1 -1 -1 1 5.1886 13 1 -1 0 1 1.4525 14 1 -1 1 1 5.8442 15 1 0 -1 1 1.4846 16 1 0 0 1 0.7409 17 1 0 1 1 4.6577 18 1 1 1 1 5.7149 19 1 1 0 1 1.5472 20 1 1 -1 1 4.3852 21 1 1 1 0 4.5208 22 1 1 0 0 0.8986 23 1 1 -1 0 4.3349 24 1 1 1 -1 5.1886 25 1 1 0 -1 1.4525 26 1 1 -1 -1 5.8442 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3399 atoms have been selected out of 3473 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 620 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 447 149 149 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1720 568 566 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 105 35 35 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.68 Total of12582 atoms and 4182 groups and 4175 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3473 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.52" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.52" Parameter: BOX -> "32.52" Parameter: BOX -> "32.52" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.52000 B = 32.52000 C = 32.52000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7138 2 1 -1 0 -1 1.5447 3 1 -1 1 -1 4.3817 4 1 0 -1 -1 4.6559 5 1 0 0 -1 0.7394 6 1 0 1 -1 1.4822 7 1 -1 -1 0 4.5191 8 1 -1 0 0 0.8972 9 1 -1 1 0 4.3325 10 1 0 -1 0 0.5658 11 1 0 1 0 0.5658 12 1 -1 -1 1 5.1859 13 1 -1 0 1 1.4508 14 1 -1 1 1 5.8413 15 1 0 -1 1 1.4822 16 1 0 0 1 0.7394 17 1 0 1 1 4.6559 18 1 1 1 1 5.7138 19 1 1 0 1 1.5447 20 1 1 -1 1 4.3817 21 1 1 1 0 4.5191 22 1 1 0 0 0.8972 23 1 1 -1 0 4.3325 24 1 1 1 -1 5.1859 25 1 1 0 -1 1.4508 26 1 1 -1 -1 5.8413 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 468 156 156 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 447 149 149 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 105 35 35 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.68 Total of12576 atoms and 4180 groups and 4173 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.518" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.518" Parameter: BOX -> "32.518" Parameter: BOX -> "32.518" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.51800 B = 32.51800 C = 32.51800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7127 2 1 -1 0 -1 1.5422 3 1 -1 1 -1 4.3783 4 1 0 -1 -1 4.6540 5 1 0 0 -1 0.7380 6 1 0 1 -1 1.4797 7 1 -1 -1 0 4.5174 8 1 -1 0 0 0.8957 9 1 -1 1 0 4.3300 10 1 0 -1 0 0.5642 11 1 0 1 0 0.5642 12 1 -1 -1 1 5.1833 13 1 -1 0 1 1.4490 14 1 -1 1 1 5.8384 15 1 0 -1 1 1.4797 16 1 0 0 1 0.7380 17 1 0 1 1 4.6540 18 1 1 1 1 5.7127 19 1 1 0 1 1.5422 20 1 1 -1 1 4.3783 21 1 1 1 0 4.5174 22 1 1 0 0 0.8957 23 1 1 -1 0 4.3300 24 1 1 1 -1 5.1833 25 1 1 0 -1 1.4490 26 1 1 -1 -1 5.8384 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 471 157 157 0.00 2 C002 has 747 249 249 0.00 3 C003 has 108 36 36 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 447 149 149 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 105 35 35 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.68 Total of12579 atoms and 4181 groups and 4174 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.516" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.516" Parameter: BOX -> "32.516" Parameter: BOX -> "32.516" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.51600 B = 32.51600 C = 32.51600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7116 2 1 -1 0 -1 1.5398 3 1 -1 1 -1 4.3749 4 1 0 -1 -1 4.6522 5 1 0 0 -1 0.7365 6 1 0 1 -1 1.4773 7 1 -1 -1 0 4.5157 8 1 -1 0 0 0.8943 9 1 -1 1 0 4.3276 10 1 0 -1 0 0.5626 11 1 0 1 0 0.5626 12 1 -1 -1 1 5.1806 13 1 -1 0 1 1.4472 14 1 -1 1 1 5.8355 15 1 0 -1 1 1.4773 16 1 0 0 1 0.7365 17 1 0 1 1 4.6522 18 1 1 1 1 5.7116 19 1 1 0 1 1.5398 20 1 1 -1 1 4.3749 21 1 1 1 0 4.5157 22 1 1 0 0 0.8943 23 1 1 -1 0 4.3276 24 1 1 1 -1 5.1806 25 1 1 0 -1 1.4472 26 1 1 -1 -1 5.8355 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 747 249 249 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 447 149 149 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 105 35 35 0.00 13 C013 has 474 158 158 0.00 14 C014 has 117 39 39 0.68 Total of12588 atoms and 4184 groups and 4177 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.514" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.514" Parameter: BOX -> "32.514" Parameter: BOX -> "32.514" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.51400 B = 32.51400 C = 32.51400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7106 2 1 -1 0 -1 1.5373 3 1 -1 1 -1 4.3715 4 1 0 -1 -1 4.6504 5 1 0 0 -1 0.7351 6 1 0 1 -1 1.4748 7 1 -1 -1 0 4.5140 8 1 -1 0 0 0.8929 9 1 -1 1 0 4.3252 10 1 0 -1 0 0.5610 11 1 0 1 0 0.5610 12 1 -1 -1 1 5.1779 13 1 -1 0 1 1.4455 14 1 -1 1 1 5.8326 15 1 0 -1 1 1.4748 16 1 0 0 1 0.7351 17 1 0 1 1 4.6504 18 1 1 1 1 5.7106 19 1 1 0 1 1.5373 20 1 1 -1 1 4.3715 21 1 1 1 0 4.5140 22 1 1 0 0 0.8929 23 1 1 -1 0 4.3252 24 1 1 1 -1 5.1779 25 1 1 0 -1 1.4455 26 1 1 -1 -1 5.8326 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 747 249 249 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 447 149 149 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 105 35 35 0.00 13 C013 has 477 159 159 0.00 14 C014 has 117 39 39 0.67 Total of12597 atoms and 4187 groups and 4180 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.512" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.512" Parameter: BOX -> "32.512" Parameter: BOX -> "32.512" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.51200 B = 32.51200 C = 32.51200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7095 2 1 -1 0 -1 1.5349 3 1 -1 1 -1 4.3681 4 1 0 -1 -1 4.6486 5 1 0 0 -1 0.7336 6 1 0 1 -1 1.4723 7 1 -1 -1 0 4.5123 8 1 -1 0 0 0.8915 9 1 -1 1 0 4.3228 10 1 0 -1 0 0.5593 11 1 0 1 0 0.5593 12 1 -1 -1 1 5.1753 13 1 -1 0 1 1.4437 14 1 -1 1 1 5.8298 15 1 0 -1 1 1.4723 16 1 0 0 1 0.7336 17 1 0 1 1 4.6486 18 1 1 1 1 5.7095 19 1 1 0 1 1.5349 20 1 1 -1 1 4.3681 21 1 1 1 0 4.5123 22 1 1 0 0 0.8915 23 1 1 -1 0 4.3228 24 1 1 1 -1 5.1753 25 1 1 0 -1 1.4437 26 1 1 -1 -1 5.8298 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 747 249 249 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 447 149 149 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 105 35 35 0.00 13 C013 has 477 159 159 0.00 14 C014 has 117 39 39 0.67 Total of12600 atoms and 4188 groups and 4181 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.51" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.51" Parameter: BOX -> "32.51" Parameter: BOX -> "32.51" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.51000 B = 32.51000 C = 32.51000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7084 2 1 -1 0 -1 1.5324 3 1 -1 1 -1 4.3647 4 1 0 -1 -1 4.6467 5 1 0 0 -1 0.7322 6 1 0 1 -1 1.4699 7 1 -1 -1 0 4.5106 8 1 -1 0 0 0.8901 9 1 -1 1 0 4.3204 10 1 0 -1 0 0.5577 11 1 0 1 0 0.5577 12 1 -1 -1 1 5.1726 13 1 -1 0 1 1.4419 14 1 -1 1 1 5.8269 15 1 0 -1 1 1.4699 16 1 0 0 1 0.7322 17 1 0 1 1 4.6467 18 1 1 1 1 5.7084 19 1 1 0 1 1.5324 20 1 1 -1 1 4.3647 21 1 1 1 0 4.5106 22 1 1 0 0 0.8901 23 1 1 -1 0 4.3204 24 1 1 1 -1 5.1726 25 1 1 0 -1 1.4419 26 1 1 -1 -1 5.8269 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 747 249 249 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 447 149 149 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 105 35 35 0.00 13 C013 has 477 159 159 0.00 14 C014 has 117 39 39 0.67 Total of12600 atoms and 4188 groups and 4181 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.508" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.508" Parameter: BOX -> "32.508" Parameter: BOX -> "32.508" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.50800 B = 32.50800 C = 32.50800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7073 2 1 -1 0 -1 1.5300 3 1 -1 1 -1 4.3613 4 1 0 -1 -1 4.6449 5 1 0 0 -1 0.7307 6 1 0 1 -1 1.4674 7 1 -1 -1 0 4.5089 8 1 -1 0 0 0.8887 9 1 -1 1 0 4.3179 10 1 0 -1 0 0.5561 11 1 0 1 0 0.5561 12 1 -1 -1 1 5.1700 13 1 -1 0 1 1.4402 14 1 -1 1 1 5.8240 15 1 0 -1 1 1.4674 16 1 0 0 1 0.7307 17 1 0 1 1 4.6449 18 1 1 1 1 5.7073 19 1 1 0 1 1.5300 20 1 1 -1 1 4.3613 21 1 1 1 0 4.5089 22 1 1 0 0 0.8887 23 1 1 -1 0 4.3179 24 1 1 1 -1 5.1700 25 1 1 0 -1 1.4402 26 1 1 -1 -1 5.8240 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 747 249 249 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 447 149 149 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 105 35 35 0.00 13 C013 has 477 159 159 0.00 14 C014 has 117 39 39 0.67 Total of12600 atoms and 4188 groups and 4181 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.506" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.506" Parameter: BOX -> "32.506" Parameter: BOX -> "32.506" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.50600 B = 32.50600 C = 32.50600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7063 2 1 -1 0 -1 1.5275 3 1 -1 1 -1 4.3579 4 1 0 -1 -1 4.6431 5 1 0 0 -1 0.7293 6 1 0 1 -1 1.4650 7 1 -1 -1 0 4.5072 8 1 -1 0 0 0.8873 9 1 -1 1 0 4.3155 10 1 0 -1 0 0.5545 11 1 0 1 0 0.5545 12 1 -1 -1 1 5.1673 13 1 -1 0 1 1.4384 14 1 -1 1 1 5.8211 15 1 0 -1 1 1.4650 16 1 0 0 1 0.7293 17 1 0 1 1 4.6431 18 1 1 1 1 5.7063 19 1 1 0 1 1.5275 20 1 1 -1 1 4.3579 21 1 1 1 0 4.5072 22 1 1 0 0 0.8873 23 1 1 -1 0 4.3155 24 1 1 1 -1 5.1673 25 1 1 0 -1 1.4384 26 1 1 -1 -1 5.8211 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 447 149 149 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 105 35 35 0.00 13 C013 has 477 159 159 0.00 14 C014 has 117 39 39 0.67 Total of12603 atoms and 4189 groups and 4182 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.504" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.504" Parameter: BOX -> "32.504" Parameter: BOX -> "32.504" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.50400 B = 32.50400 C = 32.50400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7052 2 1 -1 0 -1 1.5251 3 1 -1 1 -1 4.3544 4 1 0 -1 -1 4.6413 5 1 0 0 -1 0.7278 6 1 0 1 -1 1.4625 7 1 -1 -1 0 4.5056 8 1 -1 0 0 0.8859 9 1 -1 1 0 4.3131 10 1 0 -1 0 0.5529 11 1 0 1 0 0.5529 12 1 -1 -1 1 5.1647 13 1 -1 0 1 1.4367 14 1 -1 1 1 5.8182 15 1 0 -1 1 1.4625 16 1 0 0 1 0.7278 17 1 0 1 1 4.6413 18 1 1 1 1 5.7052 19 1 1 0 1 1.5251 20 1 1 -1 1 4.3544 21 1 1 1 0 4.5056 22 1 1 0 0 0.8859 23 1 1 -1 0 4.3131 24 1 1 1 -1 5.1647 25 1 1 0 -1 1.4367 26 1 1 -1 -1 5.8182 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 447 149 149 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 105 35 35 0.00 13 C013 has 477 159 159 0.00 14 C014 has 117 39 39 0.66 Total of12606 atoms and 4190 groups and 4183 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.502" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.502" Parameter: BOX -> "32.502" Parameter: BOX -> "32.502" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.50200 B = 32.50200 C = 32.50200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7041 2 1 -1 0 -1 1.5227 3 1 -1 1 -1 4.3510 4 1 0 -1 -1 4.6394 5 1 0 0 -1 0.7264 6 1 0 1 -1 1.4600 7 1 -1 -1 0 4.5039 8 1 -1 0 0 0.8845 9 1 -1 1 0 4.3107 10 1 0 -1 0 0.5514 11 1 0 1 0 0.5514 12 1 -1 -1 1 5.1620 13 1 -1 0 1 1.4350 14 1 -1 1 1 5.8153 15 1 0 -1 1 1.4600 16 1 0 0 1 0.7264 17 1 0 1 1 4.6394 18 1 1 1 1 5.7041 19 1 1 0 1 1.5227 20 1 1 -1 1 4.3510 21 1 1 1 0 4.5039 22 1 1 0 0 0.8845 23 1 1 -1 0 4.3107 24 1 1 1 -1 5.1620 25 1 1 0 -1 1.4350 26 1 1 -1 -1 5.8153 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 447 149 149 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 105 35 35 0.00 13 C013 has 477 159 159 0.00 14 C014 has 117 39 39 0.66 Total of12606 atoms and 4190 groups and 4183 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.5" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.5" Parameter: BOX -> "32.5" Parameter: BOX -> "32.5" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.50000 B = 32.50000 C = 32.50000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7031 2 1 -1 0 -1 1.5202 3 1 -1 1 -1 4.3476 4 1 0 -1 -1 4.6376 5 1 0 0 -1 0.7250 6 1 0 1 -1 1.4576 7 1 -1 -1 0 4.5022 8 1 -1 0 0 0.8831 9 1 -1 1 0 4.3083 10 1 0 -1 0 0.5498 11 1 0 1 0 0.5498 12 1 -1 -1 1 5.1593 13 1 -1 0 1 1.4332 14 1 -1 1 1 5.8124 15 1 0 -1 1 1.4576 16 1 0 0 1 0.7250 17 1 0 1 1 4.6376 18 1 1 1 1 5.7031 19 1 1 0 1 1.5202 20 1 1 -1 1 4.3476 21 1 1 1 0 4.5022 22 1 1 0 0 0.8831 23 1 1 -1 0 4.3083 24 1 1 1 -1 5.1593 25 1 1 0 -1 1.4332 26 1 1 -1 -1 5.8124 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 474 158 158 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 447 149 149 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 105 35 35 0.00 13 C013 has 477 159 159 0.00 14 C014 has 117 39 39 0.66 Total of12606 atoms and 4190 groups and 4183 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.498" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.498" Parameter: BOX -> "32.498" Parameter: BOX -> "32.498" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.49800 B = 32.49800 C = 32.49800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7020 2 1 -1 0 -1 1.5178 3 1 -1 1 -1 4.3442 4 1 0 -1 -1 4.6358 5 1 0 0 -1 0.7235 6 1 0 1 -1 1.4551 7 1 -1 -1 0 4.5005 8 1 -1 0 0 0.8817 9 1 -1 1 0 4.3059 10 1 0 -1 0 0.5482 11 1 0 1 0 0.5482 12 1 -1 -1 1 5.1567 13 1 -1 0 1 1.4315 14 1 -1 1 1 5.8095 15 1 0 -1 1 1.4551 16 1 0 0 1 0.7235 17 1 0 1 1 4.6358 18 1 1 1 1 5.7020 19 1 1 0 1 1.5178 20 1 1 -1 1 4.3442 21 1 1 1 0 4.5005 22 1 1 0 0 0.8817 23 1 1 -1 0 4.3059 24 1 1 1 -1 5.1567 25 1 1 0 -1 1.4315 26 1 1 -1 -1 5.8095 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 447 149 149 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 105 35 35 0.00 13 C013 has 477 159 159 0.00 14 C014 has 117 39 39 0.66 Total of12612 atoms and 4192 groups and 4185 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.496" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.496" Parameter: BOX -> "32.496" Parameter: BOX -> "32.496" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.49600 B = 32.49600 C = 32.49600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.7009 2 1 -1 0 -1 1.5153 3 1 -1 1 -1 4.3408 4 1 0 -1 -1 4.6340 5 1 0 0 -1 0.7221 6 1 0 1 -1 1.4527 7 1 -1 -1 0 4.4988 8 1 -1 0 0 0.8803 9 1 -1 1 0 4.3034 10 1 0 -1 0 0.5466 11 1 0 1 0 0.5466 12 1 -1 -1 1 5.1540 13 1 -1 0 1 1.4297 14 1 -1 1 1 5.8067 15 1 0 -1 1 1.4527 16 1 0 0 1 0.7221 17 1 0 1 1 4.6340 18 1 1 1 1 5.7009 19 1 1 0 1 1.5153 20 1 1 -1 1 4.3408 21 1 1 1 0 4.4988 22 1 1 0 0 0.8803 23 1 1 -1 0 4.3034 24 1 1 1 -1 5.1540 25 1 1 0 -1 1.4297 26 1 1 -1 -1 5.8067 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 447 149 149 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 105 35 35 0.00 13 C013 has 477 159 159 0.00 14 C014 has 117 39 39 0.66 Total of12612 atoms and 4192 groups and 4185 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.494" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.494" Parameter: BOX -> "32.494" Parameter: BOX -> "32.494" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.49400 B = 32.49400 C = 32.49400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6999 2 1 -1 0 -1 1.5129 3 1 -1 1 -1 4.3374 4 1 0 -1 -1 4.6322 5 1 0 0 -1 0.7207 6 1 0 1 -1 1.4502 7 1 -1 -1 0 4.4971 8 1 -1 0 0 0.8789 9 1 -1 1 0 4.3010 10 1 0 -1 0 0.5450 11 1 0 1 0 0.5450 12 1 -1 -1 1 5.1514 13 1 -1 0 1 1.4280 14 1 -1 1 1 5.8038 15 1 0 -1 1 1.4502 16 1 0 0 1 0.7207 17 1 0 1 1 4.6322 18 1 1 1 1 5.6999 19 1 1 0 1 1.5129 20 1 1 -1 1 4.3374 21 1 1 1 0 4.4971 22 1 1 0 0 0.8789 23 1 1 -1 0 4.3010 24 1 1 1 -1 5.1514 25 1 1 0 -1 1.4280 26 1 1 -1 -1 5.8038 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 450 150 150 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 105 35 35 0.00 13 C013 has 477 159 159 0.00 14 C014 has 117 39 39 0.65 Total of12621 atoms and 4195 groups and 4188 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.492" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.492" Parameter: BOX -> "32.492" Parameter: BOX -> "32.492" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.49200 B = 32.49200 C = 32.49200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6988 2 1 -1 0 -1 1.5104 3 1 -1 1 -1 4.3340 4 1 0 -1 -1 4.6303 5 1 0 0 -1 0.7192 6 1 0 1 -1 1.4478 7 1 -1 -1 0 4.4954 8 1 -1 0 0 0.8775 9 1 -1 1 0 4.2986 10 1 0 -1 0 0.5434 11 1 0 1 0 0.5434 12 1 -1 -1 1 5.1487 13 1 -1 0 1 1.4263 14 1 -1 1 1 5.8009 15 1 0 -1 1 1.4478 16 1 0 0 1 0.7192 17 1 0 1 1 4.6303 18 1 1 1 1 5.6988 19 1 1 0 1 1.5104 20 1 1 -1 1 4.3340 21 1 1 1 0 4.4954 22 1 1 0 0 0.8775 23 1 1 -1 0 4.2986 24 1 1 1 -1 5.1487 25 1 1 0 -1 1.4263 26 1 1 -1 -1 5.8009 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 450 150 150 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 105 35 35 0.00 13 C013 has 477 159 159 0.00 14 C014 has 117 39 39 0.65 Total of12621 atoms and 4195 groups and 4188 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.49" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.49" Parameter: BOX -> "32.49" Parameter: BOX -> "32.49" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.49000 B = 32.49000 C = 32.49000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6977 2 1 -1 0 -1 1.5080 3 1 -1 1 -1 4.3305 4 1 0 -1 -1 4.6285 5 1 0 0 -1 0.7178 6 1 0 1 -1 1.4454 7 1 -1 -1 0 4.4938 8 1 -1 0 0 0.8761 9 1 -1 1 0 4.2962 10 1 0 -1 0 0.5419 11 1 0 1 0 0.5419 12 1 -1 -1 1 5.1461 13 1 -1 0 1 1.4246 14 1 -1 1 1 5.7980 15 1 0 -1 1 1.4454 16 1 0 0 1 0.7178 17 1 0 1 1 4.6285 18 1 1 1 1 5.6977 19 1 1 0 1 1.5080 20 1 1 -1 1 4.3305 21 1 1 1 0 4.4938 22 1 1 0 0 0.8761 23 1 1 -1 0 4.2962 24 1 1 1 -1 5.1461 25 1 1 0 -1 1.4246 26 1 1 -1 -1 5.7980 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 450 150 150 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 105 35 35 0.00 13 C013 has 477 159 159 0.00 14 C014 has 117 39 39 0.65 Total of12624 atoms and 4196 groups and 4189 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.488" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.488" Parameter: BOX -> "32.488" Parameter: BOX -> "32.488" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.48800 B = 32.48800 C = 32.48800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6967 2 1 -1 0 -1 1.5056 3 1 -1 1 -1 4.3271 4 1 0 -1 -1 4.6267 5 1 0 0 -1 0.7164 6 1 0 1 -1 1.4429 7 1 -1 -1 0 4.4921 8 1 -1 0 0 0.8748 9 1 -1 1 0 4.2938 10 1 0 -1 0 0.5403 11 1 0 1 0 0.5403 12 1 -1 -1 1 5.1434 13 1 -1 0 1 1.4229 14 1 -1 1 1 5.7951 15 1 0 -1 1 1.4429 16 1 0 0 1 0.7164 17 1 0 1 1 4.6267 18 1 1 1 1 5.6967 19 1 1 0 1 1.5056 20 1 1 -1 1 4.3271 21 1 1 1 0 4.4921 22 1 1 0 0 0.8748 23 1 1 -1 0 4.2938 24 1 1 1 -1 5.1434 25 1 1 0 -1 1.4229 26 1 1 -1 -1 5.7951 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 477 159 159 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 450 150 150 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 105 35 35 0.00 13 C013 has 477 159 159 0.00 14 C014 has 117 39 39 0.65 Total of12627 atoms and 4197 groups and 4190 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.486" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.486" Parameter: BOX -> "32.486" Parameter: BOX -> "32.486" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.48600 B = 32.48600 C = 32.48600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6956 2 1 -1 0 -1 1.5031 3 1 -1 1 -1 4.3237 4 1 0 -1 -1 4.6249 5 1 0 0 -1 0.7150 6 1 0 1 -1 1.4405 7 1 -1 -1 0 4.4904 8 1 -1 0 0 0.8734 9 1 -1 1 0 4.2914 10 1 0 -1 0 0.5387 11 1 0 1 0 0.5387 12 1 -1 -1 1 5.1408 13 1 -1 0 1 1.4211 14 1 -1 1 1 5.7922 15 1 0 -1 1 1.4405 16 1 0 0 1 0.7150 17 1 0 1 1 4.6249 18 1 1 1 1 5.6956 19 1 1 0 1 1.5031 20 1 1 -1 1 4.3237 21 1 1 1 0 4.4904 22 1 1 0 0 0.8734 23 1 1 -1 0 4.2914 24 1 1 1 -1 5.1408 25 1 1 0 -1 1.4211 26 1 1 -1 -1 5.7922 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 450 150 150 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 105 35 35 0.00 13 C013 has 477 159 159 0.00 14 C014 has 117 39 39 0.65 Total of12630 atoms and 4198 groups and 4191 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.484" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.484" Parameter: BOX -> "32.484" Parameter: BOX -> "32.484" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.48400 B = 32.48400 C = 32.48400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6946 2 1 -1 0 -1 1.5007 3 1 -1 1 -1 4.3203 4 1 0 -1 -1 4.6231 5 1 0 0 -1 0.7136 6 1 0 1 -1 1.4380 7 1 -1 -1 0 4.4887 8 1 -1 0 0 0.8720 9 1 -1 1 0 4.2890 10 1 0 -1 0 0.5371 11 1 0 1 0 0.5371 12 1 -1 -1 1 5.1381 13 1 -1 0 1 1.4194 14 1 -1 1 1 5.7893 15 1 0 -1 1 1.4380 16 1 0 0 1 0.7136 17 1 0 1 1 4.6231 18 1 1 1 1 5.6946 19 1 1 0 1 1.5007 20 1 1 -1 1 4.3203 21 1 1 1 0 4.4887 22 1 1 0 0 0.8720 23 1 1 -1 0 4.2890 24 1 1 1 -1 5.1381 25 1 1 0 -1 1.4194 26 1 1 -1 -1 5.7893 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 450 150 150 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 105 35 35 0.00 13 C013 has 477 159 159 0.00 14 C014 has 117 39 39 0.64 Total of12630 atoms and 4198 groups and 4191 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.482" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.482" Parameter: BOX -> "32.482" Parameter: BOX -> "32.482" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.48200 B = 32.48200 C = 32.48200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6935 2 1 -1 0 -1 1.4983 3 1 -1 1 -1 4.3169 4 1 0 -1 -1 4.6213 5 1 0 0 -1 0.7122 6 1 0 1 -1 1.4356 7 1 -1 -1 0 4.4870 8 1 -1 0 0 0.8706 9 1 -1 1 0 4.2865 10 1 0 -1 0 0.5356 11 1 0 1 0 0.5356 12 1 -1 -1 1 5.1355 13 1 -1 0 1 1.4177 14 1 -1 1 1 5.7865 15 1 0 -1 1 1.4356 16 1 0 0 1 0.7122 17 1 0 1 1 4.6213 18 1 1 1 1 5.6935 19 1 1 0 1 1.4983 20 1 1 -1 1 4.3169 21 1 1 1 0 4.4870 22 1 1 0 0 0.8706 23 1 1 -1 0 4.2865 24 1 1 1 -1 5.1355 25 1 1 0 -1 1.4177 26 1 1 -1 -1 5.7865 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 450 150 150 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 105 35 35 0.00 13 C013 has 477 159 159 0.00 14 C014 has 117 39 39 0.64 Total of12630 atoms and 4198 groups and 4191 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.48" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.48" Parameter: BOX -> "32.48" Parameter: BOX -> "32.48" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.48000 B = 32.48000 C = 32.48000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6925 2 1 -1 0 -1 1.4958 3 1 -1 1 -1 4.3135 4 1 0 -1 -1 4.6195 5 1 0 0 -1 0.7108 6 1 0 1 -1 1.4331 7 1 -1 -1 0 4.4854 8 1 -1 0 0 0.8693 9 1 -1 1 0 4.2841 10 1 0 -1 0 0.5340 11 1 0 1 0 0.5340 12 1 -1 -1 1 5.1328 13 1 -1 0 1 1.4160 14 1 -1 1 1 5.7836 15 1 0 -1 1 1.4331 16 1 0 0 1 0.7108 17 1 0 1 1 4.6195 18 1 1 1 1 5.6925 19 1 1 0 1 1.4958 20 1 1 -1 1 4.3135 21 1 1 1 0 4.4854 22 1 1 0 0 0.8693 23 1 1 -1 0 4.2841 24 1 1 1 -1 5.1328 25 1 1 0 -1 1.4160 26 1 1 -1 -1 5.7836 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 450 150 150 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 105 35 35 0.00 13 C013 has 477 159 159 0.00 14 C014 has 117 39 39 0.64 Total of12633 atoms and 4199 groups and 4192 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.478" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.478" Parameter: BOX -> "32.478" Parameter: BOX -> "32.478" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.47800 B = 32.47800 C = 32.47800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6914 2 1 -1 0 -1 1.4934 3 1 -1 1 -1 4.3101 4 1 0 -1 -1 4.6177 5 1 0 0 -1 0.7094 6 1 0 1 -1 1.4307 7 1 -1 -1 0 4.4837 8 1 -1 0 0 0.8679 9 1 -1 1 0 4.2817 10 1 0 -1 0 0.5324 11 1 0 1 0 0.5324 12 1 -1 -1 1 5.1302 13 1 -1 0 1 1.4143 14 1 -1 1 1 5.7807 15 1 0 -1 1 1.4307 16 1 0 0 1 0.7094 17 1 0 1 1 4.6177 18 1 1 1 1 5.6914 19 1 1 0 1 1.4934 20 1 1 -1 1 4.3101 21 1 1 1 0 4.4837 22 1 1 0 0 0.8679 23 1 1 -1 0 4.2817 24 1 1 1 -1 5.1302 25 1 1 0 -1 1.4143 26 1 1 -1 -1 5.7807 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 639 213 213 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 450 150 150 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 105 35 35 0.00 13 C013 has 477 159 159 0.00 14 C014 has 117 39 39 0.64 Total of12636 atoms and 4200 groups and 4193 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.476" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.476" Parameter: BOX -> "32.476" Parameter: BOX -> "32.476" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.47600 B = 32.47600 C = 32.47600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6904 2 1 -1 0 -1 1.4910 3 1 -1 1 -1 4.3067 4 1 0 -1 -1 4.6158 5 1 0 0 -1 0.7080 6 1 0 1 -1 1.4283 7 1 -1 -1 0 4.4820 8 1 -1 0 0 0.8665 9 1 -1 1 0 4.2793 10 1 0 -1 0 0.5309 11 1 0 1 0 0.5309 12 1 -1 -1 1 5.1276 13 1 -1 0 1 1.4126 14 1 -1 1 1 5.7778 15 1 0 -1 1 1.4283 16 1 0 0 1 0.7080 17 1 0 1 1 4.6158 18 1 1 1 1 5.6904 19 1 1 0 1 1.4910 20 1 1 -1 1 4.3067 21 1 1 1 0 4.4820 22 1 1 0 0 0.8665 23 1 1 -1 0 4.2793 24 1 1 1 -1 5.1276 25 1 1 0 -1 1.4126 26 1 1 -1 -1 5.7778 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 639 213 213 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 453 151 151 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 105 35 35 0.00 13 C013 has 477 159 159 0.00 14 C014 has 117 39 39 0.64 Total of12642 atoms and 4202 groups and 4195 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.474" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.474" Parameter: BOX -> "32.474" Parameter: BOX -> "32.474" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.47400 B = 32.47400 C = 32.47400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6893 2 1 -1 0 -1 1.4886 3 1 -1 1 -1 4.3032 4 1 0 -1 -1 4.6140 5 1 0 0 -1 0.7066 6 1 0 1 -1 1.4258 7 1 -1 -1 0 4.4803 8 1 -1 0 0 0.8652 9 1 -1 1 0 4.2769 10 1 0 -1 0 0.5293 11 1 0 1 0 0.5293 12 1 -1 -1 1 5.1249 13 1 -1 0 1 1.4109 14 1 -1 1 1 5.7749 15 1 0 -1 1 1.4258 16 1 0 0 1 0.7066 17 1 0 1 1 4.6140 18 1 1 1 1 5.6893 19 1 1 0 1 1.4886 20 1 1 -1 1 4.3032 21 1 1 1 0 4.4803 22 1 1 0 0 0.8652 23 1 1 -1 0 4.2769 24 1 1 1 -1 5.1249 25 1 1 0 -1 1.4109 26 1 1 -1 -1 5.7749 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 639 213 213 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 453 151 151 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 105 35 35 0.00 13 C013 has 477 159 159 0.00 14 C014 has 117 39 39 0.63 Total of12645 atoms and 4203 groups and 4196 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.472" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.472" Parameter: BOX -> "32.472" Parameter: BOX -> "32.472" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.47200 B = 32.47200 C = 32.47200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6883 2 1 -1 0 -1 1.4861 3 1 -1 1 -1 4.2998 4 1 0 -1 -1 4.6122 5 1 0 0 -1 0.7052 6 1 0 1 -1 1.4234 7 1 -1 -1 0 4.4787 8 1 -1 0 0 0.8638 9 1 -1 1 0 4.2745 10 1 0 -1 0 0.5278 11 1 0 1 0 0.5278 12 1 -1 -1 1 5.1223 13 1 -1 0 1 1.4092 14 1 -1 1 1 5.7721 15 1 0 -1 1 1.4234 16 1 0 0 1 0.7052 17 1 0 1 1 4.6122 18 1 1 1 1 5.6883 19 1 1 0 1 1.4861 20 1 1 -1 1 4.2998 21 1 1 1 0 4.4787 22 1 1 0 0 0.8638 23 1 1 -1 0 4.2745 24 1 1 1 -1 5.1223 25 1 1 0 -1 1.4092 26 1 1 -1 -1 5.7721 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 639 213 213 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 453 151 151 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1717 567 565 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 105 35 35 0.00 13 C013 has 477 159 159 0.00 14 C014 has 117 39 39 0.63 Total of12645 atoms and 4203 groups and 4196 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.47" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.47" Parameter: BOX -> "32.47" Parameter: BOX -> "32.47" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.47000 B = 32.47000 C = 32.47000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6873 2 1 -1 0 -1 1.4837 3 1 -1 1 -1 4.2964 4 1 0 -1 -1 4.6104 5 1 0 0 -1 0.7038 6 1 0 1 -1 1.4210 7 1 -1 -1 0 4.4770 8 1 -1 0 0 0.8624 9 1 -1 1 0 4.2721 10 1 0 -1 0 0.5262 11 1 0 1 0 0.5262 12 1 -1 -1 1 5.1196 13 1 -1 0 1 1.4076 14 1 -1 1 1 5.7692 15 1 0 -1 1 1.4210 16 1 0 0 1 0.7038 17 1 0 1 1 4.6104 18 1 1 1 1 5.6873 19 1 1 0 1 1.4837 20 1 1 -1 1 4.2964 21 1 1 1 0 4.4770 22 1 1 0 0 0.8624 23 1 1 -1 0 4.2721 24 1 1 1 -1 5.1196 25 1 1 0 -1 1.4076 26 1 1 -1 -1 5.7692 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 639 213 213 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 453 151 151 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1734 569 567 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 105 35 35 0.00 13 C013 has 477 159 159 0.00 14 C014 has 117 39 39 0.63 Total of12662 atoms and 4205 groups and 4198 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.468" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.468" Parameter: BOX -> "32.468" Parameter: BOX -> "32.468" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.46800 B = 32.46800 C = 32.46800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6862 2 1 -1 0 -1 1.4813 3 1 -1 1 -1 4.2930 4 1 0 -1 -1 4.6086 5 1 0 0 -1 0.7024 6 1 0 1 -1 1.4185 7 1 -1 -1 0 4.4753 8 1 -1 0 0 0.8611 9 1 -1 1 0 4.2697 10 1 0 -1 0 0.5247 11 1 0 1 0 0.5247 12 1 -1 -1 1 5.1170 13 1 -1 0 1 1.4059 14 1 -1 1 1 5.7663 15 1 0 -1 1 1.4185 16 1 0 0 1 0.7024 17 1 0 1 1 4.6086 18 1 1 1 1 5.6862 19 1 1 0 1 1.4813 20 1 1 -1 1 4.2930 21 1 1 1 0 4.4753 22 1 1 0 0 0.8611 23 1 1 -1 0 4.2697 24 1 1 1 -1 5.1170 25 1 1 0 -1 1.4059 26 1 1 -1 -1 5.7663 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 453 151 151 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1734 569 567 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 105 35 35 0.00 13 C013 has 477 159 159 0.00 14 C014 has 117 39 39 0.63 Total of12665 atoms and 4206 groups and 4199 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.466" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.466" Parameter: BOX -> "32.466" Parameter: BOX -> "32.466" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.46600 B = 32.46600 C = 32.46600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6852 2 1 -1 0 -1 1.4789 3 1 -1 1 -1 4.2896 4 1 0 -1 -1 4.6068 5 1 0 0 -1 0.7010 6 1 0 1 -1 1.4161 7 1 -1 -1 0 4.4736 8 1 -1 0 0 0.8597 9 1 -1 1 0 4.2673 10 1 0 -1 0 0.5232 11 1 0 1 0 0.5232 12 1 -1 -1 1 5.1144 13 1 -1 0 1 1.4042 14 1 -1 1 1 5.7634 15 1 0 -1 1 1.4161 16 1 0 0 1 0.7010 17 1 0 1 1 4.6068 18 1 1 1 1 5.6852 19 1 1 0 1 1.4789 20 1 1 -1 1 4.2896 21 1 1 1 0 4.4736 22 1 1 0 0 0.8597 23 1 1 -1 0 4.2673 24 1 1 1 -1 5.1144 25 1 1 0 -1 1.4042 26 1 1 -1 -1 5.7634 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 453 151 151 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1734 569 567 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 108 36 36 0.00 13 C013 has 477 159 159 0.00 14 C014 has 123 41 41 0.63 Total of12677 atoms and 4210 groups and 4203 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.464" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.464" Parameter: BOX -> "32.464" Parameter: BOX -> "32.464" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.46400 B = 32.46400 C = 32.46400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6842 2 1 -1 0 -1 1.4765 3 1 -1 1 -1 4.2862 4 1 0 -1 -1 4.6050 5 1 0 0 -1 0.6996 6 1 0 1 -1 1.4137 7 1 -1 -1 0 4.4720 8 1 -1 0 0 0.8584 9 1 -1 1 0 4.2649 10 1 0 -1 0 0.5216 11 1 0 1 0 0.5216 12 1 -1 -1 1 5.1117 13 1 -1 0 1 1.4025 14 1 -1 1 1 5.7606 15 1 0 -1 1 1.4137 16 1 0 0 1 0.6996 17 1 0 1 1 4.6050 18 1 1 1 1 5.6842 19 1 1 0 1 1.4765 20 1 1 -1 1 4.2862 21 1 1 1 0 4.4720 22 1 1 0 0 0.8584 23 1 1 -1 0 4.2649 24 1 1 1 -1 5.1117 25 1 1 0 -1 1.4025 26 1 1 -1 -1 5.7606 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 453 151 151 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1734 569 567 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 108 36 36 0.00 13 C013 has 477 159 159 0.00 14 C014 has 123 41 41 0.62 Total of12680 atoms and 4211 groups and 4204 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.462" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.462" Parameter: BOX -> "32.462" Parameter: BOX -> "32.462" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.46200 B = 32.46200 C = 32.46200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6831 2 1 -1 0 -1 1.4740 3 1 -1 1 -1 4.2828 4 1 0 -1 -1 4.6032 5 1 0 0 -1 0.6982 6 1 0 1 -1 1.4113 7 1 -1 -1 0 4.4703 8 1 -1 0 0 0.8570 9 1 -1 1 0 4.2625 10 1 0 -1 0 0.5201 11 1 0 1 0 0.5201 12 1 -1 -1 1 5.1091 13 1 -1 0 1 1.4009 14 1 -1 1 1 5.7577 15 1 0 -1 1 1.4113 16 1 0 0 1 0.6982 17 1 0 1 1 4.6032 18 1 1 1 1 5.6831 19 1 1 0 1 1.4740 20 1 1 -1 1 4.2828 21 1 1 1 0 4.4703 22 1 1 0 0 0.8570 23 1 1 -1 0 4.2625 24 1 1 1 -1 5.1091 25 1 1 0 -1 1.4009 26 1 1 -1 -1 5.7577 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 453 151 151 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1734 569 567 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 108 36 36 0.00 13 C013 has 477 159 159 0.00 14 C014 has 123 41 41 0.62 Total of12683 atoms and 4212 groups and 4205 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.46" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.46" Parameter: BOX -> "32.46" Parameter: BOX -> "32.46" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.46000 B = 32.46000 C = 32.46000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6821 2 1 -1 0 -1 1.4716 3 1 -1 1 -1 4.2794 4 1 0 -1 -1 4.6014 5 1 0 0 -1 0.6968 6 1 0 1 -1 1.4088 7 1 -1 -1 0 4.4686 8 1 -1 0 0 0.8557 9 1 -1 1 0 4.2600 10 1 0 -1 0 0.5185 11 1 0 1 0 0.5185 12 1 -1 -1 1 5.1065 13 1 -1 0 1 1.3992 14 1 -1 1 1 5.7548 15 1 0 -1 1 1.4088 16 1 0 0 1 0.6968 17 1 0 1 1 4.6014 18 1 1 1 1 5.6821 19 1 1 0 1 1.4716 20 1 1 -1 1 4.2794 21 1 1 1 0 4.4686 22 1 1 0 0 0.8557 23 1 1 -1 0 4.2600 24 1 1 1 -1 5.1065 25 1 1 0 -1 1.3992 26 1 1 -1 -1 5.7548 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 453 151 151 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1734 569 567 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 108 36 36 0.00 13 C013 has 477 159 159 0.00 14 C014 has 123 41 41 0.62 Total of12683 atoms and 4212 groups and 4205 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.458" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.458" Parameter: BOX -> "32.458" Parameter: BOX -> "32.458" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.45800 B = 32.45800 C = 32.45800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6811 2 1 -1 0 -1 1.4692 3 1 -1 1 -1 4.2760 4 1 0 -1 -1 4.5996 5 1 0 0 -1 0.6955 6 1 0 1 -1 1.4064 7 1 -1 -1 0 4.4670 8 1 -1 0 0 0.8543 9 1 -1 1 0 4.2576 10 1 0 -1 0 0.5170 11 1 0 1 0 0.5170 12 1 -1 -1 1 5.1038 13 1 -1 0 1 1.3975 14 1 -1 1 1 5.7519 15 1 0 -1 1 1.4064 16 1 0 0 1 0.6955 17 1 0 1 1 4.5996 18 1 1 1 1 5.6811 19 1 1 0 1 1.4692 20 1 1 -1 1 4.2760 21 1 1 1 0 4.4670 22 1 1 0 0 0.8543 23 1 1 -1 0 4.2576 24 1 1 1 -1 5.1038 25 1 1 0 -1 1.3975 26 1 1 -1 -1 5.7519 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 453 151 151 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1734 569 567 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 108 36 36 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.62 Total of12689 atoms and 4214 groups and 4207 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.456" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.456" Parameter: BOX -> "32.456" Parameter: BOX -> "32.456" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.45600 B = 32.45600 C = 32.45600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6800 2 1 -1 0 -1 1.4668 3 1 -1 1 -1 4.2725 4 1 0 -1 -1 4.5978 5 1 0 0 -1 0.6941 6 1 0 1 -1 1.4040 7 1 -1 -1 0 4.4653 8 1 -1 0 0 0.8530 9 1 -1 1 0 4.2552 10 1 0 -1 0 0.5155 11 1 0 1 0 0.5155 12 1 -1 -1 1 5.1012 13 1 -1 0 1 1.3959 14 1 -1 1 1 5.7491 15 1 0 -1 1 1.4040 16 1 0 0 1 0.6941 17 1 0 1 1 4.5978 18 1 1 1 1 5.6800 19 1 1 0 1 1.4668 20 1 1 -1 1 4.2725 21 1 1 1 0 4.4653 22 1 1 0 0 0.8530 23 1 1 -1 0 4.2552 24 1 1 1 -1 5.1012 25 1 1 0 -1 1.3959 26 1 1 -1 -1 5.7491 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 453 151 151 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1734 569 567 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 108 36 36 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.62 Total of12689 atoms and 4214 groups and 4207 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.454" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.454" Parameter: BOX -> "32.454" Parameter: BOX -> "32.454" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.45400 B = 32.45400 C = 32.45400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6790 2 1 -1 0 -1 1.4644 3 1 -1 1 -1 4.2691 4 1 0 -1 -1 4.5960 5 1 0 0 -1 0.6927 6 1 0 1 -1 1.4016 7 1 -1 -1 0 4.4637 8 1 -1 0 0 0.8517 9 1 -1 1 0 4.2528 10 1 0 -1 0 0.5140 11 1 0 1 0 0.5140 12 1 -1 -1 1 5.0986 13 1 -1 0 1 1.3942 14 1 -1 1 1 5.7462 15 1 0 -1 1 1.4016 16 1 0 0 1 0.6927 17 1 0 1 1 4.5960 18 1 1 1 1 5.6790 19 1 1 0 1 1.4644 20 1 1 -1 1 4.2691 21 1 1 1 0 4.4637 22 1 1 0 0 0.8517 23 1 1 -1 0 4.2528 24 1 1 1 -1 5.0986 25 1 1 0 -1 1.3942 26 1 1 -1 -1 5.7462 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 453 151 151 0.00 7 C007 has 801 267 267 0.00 8 C008 has 1734 569 567 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 108 36 36 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.61 Total of12692 atoms and 4215 groups and 4208 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.452" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.452" Parameter: BOX -> "32.452" Parameter: BOX -> "32.452" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.45200 B = 32.45200 C = 32.45200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6780 2 1 -1 0 -1 1.4620 3 1 -1 1 -1 4.2657 4 1 0 -1 -1 4.5942 5 1 0 0 -1 0.6914 6 1 0 1 -1 1.3992 7 1 -1 -1 0 4.4620 8 1 -1 0 0 0.8503 9 1 -1 1 0 4.2504 10 1 0 -1 0 0.5124 11 1 0 1 0 0.5124 12 1 -1 -1 1 5.0959 13 1 -1 0 1 1.3926 14 1 -1 1 1 5.7433 15 1 0 -1 1 1.3992 16 1 0 0 1 0.6914 17 1 0 1 1 4.5942 18 1 1 1 1 5.6780 19 1 1 0 1 1.4620 20 1 1 -1 1 4.2657 21 1 1 1 0 4.4620 22 1 1 0 0 0.8503 23 1 1 -1 0 4.2504 24 1 1 1 -1 5.0959 25 1 1 0 -1 1.3926 26 1 1 -1 -1 5.7433 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 453 151 151 0.00 7 C007 has 801 267 267 0.00 8 C008 has 1734 569 567 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.61 Total of12695 atoms and 4216 groups and 4209 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.45" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.45" Parameter: BOX -> "32.45" Parameter: BOX -> "32.45" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.45000 B = 32.45000 C = 32.45000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6770 2 1 -1 0 -1 1.4596 3 1 -1 1 -1 4.2623 4 1 0 -1 -1 4.5924 5 1 0 0 -1 0.6900 6 1 0 1 -1 1.3967 7 1 -1 -1 0 4.4603 8 1 -1 0 0 0.8490 9 1 -1 1 0 4.2480 10 1 0 -1 0 0.5109 11 1 0 1 0 0.5109 12 1 -1 -1 1 5.0933 13 1 -1 0 1 1.3909 14 1 -1 1 1 5.7404 15 1 0 -1 1 1.3967 16 1 0 0 1 0.6900 17 1 0 1 1 4.5924 18 1 1 1 1 5.6770 19 1 1 0 1 1.4596 20 1 1 -1 1 4.2623 21 1 1 1 0 4.4603 22 1 1 0 0 0.8490 23 1 1 -1 0 4.2480 24 1 1 1 -1 5.0933 25 1 1 0 -1 1.3909 26 1 1 -1 -1 5.7404 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 456 152 152 0.00 7 C007 has 801 267 267 0.00 8 C008 has 1734 569 567 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.61 Total of12698 atoms and 4217 groups and 4210 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.448" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.448" Parameter: BOX -> "32.448" Parameter: BOX -> "32.448" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.44800 B = 32.44800 C = 32.44800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6760 2 1 -1 0 -1 1.4572 3 1 -1 1 -1 4.2589 4 1 0 -1 -1 4.5906 5 1 0 0 -1 0.6886 6 1 0 1 -1 1.3943 7 1 -1 -1 0 4.4587 8 1 -1 0 0 0.8476 9 1 -1 1 0 4.2456 10 1 0 -1 0 0.5094 11 1 0 1 0 0.5094 12 1 -1 -1 1 5.0907 13 1 -1 0 1 1.3893 14 1 -1 1 1 5.7376 15 1 0 -1 1 1.3943 16 1 0 0 1 0.6886 17 1 0 1 1 4.5906 18 1 1 1 1 5.6760 19 1 1 0 1 1.4572 20 1 1 -1 1 4.2589 21 1 1 1 0 4.4587 22 1 1 0 0 0.8476 23 1 1 -1 0 4.2456 24 1 1 1 -1 5.0907 25 1 1 0 -1 1.3893 26 1 1 -1 -1 5.7376 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 456 152 152 0.00 7 C007 has 801 267 267 0.00 8 C008 has 1734 569 567 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.61 Total of12698 atoms and 4217 groups and 4210 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.446" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.446" Parameter: BOX -> "32.446" Parameter: BOX -> "32.446" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.44600 B = 32.44600 C = 32.44600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6749 2 1 -1 0 -1 1.4548 3 1 -1 1 -1 4.2555 4 1 0 -1 -1 4.5888 5 1 0 0 -1 0.6873 6 1 0 1 -1 1.3919 7 1 -1 -1 0 4.4570 8 1 -1 0 0 0.8463 9 1 -1 1 0 4.2432 10 1 0 -1 0 0.5079 11 1 0 1 0 0.5079 12 1 -1 -1 1 5.0880 13 1 -1 0 1 1.3876 14 1 -1 1 1 5.7347 15 1 0 -1 1 1.3919 16 1 0 0 1 0.6873 17 1 0 1 1 4.5888 18 1 1 1 1 5.6749 19 1 1 0 1 1.4548 20 1 1 -1 1 4.2555 21 1 1 1 0 4.4570 22 1 1 0 0 0.8463 23 1 1 -1 0 4.2432 24 1 1 1 -1 5.0880 25 1 1 0 -1 1.3876 26 1 1 -1 -1 5.7347 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 456 152 152 0.00 7 C007 has 801 267 267 0.00 8 C008 has 1734 569 567 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.61 Total of12698 atoms and 4217 groups and 4210 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.444" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.444" Parameter: BOX -> "32.444" Parameter: BOX -> "32.444" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.44400 B = 32.44400 C = 32.44400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6739 2 1 -1 0 -1 1.4524 3 1 -1 1 -1 4.2521 4 1 0 -1 -1 4.5871 5 1 0 0 -1 0.6859 6 1 0 1 -1 1.3895 7 1 -1 -1 0 4.4554 8 1 -1 0 0 0.8450 9 1 -1 1 0 4.2408 10 1 0 -1 0 0.5064 11 1 0 1 0 0.5064 12 1 -1 -1 1 5.0854 13 1 -1 0 1 1.3860 14 1 -1 1 1 5.7318 15 1 0 -1 1 1.3895 16 1 0 0 1 0.6859 17 1 0 1 1 4.5871 18 1 1 1 1 5.6739 19 1 1 0 1 1.4524 20 1 1 -1 1 4.2521 21 1 1 1 0 4.4554 22 1 1 0 0 0.8450 23 1 1 -1 0 4.2408 24 1 1 1 -1 5.0854 25 1 1 0 -1 1.3860 26 1 1 -1 -1 5.7318 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 456 152 152 0.00 7 C007 has 801 267 267 0.00 8 C008 has 1734 569 567 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.60 Total of12698 atoms and 4217 groups and 4210 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.442" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.442" Parameter: BOX -> "32.442" Parameter: BOX -> "32.442" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.44200 B = 32.44200 C = 32.44200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6729 2 1 -1 0 -1 1.4500 3 1 -1 1 -1 4.2487 4 1 0 -1 -1 4.5853 5 1 0 0 -1 0.6846 6 1 0 1 -1 1.3871 7 1 -1 -1 0 4.4537 8 1 -1 0 0 0.8437 9 1 -1 1 0 4.2384 10 1 0 -1 0 0.5049 11 1 0 1 0 0.5049 12 1 -1 -1 1 5.0828 13 1 -1 0 1 1.3844 14 1 -1 1 1 5.7290 15 1 0 -1 1 1.3871 16 1 0 0 1 0.6846 17 1 0 1 1 4.5853 18 1 1 1 1 5.6729 19 1 1 0 1 1.4500 20 1 1 -1 1 4.2487 21 1 1 1 0 4.4537 22 1 1 0 0 0.8437 23 1 1 -1 0 4.2384 24 1 1 1 -1 5.0828 25 1 1 0 -1 1.3844 26 1 1 -1 -1 5.7290 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 456 152 152 0.00 7 C007 has 801 267 267 0.00 8 C008 has 1734 569 567 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.60 Total of12698 atoms and 4217 groups and 4210 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3470 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1145 Number of atoms = 3470 Number of groups = 1150 Number of bonds = 3463 Number of angles = 1249 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1147 Number of HB donors = 2272 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.44" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-7 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1138" Comparing "1081" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.44" Parameter: BOX -> "32.44" Parameter: BOX -> "32.44" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.44000 B = 32.44000 C = 32.44000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6719 2 1 -1 0 -1 1.4476 3 1 -1 1 -1 4.2453 4 1 0 -1 -1 4.5835 5 1 0 0 -1 0.6832 6 1 0 1 -1 1.3847 7 1 -1 -1 0 4.4521 8 1 -1 0 0 0.8423 9 1 -1 1 0 4.2360 10 1 0 -1 0 0.5034 11 1 0 1 0 0.5034 12 1 -1 -1 1 5.0802 13 1 -1 0 1 1.3827 14 1 -1 1 1 5.7261 15 1 0 -1 1 1.3847 16 1 0 0 1 0.6832 17 1 0 1 1 4.5835 18 1 1 1 1 5.6719 19 1 1 0 1 1.4476 20 1 1 -1 1 4.2453 21 1 1 1 0 4.4521 22 1 1 0 0 0.8423 23 1 1 -1 0 4.2360 24 1 1 1 -1 5.0802 25 1 1 0 -1 1.3827 26 1 1 -1 -1 5.7261 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3396 atoms have been selected out of 3470 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 724 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 759 253 253 0.00 3 C003 has 108 36 36 0.00 4 C004 has 645 215 215 0.00 5 C005 has 1512 504 504 0.00 6 C006 has 456 152 152 0.00 7 C007 has 804 268 268 0.00 8 C008 has 1734 569 567 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1599 533 533 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.60 Total of12707 atoms and 4220 groups and 4213 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3470 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1144 Number of atoms = 3467 Number of groups = 1149 Number of bonds = 3460 Number of angles = 1248 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1146 Number of HB donors = 2270 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1144 Number of atoms = 3467 Number of groups = 1149 Number of bonds = 3460 Number of angles = 1248 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1146 Number of HB donors = 2270 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.438" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1144" Evaluating: 1144-7 Parameter: NUMWAT <- "1137" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1137" Comparing "1081" and "1137". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.438" Parameter: BOX -> "32.438" Parameter: BOX -> "32.438" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.43800 B = 32.43800 C = 32.43800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6709 2 1 -1 0 -1 1.4452 3 1 -1 1 -1 5.2678 4 1 0 -1 -1 4.5817 5 1 0 0 -1 0.6819 6 1 0 1 -1 1.3823 7 1 -1 -1 0 4.4504 8 1 -1 0 0 0.8410 9 1 -1 1 0 5.3445 10 1 0 -1 0 0.5019 11 1 0 1 0 0.5019 12 1 -1 -1 1 5.0775 13 1 -1 0 1 1.3811 14 1 -1 1 1 5.7232 15 1 0 -1 1 1.3823 16 1 0 0 1 0.6819 17 1 0 1 1 4.5817 18 1 1 1 1 5.6709 19 1 1 0 1 1.4452 20 1 1 -1 1 5.2678 21 1 1 1 0 4.4504 22 1 1 0 0 0.8410 23 1 1 -1 0 5.3445 24 1 1 1 -1 5.0775 25 1 1 0 -1 1.3811 26 1 1 -1 -1 5.7232 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3393 atoms have been selected out of 3467 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 759 253 253 0.00 3 C003 has 108 36 36 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1512 504 504 0.00 6 C006 has 456 152 152 0.00 7 C007 has 801 267 267 0.00 8 C008 has 1731 568 566 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.60 Total of12689 atoms and 4214 groups and 4207 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3467 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1144 Number of atoms = 3467 Number of groups = 1149 Number of bonds = 3460 Number of angles = 1248 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1146 Number of HB donors = 2270 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1144 Number of atoms = 3467 Number of groups = 1149 Number of bonds = 3460 Number of angles = 1248 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1146 Number of HB donors = 2270 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.436" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1144" Evaluating: 1144-7 Parameter: NUMWAT <- "1137" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1137" Comparing "1081" and "1137". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.436" Parameter: BOX -> "32.436" Parameter: BOX -> "32.436" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.43600 B = 32.43600 C = 32.43600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6699 2 1 -1 0 -1 1.4428 3 1 -1 1 -1 5.2649 4 1 0 -1 -1 4.5799 5 1 0 0 -1 0.6805 6 1 0 1 -1 1.3799 7 1 -1 -1 0 4.4488 8 1 -1 0 0 0.8397 9 1 -1 1 0 5.3416 10 1 0 -1 0 0.5004 11 1 0 1 0 0.5004 12 1 -1 -1 1 5.0749 13 1 -1 0 1 1.3795 14 1 -1 1 1 5.7204 15 1 0 -1 1 1.3799 16 1 0 0 1 0.6805 17 1 0 1 1 4.5799 18 1 1 1 1 5.6699 19 1 1 0 1 1.4428 20 1 1 -1 1 5.2649 21 1 1 1 0 4.4488 22 1 1 0 0 0.8397 23 1 1 -1 0 5.3416 24 1 1 1 -1 5.0749 25 1 1 0 -1 1.3795 26 1 1 -1 -1 5.7204 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3393 atoms have been selected out of 3467 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 759 253 253 0.00 3 C003 has 108 36 36 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1515 505 505 0.00 6 C006 has 456 152 152 0.00 7 C007 has 801 267 267 0.00 8 C008 has 1731 568 566 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.60 Total of12692 atoms and 4215 groups and 4208 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3467 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1144 Number of atoms = 3467 Number of groups = 1149 Number of bonds = 3460 Number of angles = 1248 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1146 Number of HB donors = 2270 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1144 Number of atoms = 3467 Number of groups = 1149 Number of bonds = 3460 Number of angles = 1248 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1146 Number of HB donors = 2270 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.434" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1144" Evaluating: 1144-7 Parameter: NUMWAT <- "1137" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1137" Comparing "1081" and "1137". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.434" Parameter: BOX -> "32.434" Parameter: BOX -> "32.434" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.43400 B = 32.43400 C = 32.43400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6689 2 1 -1 0 -1 1.4404 3 1 -1 1 -1 5.2620 4 1 0 -1 -1 4.5781 5 1 0 0 -1 0.6792 6 1 0 1 -1 1.3775 7 1 -1 -1 0 4.4471 8 1 -1 0 0 0.8384 9 1 -1 1 0 5.3388 10 1 0 -1 0 0.4989 11 1 0 1 0 0.4989 12 1 -1 -1 1 5.0723 13 1 -1 0 1 1.3779 14 1 -1 1 1 5.7175 15 1 0 -1 1 1.3775 16 1 0 0 1 0.6792 17 1 0 1 1 4.5781 18 1 1 1 1 5.6689 19 1 1 0 1 1.4404 20 1 1 -1 1 5.2620 21 1 1 1 0 4.4471 22 1 1 0 0 0.8384 23 1 1 -1 0 5.3388 24 1 1 1 -1 5.0723 25 1 1 0 -1 1.3779 26 1 1 -1 -1 5.7175 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3393 atoms have been selected out of 3467 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 759 253 253 0.00 3 C003 has 108 36 36 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1515 505 505 0.00 6 C006 has 456 152 152 0.00 7 C007 has 801 267 267 0.00 8 C008 has 1731 568 566 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.59 Total of12692 atoms and 4215 groups and 4208 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3467 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1144 Number of atoms = 3467 Number of groups = 1149 Number of bonds = 3460 Number of angles = 1248 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1146 Number of HB donors = 2270 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1144 Number of atoms = 3467 Number of groups = 1149 Number of bonds = 3460 Number of angles = 1248 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1146 Number of HB donors = 2270 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.432" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1144" Evaluating: 1144-7 Parameter: NUMWAT <- "1137" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1137" Comparing "1081" and "1137". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.432" Parameter: BOX -> "32.432" Parameter: BOX -> "32.432" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.43200 B = 32.43200 C = 32.43200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6679 2 1 -1 0 -1 1.4380 3 1 -1 1 -1 5.2591 4 1 0 -1 -1 4.5763 5 1 0 0 -1 0.6779 6 1 0 1 -1 1.3751 7 1 -1 -1 0 4.4455 8 1 -1 0 0 0.8371 9 1 -1 1 0 5.3360 10 1 0 -1 0 0.4974 11 1 0 1 0 0.4974 12 1 -1 -1 1 5.0697 13 1 -1 0 1 1.3762 14 1 -1 1 1 5.7146 15 1 0 -1 1 1.3751 16 1 0 0 1 0.6779 17 1 0 1 1 4.5763 18 1 1 1 1 5.6679 19 1 1 0 1 1.4380 20 1 1 -1 1 5.2591 21 1 1 1 0 4.4455 22 1 1 0 0 0.8371 23 1 1 -1 0 5.3360 24 1 1 1 -1 5.0697 25 1 1 0 -1 1.3762 26 1 1 -1 -1 5.7146 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3393 atoms have been selected out of 3467 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 759 253 253 0.00 3 C003 has 108 36 36 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1515 505 505 0.00 6 C006 has 456 152 152 0.00 7 C007 has 801 267 267 0.00 8 C008 has 1731 568 566 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.59 Total of12692 atoms and 4215 groups and 4208 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3467 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1144 Number of atoms = 3467 Number of groups = 1149 Number of bonds = 3460 Number of angles = 1248 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1146 Number of HB donors = 2270 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1144 Number of atoms = 3467 Number of groups = 1149 Number of bonds = 3460 Number of angles = 1248 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1146 Number of HB donors = 2270 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.43" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1144" Evaluating: 1144-7 Parameter: NUMWAT <- "1137" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1137" Comparing "1081" and "1137". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.43" Parameter: BOX -> "32.43" Parameter: BOX -> "32.43" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.43000 B = 32.43000 C = 32.43000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6669 2 1 -1 0 -1 1.4356 3 1 -1 1 -1 5.2562 4 1 0 -1 -1 4.5745 5 1 0 0 -1 0.6765 6 1 0 1 -1 1.3727 7 1 -1 -1 0 4.4438 8 1 -1 0 0 0.8358 9 1 -1 1 0 5.3332 10 1 0 -1 0 0.4960 11 1 0 1 0 0.4960 12 1 -1 -1 1 5.0670 13 1 -1 0 1 1.3746 14 1 -1 1 1 5.7118 15 1 0 -1 1 1.3727 16 1 0 0 1 0.6765 17 1 0 1 1 4.5745 18 1 1 1 1 5.6669 19 1 1 0 1 1.4356 20 1 1 -1 1 5.2562 21 1 1 1 0 4.4438 22 1 1 0 0 0.8358 23 1 1 -1 0 5.3332 24 1 1 1 -1 5.0670 25 1 1 0 -1 1.3746 26 1 1 -1 -1 5.7118 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3393 atoms have been selected out of 3467 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 759 253 253 0.00 3 C003 has 108 36 36 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1515 505 505 0.00 6 C006 has 456 152 152 0.00 7 C007 has 801 267 267 0.00 8 C008 has 1731 568 566 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.59 Total of12692 atoms and 4215 groups and 4208 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3467 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1144 Number of atoms = 3467 Number of groups = 1149 Number of bonds = 3460 Number of angles = 1248 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1146 Number of HB donors = 2270 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1144 Number of atoms = 3467 Number of groups = 1149 Number of bonds = 3460 Number of angles = 1248 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1146 Number of HB donors = 2270 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.428" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1144" Evaluating: 1144-7 Parameter: NUMWAT <- "1137" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1137" Comparing "1081" and "1137". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.428" Parameter: BOX -> "32.428" Parameter: BOX -> "32.428" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.42800 B = 32.42800 C = 32.42800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6659 2 1 -1 0 -1 1.4332 3 1 -1 1 -1 5.2534 4 1 0 -1 -1 4.5728 5 1 0 0 -1 0.6752 6 1 0 1 -1 1.3703 7 1 -1 -1 0 4.4422 8 1 -1 0 0 0.8345 9 1 -1 1 0 5.3304 10 1 0 -1 0 0.4945 11 1 0 1 0 0.4945 12 1 -1 -1 1 5.0644 13 1 -1 0 1 1.3730 14 1 -1 1 1 5.7089 15 1 0 -1 1 1.3703 16 1 0 0 1 0.6752 17 1 0 1 1 4.5728 18 1 1 1 1 5.6659 19 1 1 0 1 1.4332 20 1 1 -1 1 5.2534 21 1 1 1 0 4.4422 22 1 1 0 0 0.8345 23 1 1 -1 0 5.3304 24 1 1 1 -1 5.0644 25 1 1 0 -1 1.3730 26 1 1 -1 -1 5.7089 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3393 atoms have been selected out of 3467 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 550 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 759 253 253 0.00 3 C003 has 108 36 36 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1515 505 505 0.00 6 C006 has 456 152 152 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1728 567 565 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 111 37 37 0.00 13 C013 has 474 158 158 0.00 14 C014 has 126 42 42 0.59 Total of12683 atoms and 4212 groups and 4205 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3467 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1143 Number of atoms = 3464 Number of groups = 1148 Number of bonds = 3457 Number of angles = 1247 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1145 Number of HB donors = 2268 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1143 Number of atoms = 3464 Number of groups = 1148 Number of bonds = 3457 Number of angles = 1247 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1145 Number of HB donors = 2268 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.426" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1143" Evaluating: 1143-7 Parameter: NUMWAT <- "1136" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1136" Comparing "1081" and "1136". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.426" Parameter: BOX -> "32.426" Parameter: BOX -> "32.426" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.42600 B = 32.42600 C = 32.42600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6649 2 1 -1 0 -1 1.4308 3 1 -1 1 -1 5.2505 4 1 0 -1 -1 4.5710 5 1 0 0 -1 0.6739 6 1 0 1 -1 1.3679 7 1 -1 -1 0 4.4405 8 1 -1 0 0 0.8332 9 1 -1 1 0 5.3275 10 1 0 -1 0 0.4930 11 1 0 1 0 0.4930 12 1 -1 -1 1 5.0618 13 1 -1 0 1 1.3714 14 1 -1 1 1 5.7060 15 1 0 -1 1 1.3679 16 1 0 0 1 0.6739 17 1 0 1 1 4.5710 18 1 1 1 1 5.6649 19 1 1 0 1 1.4308 20 1 1 -1 1 5.2505 21 1 1 1 0 4.4405 22 1 1 0 0 0.8332 23 1 1 -1 0 5.3275 24 1 1 1 -1 5.0618 25 1 1 0 -1 1.3714 26 1 1 -1 -1 5.7060 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3390 atoms have been selected out of 3464 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 762 254 254 0.00 3 C003 has 108 36 36 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1518 506 506 0.00 6 C006 has 456 152 152 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1728 567 565 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 111 37 37 0.00 13 C013 has 474 158 158 0.00 14 C014 has 126 42 42 0.59 Total of12683 atoms and 4212 groups and 4205 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3464 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1143 Number of atoms = 3464 Number of groups = 1148 Number of bonds = 3457 Number of angles = 1247 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1145 Number of HB donors = 2268 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1143 Number of atoms = 3464 Number of groups = 1148 Number of bonds = 3457 Number of angles = 1247 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1145 Number of HB donors = 2268 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.424" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1143" Evaluating: 1143-7 Parameter: NUMWAT <- "1136" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1136" Comparing "1081" and "1136". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.424" Parameter: BOX -> "32.424" Parameter: BOX -> "32.424" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.42400 B = 32.42400 C = 32.42400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6639 2 1 -1 0 -1 1.4284 3 1 -1 1 -1 5.2476 4 1 0 -1 -1 4.5692 5 1 0 0 -1 0.6726 6 1 0 1 -1 1.3655 7 1 -1 -1 0 4.4389 8 1 -1 0 0 0.8319 9 1 -1 1 0 5.3247 10 1 0 -1 0 0.4915 11 1 0 1 0 0.4915 12 1 -1 -1 1 5.0592 13 1 -1 0 1 1.3698 14 1 -1 1 1 5.7032 15 1 0 -1 1 1.3655 16 1 0 0 1 0.6726 17 1 0 1 1 4.5692 18 1 1 1 1 5.6639 19 1 1 0 1 1.4284 20 1 1 -1 1 5.2476 21 1 1 1 0 4.4389 22 1 1 0 0 0.8319 23 1 1 -1 0 5.3247 24 1 1 1 -1 5.0592 25 1 1 0 -1 1.3698 26 1 1 -1 -1 5.7032 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3390 atoms have been selected out of 3464 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 762 254 254 0.00 3 C003 has 108 36 36 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1518 506 506 0.00 6 C006 has 456 152 152 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1728 567 565 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 111 37 37 0.00 13 C013 has 474 158 158 0.00 14 C014 has 126 42 42 0.58 Total of12683 atoms and 4212 groups and 4205 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3464 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1143 Number of atoms = 3464 Number of groups = 1148 Number of bonds = 3457 Number of angles = 1247 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1145 Number of HB donors = 2268 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1143 Number of atoms = 3464 Number of groups = 1148 Number of bonds = 3457 Number of angles = 1247 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1145 Number of HB donors = 2268 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.422" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1143" Evaluating: 1143-7 Parameter: NUMWAT <- "1136" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1136" Comparing "1081" and "1136". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.422" Parameter: BOX -> "32.422" Parameter: BOX -> "32.422" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.42200 B = 32.42200 C = 32.42200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6629 2 1 -1 0 -1 1.4260 3 1 -1 1 -1 5.2447 4 1 0 -1 -1 4.5674 5 1 0 0 -1 0.6712 6 1 0 1 -1 1.3631 7 1 -1 -1 0 4.4372 8 1 -1 0 0 0.8306 9 1 -1 1 0 5.3219 10 1 0 -1 0 0.4901 11 1 0 1 0 0.4901 12 1 -1 -1 1 5.0566 13 1 -1 0 1 1.3682 14 1 -1 1 1 5.7003 15 1 0 -1 1 1.3631 16 1 0 0 1 0.6712 17 1 0 1 1 4.5674 18 1 1 1 1 5.6629 19 1 1 0 1 1.4260 20 1 1 -1 1 5.2447 21 1 1 1 0 4.4372 22 1 1 0 0 0.8306 23 1 1 -1 0 5.3219 24 1 1 1 -1 5.0566 25 1 1 0 -1 1.3682 26 1 1 -1 -1 5.7003 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3390 atoms have been selected out of 3464 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 188 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 762 254 254 0.00 3 C003 has 108 36 36 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1518 506 506 0.00 6 C006 has 456 152 152 0.00 7 C007 has 801 267 267 0.00 8 C008 has 1728 567 565 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 114 38 38 0.00 13 C013 has 474 158 158 0.00 14 C014 has 126 42 42 0.58 Total of12686 atoms and 4213 groups and 4206 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3464 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1142 Number of atoms = 3461 Number of groups = 1147 Number of bonds = 3454 Number of angles = 1246 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1144 Number of HB donors = 2266 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1142 Number of atoms = 3461 Number of groups = 1147 Number of bonds = 3454 Number of angles = 1246 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1144 Number of HB donors = 2266 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.42" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1142" Evaluating: 1142-7 Parameter: NUMWAT <- "1135" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1135" Comparing "1081" and "1135". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.42" Parameter: BOX -> "32.42" Parameter: BOX -> "32.42" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.42000 B = 32.42000 C = 32.42000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6619 2 1 -1 0 -1 1.4236 3 1 -1 1 -1 5.2418 4 1 0 -1 -1 4.5656 5 1 0 0 -1 0.6699 6 1 0 1 -1 1.3607 7 1 -1 -1 0 4.4356 8 1 -1 0 0 0.8293 9 1 -1 1 0 5.3191 10 1 0 -1 0 0.4886 11 1 0 1 0 0.4886 12 1 -1 -1 1 5.0540 13 1 -1 0 1 1.3666 14 1 -1 1 1 5.6975 15 1 0 -1 1 1.3607 16 1 0 0 1 0.6699 17 1 0 1 1 4.5656 18 1 1 1 1 5.6619 19 1 1 0 1 1.4236 20 1 1 -1 1 5.2418 21 1 1 1 0 4.4356 22 1 1 0 0 0.8293 23 1 1 -1 0 5.3191 24 1 1 1 -1 5.0540 25 1 1 0 -1 1.3666 26 1 1 -1 -1 5.6975 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3387 atoms have been selected out of 3461 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 762 254 254 0.00 3 C003 has 108 36 36 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1518 506 506 0.00 6 C006 has 456 152 152 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1725 566 564 0.00 9 C009 has 417 139 139 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 114 38 38 0.00 13 C013 has 474 158 158 0.00 14 C014 has 126 42 42 0.58 Total of12674 atoms and 4209 groups and 4202 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3461 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1142 Number of atoms = 3461 Number of groups = 1147 Number of bonds = 3454 Number of angles = 1246 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1144 Number of HB donors = 2266 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1142 Number of atoms = 3461 Number of groups = 1147 Number of bonds = 3454 Number of angles = 1246 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1144 Number of HB donors = 2266 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.418" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1142" Evaluating: 1142-7 Parameter: NUMWAT <- "1135" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1135" Comparing "1081" and "1135". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.418" Parameter: BOX -> "32.418" Parameter: BOX -> "32.418" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.41800 B = 32.41800 C = 32.41800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6609 2 1 -1 0 -1 1.4213 3 1 -1 1 -1 5.2389 4 1 0 -1 -1 4.5639 5 1 0 0 -1 0.6686 6 1 0 1 -1 1.3583 7 1 -1 -1 0 4.4339 8 1 -1 0 0 0.8280 9 1 -1 1 0 5.3162 10 1 0 -1 0 0.4871 11 1 0 1 0 0.4871 12 1 -1 -1 1 5.0513 13 1 -1 0 1 1.3651 14 1 -1 1 1 5.6946 15 1 0 -1 1 1.3583 16 1 0 0 1 0.6686 17 1 0 1 1 4.5639 18 1 1 1 1 5.6609 19 1 1 0 1 1.4213 20 1 1 -1 1 5.2389 21 1 1 1 0 4.4339 22 1 1 0 0 0.8280 23 1 1 -1 0 5.3162 24 1 1 1 -1 5.0513 25 1 1 0 -1 1.3651 26 1 1 -1 -1 5.6946 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3387 atoms have been selected out of 3461 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 762 254 254 0.00 3 C003 has 108 36 36 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1518 506 506 0.00 6 C006 has 456 152 152 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1725 566 564 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 114 38 38 0.00 13 C013 has 474 158 158 0.00 14 C014 has 126 42 42 0.58 Total of12677 atoms and 4210 groups and 4203 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3461 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1142 Number of atoms = 3461 Number of groups = 1147 Number of bonds = 3454 Number of angles = 1246 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1144 Number of HB donors = 2266 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1142 Number of atoms = 3461 Number of groups = 1147 Number of bonds = 3454 Number of angles = 1246 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1144 Number of HB donors = 2266 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.416" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1142" Evaluating: 1142-7 Parameter: NUMWAT <- "1135" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1135" Comparing "1081" and "1135". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.416" Parameter: BOX -> "32.416" Parameter: BOX -> "32.416" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.41600 B = 32.41600 C = 32.41600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6599 2 1 -1 0 -1 1.4189 3 1 -1 1 -1 5.2360 4 1 0 -1 -1 4.5621 5 1 0 0 -1 0.6673 6 1 0 1 -1 1.3559 7 1 -1 -1 0 4.4323 8 1 -1 0 0 0.8267 9 1 -1 1 0 5.3134 10 1 0 -1 0 0.4857 11 1 0 1 0 0.4857 12 1 -1 -1 1 5.0487 13 1 -1 0 1 1.3635 14 1 -1 1 1 5.6917 15 1 0 -1 1 1.3559 16 1 0 0 1 0.6673 17 1 0 1 1 4.5621 18 1 1 1 1 5.6599 19 1 1 0 1 1.4189 20 1 1 -1 1 5.2360 21 1 1 1 0 4.4323 22 1 1 0 0 0.8267 23 1 1 -1 0 5.3134 24 1 1 1 -1 5.0487 25 1 1 0 -1 1.3635 26 1 1 -1 -1 5.6917 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3387 atoms have been selected out of 3461 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 762 254 254 0.00 3 C003 has 108 36 36 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1518 506 506 0.00 6 C006 has 456 152 152 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1725 566 564 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 114 38 38 0.00 13 C013 has 474 158 158 0.00 14 C014 has 126 42 42 0.58 Total of12677 atoms and 4210 groups and 4203 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3461 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1142 Number of atoms = 3461 Number of groups = 1147 Number of bonds = 3454 Number of angles = 1246 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1144 Number of HB donors = 2266 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1142 Number of atoms = 3461 Number of groups = 1147 Number of bonds = 3454 Number of angles = 1246 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1144 Number of HB donors = 2266 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.414" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1142" Evaluating: 1142-7 Parameter: NUMWAT <- "1135" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1135" Comparing "1081" and "1135". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.414" Parameter: BOX -> "32.414" Parameter: BOX -> "32.414" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.41400 B = 32.41400 C = 32.41400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6589 2 1 -1 0 -1 1.4165 3 1 -1 1 -1 5.2332 4 1 0 -1 -1 4.5603 5 1 0 0 -1 0.6660 6 1 0 1 -1 1.3535 7 1 -1 -1 0 4.4307 8 1 -1 0 0 0.8254 9 1 -1 1 0 5.3106 10 1 0 -1 0 0.4842 11 1 0 1 0 0.4842 12 1 -1 -1 1 5.0461 13 1 -1 0 1 1.3619 14 1 -1 1 1 5.6889 15 1 0 -1 1 1.3535 16 1 0 0 1 0.6660 17 1 0 1 1 4.5603 18 1 1 1 1 5.6589 19 1 1 0 1 1.4165 20 1 1 -1 1 5.2332 21 1 1 1 0 4.4307 22 1 1 0 0 0.8254 23 1 1 -1 0 5.3106 24 1 1 1 -1 5.0461 25 1 1 0 -1 1.3619 26 1 1 -1 -1 5.6889 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3387 atoms have been selected out of 3461 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 762 254 254 0.00 3 C003 has 108 36 36 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1518 506 506 0.00 6 C006 has 456 152 152 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1725 566 564 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 114 38 38 0.00 13 C013 has 474 158 158 0.00 14 C014 has 126 42 42 0.57 Total of12677 atoms and 4210 groups and 4203 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3461 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1142 Number of atoms = 3461 Number of groups = 1147 Number of bonds = 3454 Number of angles = 1246 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1144 Number of HB donors = 2266 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1142 Number of atoms = 3461 Number of groups = 1147 Number of bonds = 3454 Number of angles = 1246 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1144 Number of HB donors = 2266 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.412" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1142" Evaluating: 1142-7 Parameter: NUMWAT <- "1135" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1135" Comparing "1081" and "1135". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.412" Parameter: BOX -> "32.412" Parameter: BOX -> "32.412" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.41200 B = 32.41200 C = 32.41200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6580 2 1 -1 0 -1 1.4141 3 1 -1 1 -1 5.2303 4 1 0 -1 -1 4.5585 5 1 0 0 -1 0.6647 6 1 0 1 -1 1.3511 7 1 -1 -1 0 4.4290 8 1 -1 0 0 0.8241 9 1 -1 1 0 5.3078 10 1 0 -1 0 0.4828 11 1 0 1 0 0.4828 12 1 -1 -1 1 5.0435 13 1 -1 0 1 1.3603 14 1 -1 1 1 5.6860 15 1 0 -1 1 1.3511 16 1 0 0 1 0.6647 17 1 0 1 1 4.5585 18 1 1 1 1 5.6580 19 1 1 0 1 1.4141 20 1 1 -1 1 5.2303 21 1 1 1 0 4.4290 22 1 1 0 0 0.8241 23 1 1 -1 0 5.3078 24 1 1 1 -1 5.0435 25 1 1 0 -1 1.3603 26 1 1 -1 -1 5.6860 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3387 atoms have been selected out of 3461 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 631 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1009 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 108 36 36 0.00 4 C004 has 645 215 215 0.00 5 C005 has 1515 505 505 0.00 6 C006 has 453 151 151 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1722 565 563 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 114 38 38 0.00 13 C013 has 474 158 158 0.00 14 C014 has 126 42 42 0.57 Total of12665 atoms and 4206 groups and 4199 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3461 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1140 Number of atoms = 3455 Number of groups = 1145 Number of bonds = 3448 Number of angles = 1244 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1142 Number of HB donors = 2262 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1140 Number of atoms = 3455 Number of groups = 1145 Number of bonds = 3448 Number of angles = 1244 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1142 Number of HB donors = 2262 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.41" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1140" Evaluating: 1140-7 Parameter: NUMWAT <- "1133" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1133" Comparing "1081" and "1133". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.41" Parameter: BOX -> "32.41" Parameter: BOX -> "32.41" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.41000 B = 32.41000 C = 32.41000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6570 2 1 -1 0 -1 1.4117 3 1 -1 1 -1 5.2274 4 1 0 -1 -1 4.5567 5 1 0 0 -1 0.6634 6 1 0 1 -1 1.3488 7 1 -1 -1 0 4.4274 8 1 -1 0 0 0.8229 9 1 -1 1 0 5.3050 10 1 0 -1 0 0.4814 11 1 0 1 0 0.4814 12 1 -1 -1 1 5.0409 13 1 -1 0 1 1.3588 14 1 -1 1 1 5.6832 15 1 0 -1 1 1.3488 16 1 0 0 1 0.6634 17 1 0 1 1 4.5567 18 1 1 1 1 5.6570 19 1 1 0 1 1.4117 20 1 1 -1 1 5.2274 21 1 1 1 0 4.4274 22 1 1 0 0 0.8229 23 1 1 -1 0 5.3050 24 1 1 1 -1 5.0409 25 1 1 0 -1 1.3588 26 1 1 -1 -1 5.6832 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3381 atoms have been selected out of 3455 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 329 OPERATED ON BY TRANSFORMATION C022 RESIDUE 476 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 762 254 254 0.00 3 C003 has 108 36 36 0.00 4 C004 has 645 215 215 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 453 151 151 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1713 562 560 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 117 39 39 0.00 13 C013 has 474 158 158 0.00 14 C014 has 126 42 42 0.57 Total of12650 atoms and 4201 groups and 4194 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3455 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1138 Number of atoms = 3449 Number of groups = 1143 Number of bonds = 3442 Number of angles = 1242 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1140 Number of HB donors = 2258 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1138 Number of atoms = 3449 Number of groups = 1143 Number of bonds = 3442 Number of angles = 1242 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1140 Number of HB donors = 2258 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.408" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1138" Evaluating: 1138-7 Parameter: NUMWAT <- "1131" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1131" Comparing "1081" and "1131". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.408" Parameter: BOX -> "32.408" Parameter: BOX -> "32.408" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.40800 B = 32.40800 C = 32.40800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6560 2 1 -1 0 -1 1.4094 3 1 -1 1 -1 5.2245 4 1 0 -1 -1 4.5550 5 1 0 0 -1 0.6621 6 1 0 1 -1 1.3464 7 1 -1 -1 0 4.4258 8 1 -1 0 0 0.8216 9 1 -1 1 0 5.3021 10 1 0 -1 0 0.4799 11 1 0 1 0 0.4799 12 1 -1 -1 1 5.0383 13 1 -1 0 1 1.3572 14 1 -1 1 1 5.6803 15 1 0 -1 1 1.3464 16 1 0 0 1 0.6621 17 1 0 1 1 4.5550 18 1 1 1 1 5.6560 19 1 1 0 1 1.4094 20 1 1 -1 1 5.2245 21 1 1 1 0 4.4258 22 1 1 0 0 0.8216 23 1 1 -1 0 5.3021 24 1 1 1 -1 5.0383 25 1 1 0 -1 1.3572 26 1 1 -1 -1 5.6803 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3375 atoms have been selected out of 3449 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 108 36 36 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 453 151 151 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1707 560 558 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 114 38 38 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.57 Total of12611 atoms and 4188 groups and 4181 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3449 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1138 Number of atoms = 3449 Number of groups = 1143 Number of bonds = 3442 Number of angles = 1242 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1140 Number of HB donors = 2258 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1138 Number of atoms = 3449 Number of groups = 1143 Number of bonds = 3442 Number of angles = 1242 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1140 Number of HB donors = 2258 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.406" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1138" Evaluating: 1138-7 Parameter: NUMWAT <- "1131" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1131" Comparing "1081" and "1131". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.406" Parameter: BOX -> "32.406" Parameter: BOX -> "32.406" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.40600 B = 32.40600 C = 32.40600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6550 2 1 -1 0 -1 1.4070 3 1 -1 1 -1 5.2216 4 1 0 -1 -1 4.5532 5 1 0 0 -1 0.6608 6 1 0 1 -1 1.3440 7 1 -1 -1 0 4.4241 8 1 -1 0 0 0.8203 9 1 -1 1 0 5.2993 10 1 0 -1 0 0.4785 11 1 0 1 0 0.4785 12 1 -1 -1 1 5.0357 13 1 -1 0 1 1.3556 14 1 -1 1 1 5.6774 15 1 0 -1 1 1.3440 16 1 0 0 1 0.6608 17 1 0 1 1 4.5532 18 1 1 1 1 5.6550 19 1 1 0 1 1.4070 20 1 1 -1 1 5.2216 21 1 1 1 0 4.4241 22 1 1 0 0 0.8203 23 1 1 -1 0 5.2993 24 1 1 1 -1 5.0357 25 1 1 0 -1 1.3556 26 1 1 -1 -1 5.6774 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3375 atoms have been selected out of 3449 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 108 36 36 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 453 151 151 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1707 560 558 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 114 38 38 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.57 Total of12611 atoms and 4188 groups and 4181 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3449 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1138 Number of atoms = 3449 Number of groups = 1143 Number of bonds = 3442 Number of angles = 1242 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1140 Number of HB donors = 2258 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1138 Number of atoms = 3449 Number of groups = 1143 Number of bonds = 3442 Number of angles = 1242 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1140 Number of HB donors = 2258 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.404" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1138" Evaluating: 1138-7 Parameter: NUMWAT <- "1131" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1131" Comparing "1081" and "1131". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.404" Parameter: BOX -> "32.404" Parameter: BOX -> "32.404" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.40400 B = 32.40400 C = 32.40400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6541 2 1 -1 0 -1 1.4046 3 1 -1 1 -1 5.2187 4 1 0 -1 -1 4.5514 5 1 0 0 -1 0.6595 6 1 0 1 -1 1.3416 7 1 -1 -1 0 4.4225 8 1 -1 0 0 0.8190 9 1 -1 1 0 5.2965 10 1 0 -1 0 0.4770 11 1 0 1 0 0.4770 12 1 -1 -1 1 5.0331 13 1 -1 0 1 1.3541 14 1 -1 1 1 5.6746 15 1 0 -1 1 1.3416 16 1 0 0 1 0.6595 17 1 0 1 1 4.5514 18 1 1 1 1 5.6541 19 1 1 0 1 1.4046 20 1 1 -1 1 5.2187 21 1 1 1 0 4.4225 22 1 1 0 0 0.8190 23 1 1 -1 0 5.2965 24 1 1 1 -1 5.0331 25 1 1 0 -1 1.3541 26 1 1 -1 -1 5.6746 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3375 atoms have been selected out of 3449 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 762 254 254 0.00 3 C003 has 108 36 36 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 453 151 151 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1707 560 558 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 114 38 38 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.56 Total of12614 atoms and 4189 groups and 4182 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3449 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1138 Number of atoms = 3449 Number of groups = 1143 Number of bonds = 3442 Number of angles = 1242 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1140 Number of HB donors = 2258 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1138 Number of atoms = 3449 Number of groups = 1143 Number of bonds = 3442 Number of angles = 1242 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1140 Number of HB donors = 2258 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.402" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1138" Evaluating: 1138-7 Parameter: NUMWAT <- "1131" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1131" Comparing "1081" and "1131". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.402" Parameter: BOX -> "32.402" Parameter: BOX -> "32.402" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.40200 B = 32.40200 C = 32.40200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6531 2 1 -1 0 -1 1.4023 3 1 -1 1 -1 5.2159 4 1 0 -1 -1 4.5497 5 1 0 0 -1 0.6582 6 1 0 1 -1 1.3392 7 1 -1 -1 0 4.4209 8 1 -1 0 0 0.8178 9 1 -1 1 0 5.2937 10 1 0 -1 0 0.4756 11 1 0 1 0 0.4756 12 1 -1 -1 1 5.0305 13 1 -1 0 1 1.3525 14 1 -1 1 1 5.6717 15 1 0 -1 1 1.3392 16 1 0 0 1 0.6582 17 1 0 1 1 4.5497 18 1 1 1 1 5.6531 19 1 1 0 1 1.4023 20 1 1 -1 1 5.2159 21 1 1 1 0 4.4209 22 1 1 0 0 0.8178 23 1 1 -1 0 5.2937 24 1 1 1 -1 5.0305 25 1 1 0 -1 1.3525 26 1 1 -1 -1 5.6717 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3375 atoms have been selected out of 3449 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 762 254 254 0.00 3 C003 has 108 36 36 0.00 4 C004 has 642 214 214 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 453 151 151 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1707 560 558 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.56 Total of12617 atoms and 4190 groups and 4183 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3449 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1138 Number of atoms = 3449 Number of groups = 1143 Number of bonds = 3442 Number of angles = 1242 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1140 Number of HB donors = 2258 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1138 Number of atoms = 3449 Number of groups = 1143 Number of bonds = 3442 Number of angles = 1242 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1140 Number of HB donors = 2258 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.4" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1138" Evaluating: 1138-7 Parameter: NUMWAT <- "1131" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1131" Comparing "1081" and "1131". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.4" Parameter: BOX -> "32.4" Parameter: BOX -> "32.4" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.40000 B = 32.40000 C = 32.40000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6521 2 1 -1 0 -1 1.3999 3 1 -1 1 -1 5.2130 4 1 0 -1 -1 4.5479 5 1 0 0 -1 0.6570 6 1 0 1 -1 1.3369 7 1 -1 -1 0 4.4192 8 1 -1 0 0 0.8165 9 1 -1 1 0 5.2908 10 1 0 -1 0 0.4742 11 1 0 1 0 0.4742 12 1 -1 -1 1 5.0279 13 1 -1 0 1 1.3510 14 1 -1 1 1 5.6689 15 1 0 -1 1 1.3369 16 1 0 0 1 0.6570 17 1 0 1 1 4.5479 18 1 1 1 1 5.6521 19 1 1 0 1 1.3999 20 1 1 -1 1 5.2130 21 1 1 1 0 4.4192 22 1 1 0 0 0.8165 23 1 1 -1 0 5.2908 24 1 1 1 -1 5.0279 25 1 1 0 -1 1.3510 26 1 1 -1 -1 5.6689 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3375 atoms have been selected out of 3449 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 762 254 254 0.00 3 C003 has 108 36 36 0.00 4 C004 has 645 215 215 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 453 151 151 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1707 560 558 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 117 39 39 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.56 Total of12620 atoms and 4191 groups and 4184 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3449 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1138 Number of atoms = 3449 Number of groups = 1143 Number of bonds = 3442 Number of angles = 1242 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1140 Number of HB donors = 2258 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1138 Number of atoms = 3449 Number of groups = 1143 Number of bonds = 3442 Number of angles = 1242 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1140 Number of HB donors = 2258 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.398" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1138" Evaluating: 1138-7 Parameter: NUMWAT <- "1131" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1131" Comparing "1081" and "1131". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.398" Parameter: BOX -> "32.398" Parameter: BOX -> "32.398" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.39800 B = 32.39800 C = 32.39800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6511 2 1 -1 0 -1 1.3975 3 1 -1 1 -1 5.2101 4 1 0 -1 -1 4.5461 5 1 0 0 -1 0.6557 6 1 0 1 -1 1.3345 7 1 -1 -1 0 4.4176 8 1 -1 0 0 0.8152 9 1 -1 1 0 5.2880 10 1 0 -1 0 0.4728 11 1 0 1 0 0.4728 12 1 -1 -1 1 5.0253 13 1 -1 0 1 1.3494 14 1 -1 1 1 5.6660 15 1 0 -1 1 1.3345 16 1 0 0 1 0.6557 17 1 0 1 1 4.5461 18 1 1 1 1 5.6511 19 1 1 0 1 1.3975 20 1 1 -1 1 5.2101 21 1 1 1 0 4.4176 22 1 1 0 0 0.8152 23 1 1 -1 0 5.2880 24 1 1 1 -1 5.0253 25 1 1 0 -1 1.3494 26 1 1 -1 -1 5.6660 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3375 atoms have been selected out of 3449 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 638 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 762 254 254 0.00 3 C003 has 108 36 36 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1707 560 558 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 108 36 36 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.56 Total of12614 atoms and 4189 groups and 4182 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3449 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1137 Number of atoms = 3446 Number of groups = 1142 Number of bonds = 3439 Number of angles = 1241 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1139 Number of HB donors = 2256 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1137 Number of atoms = 3446 Number of groups = 1142 Number of bonds = 3439 Number of angles = 1241 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1139 Number of HB donors = 2256 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.396" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1137" Evaluating: 1137-7 Parameter: NUMWAT <- "1130" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1130" Comparing "1081" and "1130". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.396" Parameter: BOX -> "32.396" Parameter: BOX -> "32.396" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.39600 B = 32.39600 C = 32.39600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6502 2 1 -1 0 -1 1.3952 3 1 -1 1 -1 5.2072 4 1 0 -1 -1 4.5444 5 1 0 0 -1 0.6544 6 1 0 1 -1 1.3321 7 1 -1 -1 0 4.4160 8 1 -1 0 0 0.8140 9 1 -1 1 0 5.2852 10 1 0 -1 0 0.4714 11 1 0 1 0 0.4714 12 1 -1 -1 1 5.0227 13 1 -1 0 1 1.3479 14 1 -1 1 1 5.6632 15 1 0 -1 1 1.3321 16 1 0 0 1 0.6544 17 1 0 1 1 4.5444 18 1 1 1 1 5.6502 19 1 1 0 1 1.3952 20 1 1 -1 1 5.2072 21 1 1 1 0 4.4160 22 1 1 0 0 0.8140 23 1 1 -1 0 5.2852 24 1 1 1 -1 5.0227 25 1 1 0 -1 1.3479 26 1 1 -1 -1 5.6632 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3372 atoms have been selected out of 3446 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 762 254 254 0.00 3 C003 has 108 36 36 0.00 4 C004 has 645 215 215 0.00 5 C005 has 1503 501 501 0.00 6 C006 has 450 150 150 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1707 560 558 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 108 36 36 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.56 Total of12602 atoms and 4185 groups and 4178 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3446 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1137 Number of atoms = 3446 Number of groups = 1142 Number of bonds = 3439 Number of angles = 1241 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1139 Number of HB donors = 2256 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1137 Number of atoms = 3446 Number of groups = 1142 Number of bonds = 3439 Number of angles = 1241 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1139 Number of HB donors = 2256 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.394" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1137" Evaluating: 1137-7 Parameter: NUMWAT <- "1130" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1130" Comparing "1081" and "1130". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.394" Parameter: BOX -> "32.394" Parameter: BOX -> "32.394" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.39400 B = 32.39400 C = 32.39400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6492 2 1 -1 0 -1 1.3928 3 1 -1 1 -1 5.2044 4 1 0 -1 -1 4.5426 5 1 0 0 -1 0.6531 6 1 0 1 -1 1.3298 7 1 -1 -1 0 4.4144 8 1 -1 0 0 0.8127 9 1 -1 1 0 5.2824 10 1 0 -1 0 0.4700 11 1 0 1 0 0.4700 12 1 -1 -1 1 5.0201 13 1 -1 0 1 1.3464 14 1 -1 1 1 5.6603 15 1 0 -1 1 1.3298 16 1 0 0 1 0.6531 17 1 0 1 1 4.5426 18 1 1 1 1 5.6492 19 1 1 0 1 1.3928 20 1 1 -1 1 5.2044 21 1 1 1 0 4.4144 22 1 1 0 0 0.8127 23 1 1 -1 0 5.2824 24 1 1 1 -1 5.0201 25 1 1 0 -1 1.3464 26 1 1 -1 -1 5.6603 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3372 atoms have been selected out of 3446 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 762 254 254 0.00 3 C003 has 108 36 36 0.00 4 C004 has 645 215 215 0.00 5 C005 has 1503 501 501 0.00 6 C006 has 450 150 150 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1707 560 558 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 108 36 36 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.55 Total of12602 atoms and 4185 groups and 4178 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3446 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1137 Number of atoms = 3446 Number of groups = 1142 Number of bonds = 3439 Number of angles = 1241 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1139 Number of HB donors = 2256 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1137 Number of atoms = 3446 Number of groups = 1142 Number of bonds = 3439 Number of angles = 1241 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1139 Number of HB donors = 2256 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.392" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1137" Evaluating: 1137-7 Parameter: NUMWAT <- "1130" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1130" Comparing "1081" and "1130". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.392" Parameter: BOX -> "32.392" Parameter: BOX -> "32.392" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.39200 B = 32.39200 C = 32.39200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6482 2 1 -1 0 -1 1.3904 3 1 -1 1 -1 5.2015 4 1 0 -1 -1 4.5408 5 1 0 0 -1 0.6519 6 1 0 1 -1 1.3274 7 1 -1 -1 0 4.4127 8 1 -1 0 0 0.8115 9 1 -1 1 0 5.2796 10 1 0 -1 0 0.4685 11 1 0 1 0 0.4685 12 1 -1 -1 1 5.0175 13 1 -1 0 1 1.3448 14 1 -1 1 1 5.6575 15 1 0 -1 1 1.3274 16 1 0 0 1 0.6519 17 1 0 1 1 4.5408 18 1 1 1 1 5.6482 19 1 1 0 1 1.3904 20 1 1 -1 1 5.2015 21 1 1 1 0 4.4127 22 1 1 0 0 0.8115 23 1 1 -1 0 5.2796 24 1 1 1 -1 5.0175 25 1 1 0 -1 1.3448 26 1 1 -1 -1 5.6575 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3372 atoms have been selected out of 3446 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 762 254 254 0.00 3 C003 has 108 36 36 0.00 4 C004 has 645 215 215 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1707 560 558 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 108 36 36 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.55 Total of12605 atoms and 4186 groups and 4179 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3446 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1137 Number of atoms = 3446 Number of groups = 1142 Number of bonds = 3439 Number of angles = 1241 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1139 Number of HB donors = 2256 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1137 Number of atoms = 3446 Number of groups = 1142 Number of bonds = 3439 Number of angles = 1241 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1139 Number of HB donors = 2256 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.39" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1137" Evaluating: 1137-7 Parameter: NUMWAT <- "1130" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1130" Comparing "1081" and "1130". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.39" Parameter: BOX -> "32.39" Parameter: BOX -> "32.39" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.39000 B = 32.39000 C = 32.39000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6473 2 1 -1 0 -1 1.3881 3 1 -1 1 -1 5.1986 4 1 0 -1 -1 4.5391 5 1 0 0 -1 0.6506 6 1 0 1 -1 1.3250 7 1 -1 -1 0 4.4111 8 1 -1 0 0 0.8102 9 1 -1 1 0 5.2767 10 1 0 -1 0 0.4671 11 1 0 1 0 0.4671 12 1 -1 -1 1 5.0149 13 1 -1 0 1 1.3433 14 1 -1 1 1 5.6546 15 1 0 -1 1 1.3250 16 1 0 0 1 0.6506 17 1 0 1 1 4.5391 18 1 1 1 1 5.6473 19 1 1 0 1 1.3881 20 1 1 -1 1 5.1986 21 1 1 1 0 4.4111 22 1 1 0 0 0.8102 23 1 1 -1 0 5.2767 24 1 1 1 -1 5.0149 25 1 1 0 -1 1.3433 26 1 1 -1 -1 5.6546 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3372 atoms have been selected out of 3446 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 762 254 254 0.00 3 C003 has 108 36 36 0.00 4 C004 has 645 215 215 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1707 560 558 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 108 36 36 0.00 13 C013 has 471 157 157 0.00 14 C014 has 126 42 42 0.55 Total of12605 atoms and 4186 groups and 4179 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3446 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1137 Number of atoms = 3446 Number of groups = 1142 Number of bonds = 3439 Number of angles = 1241 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1139 Number of HB donors = 2256 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1137 Number of atoms = 3446 Number of groups = 1142 Number of bonds = 3439 Number of angles = 1241 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1139 Number of HB donors = 2256 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.388" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1137" Evaluating: 1137-7 Parameter: NUMWAT <- "1130" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1130" Comparing "1081" and "1130". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.388" Parameter: BOX -> "32.388" Parameter: BOX -> "32.388" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.38800 B = 32.38800 C = 32.38800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6463 2 1 -1 0 -1 1.3857 3 1 -1 1 -1 5.1957 4 1 0 -1 -1 4.5373 5 1 0 0 -1 0.6494 6 1 0 1 -1 1.3227 7 1 -1 -1 0 4.4095 8 1 -1 0 0 0.8090 9 1 -1 1 0 5.2739 10 1 0 -1 0 0.4657 11 1 0 1 0 0.4657 12 1 -1 -1 1 5.0123 13 1 -1 0 1 1.3418 14 1 -1 1 1 5.6518 15 1 0 -1 1 1.3227 16 1 0 0 1 0.6494 17 1 0 1 1 4.5373 18 1 1 1 1 5.6463 19 1 1 0 1 1.3857 20 1 1 -1 1 5.1957 21 1 1 1 0 4.4095 22 1 1 0 0 0.8090 23 1 1 -1 0 5.2739 24 1 1 1 -1 5.0123 25 1 1 0 -1 1.3418 26 1 1 -1 -1 5.6518 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3372 atoms have been selected out of 3446 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 762 254 254 0.00 3 C003 has 108 36 36 0.00 4 C004 has 645 215 215 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1707 560 558 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 108 36 36 0.00 13 C013 has 474 158 158 0.00 14 C014 has 126 42 42 0.55 Total of12608 atoms and 4187 groups and 4180 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3446 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1137 Number of atoms = 3446 Number of groups = 1142 Number of bonds = 3439 Number of angles = 1241 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1139 Number of HB donors = 2256 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1137 Number of atoms = 3446 Number of groups = 1142 Number of bonds = 3439 Number of angles = 1241 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1139 Number of HB donors = 2256 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.386" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1137" Evaluating: 1137-7 Parameter: NUMWAT <- "1130" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1130" Comparing "1081" and "1130". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.386" Parameter: BOX -> "32.386" Parameter: BOX -> "32.386" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.38600 B = 32.38600 C = 32.38600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6454 2 1 -1 0 -1 1.3834 3 1 -1 1 -1 5.1929 4 1 0 -1 -1 4.5355 5 1 0 0 -1 0.6481 6 1 0 1 -1 1.3203 7 1 -1 -1 0 4.4079 8 1 -1 0 0 0.8077 9 1 -1 1 0 5.2711 10 1 0 -1 0 0.4644 11 1 0 1 0 0.4644 12 1 -1 -1 1 5.0097 13 1 -1 0 1 1.3403 14 1 -1 1 1 5.6489 15 1 0 -1 1 1.3203 16 1 0 0 1 0.6481 17 1 0 1 1 4.5355 18 1 1 1 1 5.6454 19 1 1 0 1 1.3834 20 1 1 -1 1 5.1929 21 1 1 1 0 4.4079 22 1 1 0 0 0.8077 23 1 1 -1 0 5.2711 24 1 1 1 -1 5.0097 25 1 1 0 -1 1.3403 26 1 1 -1 -1 5.6489 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3372 atoms have been selected out of 3446 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 762 254 254 0.00 3 C003 has 108 36 36 0.00 4 C004 has 645 215 215 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1707 560 558 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 108 36 36 0.00 13 C013 has 474 158 158 0.00 14 C014 has 126 42 42 0.55 Total of12608 atoms and 4187 groups and 4180 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3446 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1137 Number of atoms = 3446 Number of groups = 1142 Number of bonds = 3439 Number of angles = 1241 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1139 Number of HB donors = 2256 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1137 Number of atoms = 3446 Number of groups = 1142 Number of bonds = 3439 Number of angles = 1241 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1139 Number of HB donors = 2256 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.384" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1137" Evaluating: 1137-7 Parameter: NUMWAT <- "1130" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1130" Comparing "1081" and "1130". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.384" Parameter: BOX -> "32.384" Parameter: BOX -> "32.384" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.38400 B = 32.38400 C = 32.38400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6444 2 1 -1 0 -1 1.3810 3 1 -1 1 -1 5.1900 4 1 0 -1 -1 4.5338 5 1 0 0 -1 0.6468 6 1 0 1 -1 1.3179 7 1 -1 -1 0 4.4062 8 1 -1 0 0 0.8065 9 1 -1 1 0 5.2683 10 1 0 -1 0 0.4630 11 1 0 1 0 0.4630 12 1 -1 -1 1 5.0071 13 1 -1 0 1 1.3387 14 1 -1 1 1 5.6461 15 1 0 -1 1 1.3179 16 1 0 0 1 0.6468 17 1 0 1 1 4.5338 18 1 1 1 1 5.6444 19 1 1 0 1 1.3810 20 1 1 -1 1 5.1900 21 1 1 1 0 4.4062 22 1 1 0 0 0.8065 23 1 1 -1 0 5.2683 24 1 1 1 -1 5.0071 25 1 1 0 -1 1.3387 26 1 1 -1 -1 5.6461 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3372 atoms have been selected out of 3446 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 762 254 254 0.00 3 C003 has 108 36 36 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 450 150 150 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1707 560 558 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 108 36 36 0.00 13 C013 has 474 158 158 0.00 14 C014 has 126 42 42 0.54 Total of12617 atoms and 4190 groups and 4183 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3446 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1137 Number of atoms = 3446 Number of groups = 1142 Number of bonds = 3439 Number of angles = 1241 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1139 Number of HB donors = 2256 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1137 Number of atoms = 3446 Number of groups = 1142 Number of bonds = 3439 Number of angles = 1241 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1139 Number of HB donors = 2256 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.382" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1137" Evaluating: 1137-7 Parameter: NUMWAT <- "1130" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1130" Comparing "1081" and "1130". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.382" Parameter: BOX -> "32.382" Parameter: BOX -> "32.382" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.38200 B = 32.38200 C = 32.38200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6435 2 1 -1 0 -1 1.3786 3 1 -1 1 -1 5.1871 4 1 0 -1 -1 4.5320 5 1 0 0 -1 0.6456 6 1 0 1 -1 1.3156 7 1 -1 -1 0 4.4046 8 1 -1 0 0 0.8052 9 1 -1 1 0 5.2654 10 1 0 -1 0 0.4616 11 1 0 1 0 0.4616 12 1 -1 -1 1 5.0045 13 1 -1 0 1 1.3372 14 1 -1 1 1 5.6432 15 1 0 -1 1 1.3156 16 1 0 0 1 0.6456 17 1 0 1 1 4.5320 18 1 1 1 1 5.6435 19 1 1 0 1 1.3786 20 1 1 -1 1 5.1871 21 1 1 1 0 4.4046 22 1 1 0 0 0.8052 23 1 1 -1 0 5.2654 24 1 1 1 -1 5.0045 25 1 1 0 -1 1.3372 26 1 1 -1 -1 5.6432 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3372 atoms have been selected out of 3446 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 765 255 255 0.00 3 C003 has 108 36 36 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 450 150 150 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1707 560 558 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 108 36 36 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.54 Total of12626 atoms and 4193 groups and 4186 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3446 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1137 Number of atoms = 3446 Number of groups = 1142 Number of bonds = 3439 Number of angles = 1241 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1139 Number of HB donors = 2256 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1137 Number of atoms = 3446 Number of groups = 1142 Number of bonds = 3439 Number of angles = 1241 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1139 Number of HB donors = 2256 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.38" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1137" Evaluating: 1137-7 Parameter: NUMWAT <- "1130" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1130" Comparing "1081" and "1130". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.38" Parameter: BOX -> "32.38" Parameter: BOX -> "32.38" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.38000 B = 32.38000 C = 32.38000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6425 2 1 -1 0 -1 1.3763 3 1 -1 1 -1 5.1842 4 1 0 -1 -1 4.5303 5 1 0 0 -1 0.6444 6 1 0 1 -1 1.3132 7 1 -1 -1 0 4.4030 8 1 -1 0 0 0.8040 9 1 -1 1 0 5.2626 10 1 0 -1 0 0.4602 11 1 0 1 0 0.4602 12 1 -1 -1 1 5.0019 13 1 -1 0 1 1.3357 14 1 -1 1 1 5.6404 15 1 0 -1 1 1.3132 16 1 0 0 1 0.6444 17 1 0 1 1 4.5303 18 1 1 1 1 5.6425 19 1 1 0 1 1.3763 20 1 1 -1 1 5.1842 21 1 1 1 0 4.4030 22 1 1 0 0 0.8040 23 1 1 -1 0 5.2626 24 1 1 1 -1 5.0019 25 1 1 0 -1 1.3357 26 1 1 -1 -1 5.6404 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3372 atoms have been selected out of 3446 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1050 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 762 254 254 0.00 3 C003 has 108 36 36 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 450 150 150 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1713 562 560 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 108 36 36 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 0.54 Total of12626 atoms and 4193 groups and 4186 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3446 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1136 Number of atoms = 3443 Number of groups = 1141 Number of bonds = 3436 Number of angles = 1240 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1138 Number of HB donors = 2254 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1136 Number of atoms = 3443 Number of groups = 1141 Number of bonds = 3436 Number of angles = 1240 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1138 Number of HB donors = 2254 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.378" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1136" Evaluating: 1136-7 Parameter: NUMWAT <- "1129" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1129" Comparing "1081" and "1129". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.378" Parameter: BOX -> "32.378" Parameter: BOX -> "32.378" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.37800 B = 32.37800 C = 32.37800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6415 2 1 -1 0 -1 1.3740 3 1 -1 1 -1 5.1814 4 1 0 -1 -1 4.5285 5 1 0 0 -1 0.6431 6 1 0 1 -1 1.3109 7 1 -1 -1 0 4.4014 8 1 -1 0 0 0.8028 9 1 -1 1 0 5.2598 10 1 0 -1 0 0.4588 11 1 0 1 0 0.4588 12 1 -1 -1 1 4.9993 13 1 -1 0 1 1.3342 14 1 -1 1 1 5.6375 15 1 0 -1 1 1.3109 16 1 0 0 1 0.6431 17 1 0 1 1 4.5285 18 1 1 1 1 5.6415 19 1 1 0 1 1.3740 20 1 1 -1 1 5.1814 21 1 1 1 0 4.4014 22 1 1 0 0 0.8028 23 1 1 -1 0 5.2598 24 1 1 1 -1 4.9993 25 1 1 0 -1 1.3342 26 1 1 -1 -1 5.6375 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3369 atoms have been selected out of 3443 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 762 254 254 0.00 3 C003 has 108 36 36 0.00 4 C004 has 645 215 215 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1704 559 557 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 108 36 36 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.54 Total of12611 atoms and 4188 groups and 4181 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3443 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1136 Number of atoms = 3443 Number of groups = 1141 Number of bonds = 3436 Number of angles = 1240 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1138 Number of HB donors = 2254 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1136 Number of atoms = 3443 Number of groups = 1141 Number of bonds = 3436 Number of angles = 1240 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1138 Number of HB donors = 2254 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.376" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1136" Evaluating: 1136-7 Parameter: NUMWAT <- "1129" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1129" Comparing "1081" and "1129". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.376" Parameter: BOX -> "32.376" Parameter: BOX -> "32.376" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.37600 B = 32.37600 C = 32.37600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6406 2 1 -1 0 -1 1.3716 3 1 -1 1 -1 5.1785 4 1 0 -1 -1 4.5268 5 1 0 0 -1 0.6419 6 1 0 1 -1 1.3085 7 1 -1 -1 0 4.3998 8 1 -1 0 0 0.8016 9 1 -1 1 0 5.2570 10 1 0 -1 0 0.4575 11 1 0 1 0 0.4575 12 1 -1 -1 1 4.9967 13 1 -1 0 1 1.3327 14 1 -1 1 1 5.6347 15 1 0 -1 1 1.3085 16 1 0 0 1 0.6419 17 1 0 1 1 4.5268 18 1 1 1 1 5.6406 19 1 1 0 1 1.3716 20 1 1 -1 1 5.1785 21 1 1 1 0 4.3998 22 1 1 0 0 0.8016 23 1 1 -1 0 5.2570 24 1 1 1 -1 4.9967 25 1 1 0 -1 1.3327 26 1 1 -1 -1 5.6347 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3369 atoms have been selected out of 3443 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 762 254 254 0.00 3 C003 has 108 36 36 0.00 4 C004 has 645 215 215 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1704 559 557 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 108 36 36 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.54 Total of12611 atoms and 4188 groups and 4181 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3443 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1136 Number of atoms = 3443 Number of groups = 1141 Number of bonds = 3436 Number of angles = 1240 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1138 Number of HB donors = 2254 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1136 Number of atoms = 3443 Number of groups = 1141 Number of bonds = 3436 Number of angles = 1240 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1138 Number of HB donors = 2254 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.374" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1136" Evaluating: 1136-7 Parameter: NUMWAT <- "1129" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1129" Comparing "1081" and "1129". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.374" Parameter: BOX -> "32.374" Parameter: BOX -> "32.374" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.37400 B = 32.37400 C = 32.37400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6397 2 1 -1 0 -1 1.3693 3 1 -1 1 -1 5.1756 4 1 0 -1 -1 4.5250 5 1 0 0 -1 0.6407 6 1 0 1 -1 1.3062 7 1 -1 -1 0 4.3982 8 1 -1 0 0 0.8003 9 1 -1 1 0 5.2542 10 1 0 -1 0 0.4561 11 1 0 1 0 0.4561 12 1 -1 -1 1 4.9941 13 1 -1 0 1 1.3312 14 1 -1 1 1 5.6318 15 1 0 -1 1 1.3062 16 1 0 0 1 0.6407 17 1 0 1 1 4.5250 18 1 1 1 1 5.6397 19 1 1 0 1 1.3693 20 1 1 -1 1 5.1756 21 1 1 1 0 4.3982 22 1 1 0 0 0.8003 23 1 1 -1 0 5.2542 24 1 1 1 -1 4.9941 25 1 1 0 -1 1.3312 26 1 1 -1 -1 5.6318 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3369 atoms have been selected out of 3443 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 762 254 254 0.00 3 C003 has 108 36 36 0.00 4 C004 has 645 215 215 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1704 559 557 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 108 36 36 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.53 Total of12611 atoms and 4188 groups and 4181 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3443 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1136 Number of atoms = 3443 Number of groups = 1141 Number of bonds = 3436 Number of angles = 1240 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1138 Number of HB donors = 2254 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1136 Number of atoms = 3443 Number of groups = 1141 Number of bonds = 3436 Number of angles = 1240 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1138 Number of HB donors = 2254 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.372" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1136" Evaluating: 1136-7 Parameter: NUMWAT <- "1129" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1129" Comparing "1081" and "1129". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.372" Parameter: BOX -> "32.372" Parameter: BOX -> "32.372" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.37200 B = 32.37200 C = 32.37200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6387 2 1 -1 0 -1 1.3669 3 1 -1 1 -1 5.1728 4 1 0 -1 -1 4.5232 5 1 0 0 -1 0.6394 6 1 0 1 -1 1.3038 7 1 -1 -1 0 4.3965 8 1 -1 0 0 0.7991 9 1 -1 1 0 5.2513 10 1 0 -1 0 0.4547 11 1 0 1 0 0.4547 12 1 -1 -1 1 4.9915 13 1 -1 0 1 1.3297 14 1 -1 1 1 5.6290 15 1 0 -1 1 1.3038 16 1 0 0 1 0.6394 17 1 0 1 1 4.5232 18 1 1 1 1 5.6387 19 1 1 0 1 1.3669 20 1 1 -1 1 5.1728 21 1 1 1 0 4.3965 22 1 1 0 0 0.7991 23 1 1 -1 0 5.2513 24 1 1 1 -1 4.9915 25 1 1 0 -1 1.3297 26 1 1 -1 -1 5.6290 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3369 atoms have been selected out of 3443 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 318 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 645 215 215 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1707 560 558 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 111 37 37 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 0.53 Total of12623 atoms and 4192 groups and 4185 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3443 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1135 Number of atoms = 3440 Number of groups = 1140 Number of bonds = 3433 Number of angles = 1239 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1137 Number of HB donors = 2252 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1135 Number of atoms = 3440 Number of groups = 1140 Number of bonds = 3433 Number of angles = 1239 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1137 Number of HB donors = 2252 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.37" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1135" Evaluating: 1135-7 Parameter: NUMWAT <- "1128" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1128" Comparing "1081" and "1128". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.37" Parameter: BOX -> "32.37" Parameter: BOX -> "32.37" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.37000 B = 32.37000 C = 32.37000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6378 2 1 -1 0 -1 1.3646 3 1 -1 1 -1 5.1699 4 1 0 -1 -1 4.5215 5 1 0 0 -1 0.6382 6 1 0 1 -1 1.3015 7 1 -1 -1 0 4.3949 8 1 -1 0 0 0.7979 9 1 -1 1 0 5.2485 10 1 0 -1 0 0.4534 11 1 0 1 0 0.4534 12 1 -1 -1 1 4.9889 13 1 -1 0 1 1.3283 14 1 -1 1 1 5.6261 15 1 0 -1 1 1.3015 16 1 0 0 1 0.6382 17 1 0 1 1 4.5215 18 1 1 1 1 5.6378 19 1 1 0 1 1.3646 20 1 1 -1 1 5.1699 21 1 1 1 0 4.3949 22 1 1 0 0 0.7979 23 1 1 -1 0 5.2485 24 1 1 1 -1 4.9889 25 1 1 0 -1 1.3283 26 1 1 -1 -1 5.6261 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3366 atoms have been selected out of 3440 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1704 559 557 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 108 36 36 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 0.53 Total of12614 atoms and 4189 groups and 4182 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3440 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1135 Number of atoms = 3440 Number of groups = 1140 Number of bonds = 3433 Number of angles = 1239 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1137 Number of HB donors = 2252 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1135 Number of atoms = 3440 Number of groups = 1140 Number of bonds = 3433 Number of angles = 1239 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1137 Number of HB donors = 2252 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.368" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1135" Evaluating: 1135-7 Parameter: NUMWAT <- "1128" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1128" Comparing "1081" and "1128". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.368" Parameter: BOX -> "32.368" Parameter: BOX -> "32.368" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.36800 B = 32.36800 C = 32.36800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6368 2 1 -1 0 -1 1.3622 3 1 -1 1 -1 5.1670 4 1 0 -1 -1 4.5197 5 1 0 0 -1 0.6370 6 1 0 1 -1 1.2991 7 1 -1 -1 0 4.3933 8 1 -1 0 0 0.7967 9 1 -1 1 0 5.2457 10 1 0 -1 0 0.4520 11 1 0 1 0 0.4520 12 1 -1 -1 1 4.9863 13 1 -1 0 1 1.3268 14 1 -1 1 1 5.6233 15 1 0 -1 1 1.2991 16 1 0 0 1 0.6370 17 1 0 1 1 4.5197 18 1 1 1 1 5.6368 19 1 1 0 1 1.3622 20 1 1 -1 1 5.1670 21 1 1 1 0 4.3933 22 1 1 0 0 0.7967 23 1 1 -1 0 5.2457 24 1 1 1 -1 4.9863 25 1 1 0 -1 1.3268 26 1 1 -1 -1 5.6233 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3366 atoms have been selected out of 3440 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 759 253 253 0.00 3 C003 has 114 38 38 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1704 559 557 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 108 36 36 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 0.53 Total of12623 atoms and 4192 groups and 4185 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3440 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1135 Number of atoms = 3440 Number of groups = 1140 Number of bonds = 3433 Number of angles = 1239 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1137 Number of HB donors = 2252 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1135 Number of atoms = 3440 Number of groups = 1140 Number of bonds = 3433 Number of angles = 1239 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1137 Number of HB donors = 2252 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.366" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1135" Evaluating: 1135-7 Parameter: NUMWAT <- "1128" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1128" Comparing "1081" and "1128". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.366" Parameter: BOX -> "32.366" Parameter: BOX -> "32.366" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.36600 B = 32.36600 C = 32.36600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6359 2 1 -1 0 -1 1.3599 3 1 -1 1 -1 5.1642 4 1 0 -1 -1 4.5180 5 1 0 0 -1 0.6358 6 1 0 1 -1 1.2968 7 1 -1 -1 0 4.3917 8 1 -1 0 0 0.7955 9 1 -1 1 0 5.2429 10 1 0 -1 0 0.4507 11 1 0 1 0 0.4507 12 1 -1 -1 1 4.9837 13 1 -1 0 1 1.3253 14 1 -1 1 1 5.6204 15 1 0 -1 1 1.2968 16 1 0 0 1 0.6358 17 1 0 1 1 4.5180 18 1 1 1 1 5.6359 19 1 1 0 1 1.3599 20 1 1 -1 1 5.1642 21 1 1 1 0 4.3917 22 1 1 0 0 0.7955 23 1 1 -1 0 5.2429 24 1 1 1 -1 4.9837 25 1 1 0 -1 1.3253 26 1 1 -1 -1 5.6204 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3366 atoms have been selected out of 3440 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 759 253 253 0.00 3 C003 has 114 38 38 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1704 559 557 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 108 36 36 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 0.53 Total of12623 atoms and 4192 groups and 4185 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3440 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1135 Number of atoms = 3440 Number of groups = 1140 Number of bonds = 3433 Number of angles = 1239 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1137 Number of HB donors = 2252 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1135 Number of atoms = 3440 Number of groups = 1140 Number of bonds = 3433 Number of angles = 1239 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1137 Number of HB donors = 2252 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.364" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1135" Evaluating: 1135-7 Parameter: NUMWAT <- "1128" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1128" Comparing "1081" and "1128". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.364" Parameter: BOX -> "32.364" Parameter: BOX -> "32.364" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.36400 B = 32.36400 C = 32.36400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6350 2 1 -1 0 -1 1.3576 3 1 -1 1 -1 5.1613 4 1 0 -1 -1 4.5162 5 1 0 0 -1 0.6346 6 1 0 1 -1 1.2944 7 1 -1 -1 0 4.3901 8 1 -1 0 0 0.7942 9 1 -1 1 0 5.2400 10 1 0 -1 0 0.4493 11 1 0 1 0 0.4493 12 1 -1 -1 1 4.9812 13 1 -1 0 1 1.3238 14 1 -1 1 1 5.6176 15 1 0 -1 1 1.2944 16 1 0 0 1 0.6346 17 1 0 1 1 4.5162 18 1 1 1 1 5.6350 19 1 1 0 1 1.3576 20 1 1 -1 1 5.1613 21 1 1 1 0 4.3901 22 1 1 0 0 0.7942 23 1 1 -1 0 5.2400 24 1 1 1 -1 4.9812 25 1 1 0 -1 1.3238 26 1 1 -1 -1 5.6176 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3366 atoms have been selected out of 3440 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 759 253 253 0.00 3 C003 has 114 38 38 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1704 559 557 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 108 36 36 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 0.52 Total of12623 atoms and 4192 groups and 4185 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3440 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1135 Number of atoms = 3440 Number of groups = 1140 Number of bonds = 3433 Number of angles = 1239 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1137 Number of HB donors = 2252 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1135 Number of atoms = 3440 Number of groups = 1140 Number of bonds = 3433 Number of angles = 1239 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1137 Number of HB donors = 2252 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.362" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1135" Evaluating: 1135-7 Parameter: NUMWAT <- "1128" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1128" Comparing "1081" and "1128". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.362" Parameter: BOX -> "32.362" Parameter: BOX -> "32.362" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.36200 B = 32.36200 C = 32.36200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6340 2 1 -1 0 -1 1.3552 3 1 -1 1 -1 5.1584 4 1 0 -1 -1 4.5145 5 1 0 0 -1 0.6333 6 1 0 1 -1 1.2921 7 1 -1 -1 0 4.3885 8 1 -1 0 0 0.7930 9 1 -1 1 0 5.2372 10 1 0 -1 0 0.4480 11 1 0 1 0 0.4480 12 1 -1 -1 1 4.9786 13 1 -1 0 1 1.3224 14 1 -1 1 1 5.6148 15 1 0 -1 1 1.2921 16 1 0 0 1 0.6333 17 1 0 1 1 4.5145 18 1 1 1 1 5.6340 19 1 1 0 1 1.3552 20 1 1 -1 1 5.1584 21 1 1 1 0 4.3885 22 1 1 0 0 0.7930 23 1 1 -1 0 5.2372 24 1 1 1 -1 4.9786 25 1 1 0 -1 1.3224 26 1 1 -1 -1 5.6148 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3366 atoms have been selected out of 3440 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 34 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 759 253 253 0.00 3 C003 has 114 38 38 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1704 559 557 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 108 36 36 0.00 13 C013 has 483 161 161 0.00 14 C014 has 126 42 42 0.52 Total of12629 atoms and 4194 groups and 4187 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3440 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1134 Number of atoms = 3437 Number of groups = 1139 Number of bonds = 3430 Number of angles = 1238 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1136 Number of HB donors = 2250 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1134 Number of atoms = 3437 Number of groups = 1139 Number of bonds = 3430 Number of angles = 1238 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1136 Number of HB donors = 2250 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.36" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1134" Evaluating: 1134-7 Parameter: NUMWAT <- "1127" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1127" Comparing "1081" and "1127". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.36" Parameter: BOX -> "32.36" Parameter: BOX -> "32.36" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.36000 B = 32.36000 C = 32.36000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6331 2 1 -1 0 -1 1.3529 3 1 -1 1 -1 5.1556 4 1 0 -1 -1 4.5127 5 1 0 0 -1 0.6321 6 1 0 1 -1 1.2898 7 1 -1 -1 0 4.3869 8 1 -1 0 0 0.7918 9 1 -1 1 0 5.2344 10 1 0 -1 0 0.4467 11 1 0 1 0 0.4467 12 1 -1 -1 1 4.9760 13 1 -1 0 1 1.3209 14 1 -1 1 1 5.6119 15 1 0 -1 1 1.2898 16 1 0 0 1 0.6321 17 1 0 1 1 4.5127 18 1 1 1 1 5.6331 19 1 1 0 1 1.3529 20 1 1 -1 1 5.1556 21 1 1 1 0 4.3869 22 1 1 0 0 0.7918 23 1 1 -1 0 5.2344 24 1 1 1 -1 4.9760 25 1 1 0 -1 1.3209 26 1 1 -1 -1 5.6119 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3363 atoms have been selected out of 3437 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 129 OPERATED ON BY TRANSFORMATION C016 RESIDUE 149 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 453 151 151 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1701 558 556 0.00 9 C009 has 420 140 140 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 108 36 36 0.00 13 C013 has 483 161 161 0.00 14 C014 has 126 42 42 0.52 Total of12635 atoms and 4196 groups and 4189 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3437 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1132 Number of atoms = 3431 Number of groups = 1137 Number of bonds = 3424 Number of angles = 1236 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1134 Number of HB donors = 2246 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1132 Number of atoms = 3431 Number of groups = 1137 Number of bonds = 3424 Number of angles = 1236 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1134 Number of HB donors = 2246 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.358" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1132" Evaluating: 1132-7 Parameter: NUMWAT <- "1125" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1125" Comparing "1081" and "1125". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.358" Parameter: BOX -> "32.358" Parameter: BOX -> "32.358" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.35800 B = 32.35800 C = 32.35800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6322 2 1 -1 0 -1 1.3506 3 1 -1 1 -1 5.1527 4 1 0 -1 -1 4.5110 5 1 0 0 -1 0.6309 6 1 0 1 -1 1.2874 7 1 -1 -1 0 4.3853 8 1 -1 0 0 0.7906 9 1 -1 1 0 5.2316 10 1 0 -1 0 0.4453 11 1 0 1 0 0.4453 12 1 -1 -1 1 4.9734 13 1 -1 0 1 1.3194 14 1 -1 1 1 5.6091 15 1 0 -1 1 1.2874 16 1 0 0 1 0.6309 17 1 0 1 1 4.5110 18 1 1 1 1 5.6322 19 1 1 0 1 1.3506 20 1 1 -1 1 5.1527 21 1 1 1 0 4.3853 22 1 1 0 0 0.7906 23 1 1 -1 0 5.2316 24 1 1 1 -1 4.9734 25 1 1 0 -1 1.3194 26 1 1 -1 -1 5.6091 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3357 atoms have been selected out of 3431 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 759 253 253 0.00 3 C003 has 114 38 38 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1701 558 556 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 108 36 36 0.00 13 C013 has 483 161 161 0.00 14 C014 has 126 42 42 0.52 Total of12620 atoms and 4191 groups and 4184 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3431 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1132 Number of atoms = 3431 Number of groups = 1137 Number of bonds = 3424 Number of angles = 1236 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1134 Number of HB donors = 2246 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1132 Number of atoms = 3431 Number of groups = 1137 Number of bonds = 3424 Number of angles = 1236 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1134 Number of HB donors = 2246 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.356" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1132" Evaluating: 1132-7 Parameter: NUMWAT <- "1125" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1125" Comparing "1081" and "1125". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.356" Parameter: BOX -> "32.356" Parameter: BOX -> "32.356" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.35600 B = 32.35600 C = 32.35600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6312 2 1 -1 0 -1 1.3482 3 1 -1 1 -1 5.1498 4 1 0 -1 -1 4.5093 5 1 0 0 -1 0.6297 6 1 0 1 -1 1.2851 7 1 -1 -1 0 4.3837 8 1 -1 0 0 0.7894 9 1 -1 1 0 5.2287 10 1 0 -1 0 0.4440 11 1 0 1 0 0.4440 12 1 -1 -1 1 4.9708 13 1 -1 0 1 1.3180 14 1 -1 1 1 5.6062 15 1 0 -1 1 1.2851 16 1 0 0 1 0.6297 17 1 0 1 1 4.5093 18 1 1 1 1 5.6312 19 1 1 0 1 1.3482 20 1 1 -1 1 5.1498 21 1 1 1 0 4.3837 22 1 1 0 0 0.7894 23 1 1 -1 0 5.2287 24 1 1 1 -1 4.9708 25 1 1 0 -1 1.3180 26 1 1 -1 -1 5.6062 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3357 atoms have been selected out of 3431 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 759 253 253 0.00 3 C003 has 114 38 38 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1701 558 556 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 108 36 36 0.00 13 C013 has 486 162 162 0.00 14 C014 has 126 42 42 0.52 Total of12623 atoms and 4192 groups and 4185 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3431 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1132 Number of atoms = 3431 Number of groups = 1137 Number of bonds = 3424 Number of angles = 1236 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1134 Number of HB donors = 2246 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1132 Number of atoms = 3431 Number of groups = 1137 Number of bonds = 3424 Number of angles = 1236 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1134 Number of HB donors = 2246 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.354" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1132" Evaluating: 1132-7 Parameter: NUMWAT <- "1125" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1125" Comparing "1081" and "1125". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.354" Parameter: BOX -> "32.354" Parameter: BOX -> "32.354" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.35400 B = 32.35400 C = 32.35400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6303 2 1 -1 0 -1 1.3459 3 1 -1 1 -1 5.1470 4 1 0 -1 -1 4.5075 5 1 0 0 -1 0.6286 6 1 0 1 -1 1.2828 7 1 -1 -1 0 4.3821 8 1 -1 0 0 0.7882 9 1 -1 1 0 5.2259 10 1 0 -1 0 0.4427 11 1 0 1 0 0.4427 12 1 -1 -1 1 4.9683 13 1 -1 0 1 1.3165 14 1 -1 1 1 5.6034 15 1 0 -1 1 1.2828 16 1 0 0 1 0.6286 17 1 0 1 1 4.5075 18 1 1 1 1 5.6303 19 1 1 0 1 1.3459 20 1 1 -1 1 5.1470 21 1 1 1 0 4.3821 22 1 1 0 0 0.7882 23 1 1 -1 0 5.2259 24 1 1 1 -1 4.9683 25 1 1 0 -1 1.3165 26 1 1 -1 -1 5.6034 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3357 atoms have been selected out of 3431 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 759 253 253 0.00 3 C003 has 114 38 38 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1701 558 556 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 108 36 36 0.00 13 C013 has 486 162 162 0.00 14 C014 has 126 42 42 0.51 Total of12623 atoms and 4192 groups and 4185 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3431 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1132 Number of atoms = 3431 Number of groups = 1137 Number of bonds = 3424 Number of angles = 1236 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1134 Number of HB donors = 2246 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1132 Number of atoms = 3431 Number of groups = 1137 Number of bonds = 3424 Number of angles = 1236 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1134 Number of HB donors = 2246 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.352" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1132" Evaluating: 1132-7 Parameter: NUMWAT <- "1125" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1125" Comparing "1081" and "1125". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.352" Parameter: BOX -> "32.352" Parameter: BOX -> "32.352" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.35200 B = 32.35200 C = 32.35200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6294 2 1 -1 0 -1 1.3436 3 1 -1 1 -1 5.1441 4 1 0 -1 -1 4.5058 5 1 0 0 -1 0.6274 6 1 0 1 -1 1.2804 7 1 -1 -1 0 4.3805 8 1 -1 0 0 0.7871 9 1 -1 1 0 5.2231 10 1 0 -1 0 0.4414 11 1 0 1 0 0.4414 12 1 -1 -1 1 4.9657 13 1 -1 0 1 1.3151 14 1 -1 1 1 5.6006 15 1 0 -1 1 1.2804 16 1 0 0 1 0.6274 17 1 0 1 1 4.5058 18 1 1 1 1 5.6294 19 1 1 0 1 1.3436 20 1 1 -1 1 5.1441 21 1 1 1 0 4.3805 22 1 1 0 0 0.7871 23 1 1 -1 0 5.2231 24 1 1 1 -1 4.9657 25 1 1 0 -1 1.3151 26 1 1 -1 -1 5.6006 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3357 atoms have been selected out of 3431 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 759 253 253 0.00 3 C003 has 114 38 38 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1701 558 556 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 108 36 36 0.00 13 C013 has 486 162 162 0.00 14 C014 has 126 42 42 0.51 Total of12626 atoms and 4193 groups and 4186 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3431 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1132 Number of atoms = 3431 Number of groups = 1137 Number of bonds = 3424 Number of angles = 1236 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1134 Number of HB donors = 2246 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1132 Number of atoms = 3431 Number of groups = 1137 Number of bonds = 3424 Number of angles = 1236 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1134 Number of HB donors = 2246 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.35" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1132" Evaluating: 1132-7 Parameter: NUMWAT <- "1125" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1125" Comparing "1081" and "1125". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.35" Parameter: BOX -> "32.35" Parameter: BOX -> "32.35" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.35000 B = 32.35000 C = 32.35000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6285 2 1 -1 0 -1 1.3413 3 1 -1 1 -1 5.1413 4 1 0 -1 -1 4.5040 5 1 0 0 -1 0.6262 6 1 0 1 -1 1.2781 7 1 -1 -1 0 4.3789 8 1 -1 0 0 0.7859 9 1 -1 1 0 5.2203 10 1 0 -1 0 0.4401 11 1 0 1 0 0.4401 12 1 -1 -1 1 4.9631 13 1 -1 0 1 1.3136 14 1 -1 1 1 5.5977 15 1 0 -1 1 1.2781 16 1 0 0 1 0.6262 17 1 0 1 1 4.5040 18 1 1 1 1 5.6285 19 1 1 0 1 1.3413 20 1 1 -1 1 5.1413 21 1 1 1 0 4.3789 22 1 1 0 0 0.7859 23 1 1 -1 0 5.2203 24 1 1 1 -1 4.9631 25 1 1 0 -1 1.3136 26 1 1 -1 -1 5.5977 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3357 atoms have been selected out of 3431 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 759 253 253 0.00 3 C003 has 114 38 38 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1701 558 556 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 108 36 36 0.00 13 C013 has 489 163 163 0.00 14 C014 has 126 42 42 0.51 Total of12632 atoms and 4195 groups and 4188 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3431 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1132 Number of atoms = 3431 Number of groups = 1137 Number of bonds = 3424 Number of angles = 1236 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1134 Number of HB donors = 2246 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1132 Number of atoms = 3431 Number of groups = 1137 Number of bonds = 3424 Number of angles = 1236 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1134 Number of HB donors = 2246 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.348" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1132" Evaluating: 1132-7 Parameter: NUMWAT <- "1125" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1125" Comparing "1081" and "1125". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.348" Parameter: BOX -> "32.348" Parameter: BOX -> "32.348" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.34800 B = 32.34800 C = 32.34800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6275 2 1 -1 0 -1 1.3389 3 1 -1 1 -1 5.1384 4 1 0 -1 -1 4.5023 5 1 0 0 -1 0.6250 6 1 0 1 -1 1.2758 7 1 -1 -1 0 4.3773 8 1 -1 0 0 0.7847 9 1 -1 1 0 5.2175 10 1 0 -1 0 0.4388 11 1 0 1 0 0.4388 12 1 -1 -1 1 4.9605 13 1 -1 0 1 1.3122 14 1 -1 1 1 5.5949 15 1 0 -1 1 1.2758 16 1 0 0 1 0.6250 17 1 0 1 1 4.5023 18 1 1 1 1 5.6275 19 1 1 0 1 1.3389 20 1 1 -1 1 5.1384 21 1 1 1 0 4.3773 22 1 1 0 0 0.7847 23 1 1 -1 0 5.2175 24 1 1 1 -1 4.9605 25 1 1 0 -1 1.3122 26 1 1 -1 -1 5.5949 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3357 atoms have been selected out of 3431 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 759 253 253 0.00 3 C003 has 114 38 38 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1701 558 556 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 108 36 36 0.00 13 C013 has 489 163 163 0.00 14 C014 has 126 42 42 0.51 Total of12632 atoms and 4195 groups and 4188 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3431 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1132 Number of atoms = 3431 Number of groups = 1137 Number of bonds = 3424 Number of angles = 1236 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1134 Number of HB donors = 2246 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1132 Number of atoms = 3431 Number of groups = 1137 Number of bonds = 3424 Number of angles = 1236 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1134 Number of HB donors = 2246 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.346" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1132" Evaluating: 1132-7 Parameter: NUMWAT <- "1125" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1125" Comparing "1081" and "1125". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.346" Parameter: BOX -> "32.346" Parameter: BOX -> "32.346" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.34600 B = 32.34600 C = 32.34600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6266 2 1 -1 0 -1 1.3366 3 1 -1 1 -1 5.1355 4 1 0 -1 -1 4.5005 5 1 0 0 -1 0.6238 6 1 0 1 -1 1.2735 7 1 -1 -1 0 4.3757 8 1 -1 0 0 0.7835 9 1 -1 1 0 5.2146 10 1 0 -1 0 0.4375 11 1 0 1 0 0.4375 12 1 -1 -1 1 4.9579 13 1 -1 0 1 1.3108 14 1 -1 1 1 5.5921 15 1 0 -1 1 1.2735 16 1 0 0 1 0.6238 17 1 0 1 1 4.5005 18 1 1 1 1 5.6266 19 1 1 0 1 1.3366 20 1 1 -1 1 5.1355 21 1 1 1 0 4.3757 22 1 1 0 0 0.7835 23 1 1 -1 0 5.2146 24 1 1 1 -1 4.9579 25 1 1 0 -1 1.3108 26 1 1 -1 -1 5.5921 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3357 atoms have been selected out of 3431 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 759 253 253 0.00 3 C003 has 114 38 38 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1701 558 556 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 108 36 36 0.00 13 C013 has 489 163 163 0.00 14 C014 has 126 42 42 0.51 Total of12632 atoms and 4195 groups and 4188 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3431 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1132 Number of atoms = 3431 Number of groups = 1137 Number of bonds = 3424 Number of angles = 1236 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1134 Number of HB donors = 2246 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1132 Number of atoms = 3431 Number of groups = 1137 Number of bonds = 3424 Number of angles = 1236 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1134 Number of HB donors = 2246 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.344" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1132" Evaluating: 1132-7 Parameter: NUMWAT <- "1125" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1125" Comparing "1081" and "1125". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.344" Parameter: BOX -> "32.344" Parameter: BOX -> "32.344" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.34400 B = 32.34400 C = 32.34400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6257 2 1 -1 0 -1 1.3343 3 1 -1 1 -1 5.1327 4 1 0 -1 -1 4.4988 5 1 0 0 -1 0.6227 6 1 0 1 -1 1.2711 7 1 -1 -1 0 4.3741 8 1 -1 0 0 0.7823 9 1 -1 1 0 5.2118 10 1 0 -1 0 0.4362 11 1 0 1 0 0.4362 12 1 -1 -1 1 4.9554 13 1 -1 0 1 1.3093 14 1 -1 1 1 5.5892 15 1 0 -1 1 1.2711 16 1 0 0 1 0.6227 17 1 0 1 1 4.4988 18 1 1 1 1 5.6257 19 1 1 0 1 1.3343 20 1 1 -1 1 5.1327 21 1 1 1 0 4.3741 22 1 1 0 0 0.7823 23 1 1 -1 0 5.2118 24 1 1 1 -1 4.9554 25 1 1 0 -1 1.3093 26 1 1 -1 -1 5.5892 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3357 atoms have been selected out of 3431 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 759 253 253 0.00 3 C003 has 114 38 38 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1701 558 556 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 108 36 36 0.00 13 C013 has 489 163 163 0.00 14 C014 has 126 42 42 0.50 Total of12632 atoms and 4195 groups and 4188 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3431 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1132 Number of atoms = 3431 Number of groups = 1137 Number of bonds = 3424 Number of angles = 1236 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1134 Number of HB donors = 2246 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1132 Number of atoms = 3431 Number of groups = 1137 Number of bonds = 3424 Number of angles = 1236 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1134 Number of HB donors = 2246 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.342" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1132" Evaluating: 1132-7 Parameter: NUMWAT <- "1125" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1125" Comparing "1081" and "1125". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.342" Parameter: BOX -> "32.342" Parameter: BOX -> "32.342" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.34200 B = 32.34200 C = 32.34200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6248 2 1 -1 0 -1 1.3320 3 1 -1 1 -1 5.1298 4 1 0 -1 -1 4.4971 5 1 0 0 -1 0.6215 6 1 0 1 -1 1.2688 7 1 -1 -1 0 4.3725 8 1 -1 0 0 0.7811 9 1 -1 1 0 5.2090 10 1 0 -1 0 0.4349 11 1 0 1 0 0.4349 12 1 -1 -1 1 4.9528 13 1 -1 0 1 1.3079 14 1 -1 1 1 5.5864 15 1 0 -1 1 1.2688 16 1 0 0 1 0.6215 17 1 0 1 1 4.4971 18 1 1 1 1 5.6248 19 1 1 0 1 1.3320 20 1 1 -1 1 5.1298 21 1 1 1 0 4.3725 22 1 1 0 0 0.7811 23 1 1 -1 0 5.2090 24 1 1 1 -1 4.9528 25 1 1 0 -1 1.3079 26 1 1 -1 -1 5.5864 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3357 atoms have been selected out of 3431 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 493 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1067 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.00 4 C004 has 651 217 217 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1698 557 555 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1596 532 532 0.00 12 C012 has 108 36 36 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 0.50 Total of12635 atoms and 4196 groups and 4189 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3431 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1130 Number of atoms = 3425 Number of groups = 1135 Number of bonds = 3418 Number of angles = 1234 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1132 Number of HB donors = 2242 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1130 Number of atoms = 3425 Number of groups = 1135 Number of bonds = 3418 Number of angles = 1234 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1132 Number of HB donors = 2242 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.34" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1130" Evaluating: 1130-7 Parameter: NUMWAT <- "1123" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1123" Comparing "1081" and "1123". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.34" Parameter: BOX -> "32.34" Parameter: BOX -> "32.34" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.34000 B = 32.34000 C = 32.34000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6239 2 1 -1 0 -1 1.3297 3 1 -1 1 -1 5.1270 4 1 0 -1 -1 4.4953 5 1 0 0 -1 0.6203 6 1 0 1 -1 1.2665 7 1 -1 -1 0 4.3709 8 1 -1 0 0 0.7800 9 1 -1 1 0 5.2062 10 1 0 -1 0 0.4336 11 1 0 1 0 0.4336 12 1 -1 -1 1 4.9502 13 1 -1 0 1 1.3065 14 1 -1 1 1 5.5836 15 1 0 -1 1 1.2665 16 1 0 0 1 0.6203 17 1 0 1 1 4.4953 18 1 1 1 1 5.6239 19 1 1 0 1 1.3297 20 1 1 -1 1 5.1270 21 1 1 1 0 4.3709 22 1 1 0 0 0.7800 23 1 1 -1 0 5.2062 24 1 1 1 -1 4.9502 25 1 1 0 -1 1.3065 26 1 1 -1 -1 5.5836 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3351 atoms have been selected out of 3425 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 756 252 252 0.00 3 C003 has 114 38 38 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1503 501 501 0.00 6 C006 has 450 150 150 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1698 557 555 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 108 36 36 0.00 13 C013 has 486 162 162 0.00 14 C014 has 126 42 42 0.50 Total of12614 atoms and 4189 groups and 4182 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3425 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1130 Number of atoms = 3425 Number of groups = 1135 Number of bonds = 3418 Number of angles = 1234 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1132 Number of HB donors = 2242 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1130 Number of atoms = 3425 Number of groups = 1135 Number of bonds = 3418 Number of angles = 1234 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1132 Number of HB donors = 2242 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.338" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1130" Evaluating: 1130-7 Parameter: NUMWAT <- "1123" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1123" Comparing "1081" and "1123". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.338" Parameter: BOX -> "32.338" Parameter: BOX -> "32.338" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.33800 B = 32.33800 C = 32.33800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6230 2 1 -1 0 -1 1.3274 3 1 -1 1 -1 5.1241 4 1 0 -1 -1 4.4936 5 1 0 0 -1 0.6192 6 1 0 1 -1 1.2642 7 1 -1 -1 0 4.3693 8 1 -1 0 0 0.7788 9 1 -1 1 0 5.2033 10 1 0 -1 0 0.4324 11 1 0 1 0 0.4324 12 1 -1 -1 1 4.9476 13 1 -1 0 1 1.3051 14 1 -1 1 1 5.5807 15 1 0 -1 1 1.2642 16 1 0 0 1 0.6192 17 1 0 1 1 4.4936 18 1 1 1 1 5.6230 19 1 1 0 1 1.3274 20 1 1 -1 1 5.1241 21 1 1 1 0 4.3693 22 1 1 0 0 0.7788 23 1 1 -1 0 5.2033 24 1 1 1 -1 4.9476 25 1 1 0 -1 1.3051 26 1 1 -1 -1 5.5807 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3351 atoms have been selected out of 3425 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 756 252 252 0.00 3 C003 has 114 38 38 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1503 501 501 0.00 6 C006 has 450 150 150 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1698 557 555 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 111 37 37 0.00 13 C013 has 489 163 163 0.00 14 C014 has 126 42 42 0.50 Total of12620 atoms and 4191 groups and 4184 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3425 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1130 Number of atoms = 3425 Number of groups = 1135 Number of bonds = 3418 Number of angles = 1234 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1132 Number of HB donors = 2242 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1130 Number of atoms = 3425 Number of groups = 1135 Number of bonds = 3418 Number of angles = 1234 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1132 Number of HB donors = 2242 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.336" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1130" Evaluating: 1130-7 Parameter: NUMWAT <- "1123" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1123" Comparing "1081" and "1123". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.336" Parameter: BOX -> "32.336" Parameter: BOX -> "32.336" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.33600 B = 32.33600 C = 32.33600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6221 2 1 -1 0 -1 1.3251 3 1 -1 1 -1 5.1213 4 1 0 -1 -1 4.4919 5 1 0 0 -1 0.6180 6 1 0 1 -1 1.2619 7 1 -1 -1 0 4.3677 8 1 -1 0 0 0.7776 9 1 -1 1 0 5.2005 10 1 0 -1 0 0.4311 11 1 0 1 0 0.4311 12 1 -1 -1 1 4.9451 13 1 -1 0 1 1.3037 14 1 -1 1 1 5.5779 15 1 0 -1 1 1.2619 16 1 0 0 1 0.6180 17 1 0 1 1 4.4919 18 1 1 1 1 5.6221 19 1 1 0 1 1.3251 20 1 1 -1 1 5.1213 21 1 1 1 0 4.3677 22 1 1 0 0 0.7776 23 1 1 -1 0 5.2005 24 1 1 1 -1 4.9451 25 1 1 0 -1 1.3037 26 1 1 -1 -1 5.5779 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3351 atoms have been selected out of 3425 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 756 252 252 0.00 3 C003 has 114 38 38 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1503 501 501 0.00 6 C006 has 450 150 150 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1698 557 555 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 111 37 37 0.00 13 C013 has 489 163 163 0.00 14 C014 has 126 42 42 0.50 Total of12620 atoms and 4191 groups and 4184 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3425 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1130 Number of atoms = 3425 Number of groups = 1135 Number of bonds = 3418 Number of angles = 1234 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1132 Number of HB donors = 2242 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1130 Number of atoms = 3425 Number of groups = 1135 Number of bonds = 3418 Number of angles = 1234 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1132 Number of HB donors = 2242 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.334" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1130" Evaluating: 1130-7 Parameter: NUMWAT <- "1123" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1123" Comparing "1081" and "1123". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.334" Parameter: BOX -> "32.334" Parameter: BOX -> "32.334" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.33400 B = 32.33400 C = 32.33400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6212 2 1 -1 0 -1 1.3228 3 1 -1 1 -1 5.1184 4 1 0 -1 -1 4.4901 5 1 0 0 -1 0.6169 6 1 0 1 -1 1.2596 7 1 -1 -1 0 4.3661 8 1 -1 0 0 0.7765 9 1 -1 1 0 5.1977 10 1 0 -1 0 0.4298 11 1 0 1 0 0.4298 12 1 -1 -1 1 4.9425 13 1 -1 0 1 1.3023 14 1 -1 1 1 5.5751 15 1 0 -1 1 1.2596 16 1 0 0 1 0.6169 17 1 0 1 1 4.4901 18 1 1 1 1 5.6212 19 1 1 0 1 1.3228 20 1 1 -1 1 5.1184 21 1 1 1 0 4.3661 22 1 1 0 0 0.7765 23 1 1 -1 0 5.1977 24 1 1 1 -1 4.9425 25 1 1 0 -1 1.3023 26 1 1 -1 -1 5.5751 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3351 atoms have been selected out of 3425 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 756 252 252 0.00 3 C003 has 114 38 38 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1698 557 555 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 0.49 Total of12626 atoms and 4193 groups and 4186 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3425 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1130 Number of atoms = 3425 Number of groups = 1135 Number of bonds = 3418 Number of angles = 1234 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1132 Number of HB donors = 2242 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1130 Number of atoms = 3425 Number of groups = 1135 Number of bonds = 3418 Number of angles = 1234 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1132 Number of HB donors = 2242 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.332" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1130" Evaluating: 1130-7 Parameter: NUMWAT <- "1123" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1123" Comparing "1081" and "1123". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.332" Parameter: BOX -> "32.332" Parameter: BOX -> "32.332" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.33200 B = 32.33200 C = 32.33200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6202 2 1 -1 0 -1 1.3205 3 1 -1 1 -1 5.1156 4 1 0 -1 -1 4.4884 5 1 0 0 -1 0.6157 6 1 0 1 -1 1.2572 7 1 -1 -1 0 4.3646 8 1 -1 0 0 0.7753 9 1 -1 1 0 5.1949 10 1 0 -1 0 0.4286 11 1 0 1 0 0.4286 12 1 -1 -1 1 4.9399 13 1 -1 0 1 1.3009 14 1 -1 1 1 5.5722 15 1 0 -1 1 1.2572 16 1 0 0 1 0.6157 17 1 0 1 1 4.4884 18 1 1 1 1 5.6202 19 1 1 0 1 1.3205 20 1 1 -1 1 5.1156 21 1 1 1 0 4.3646 22 1 1 0 0 0.7753 23 1 1 -1 0 5.1949 24 1 1 1 -1 4.9399 25 1 1 0 -1 1.3009 26 1 1 -1 -1 5.5722 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3351 atoms have been selected out of 3425 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 756 252 252 0.00 3 C003 has 114 38 38 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 801 267 267 0.00 8 C008 has 1698 557 555 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1593 531 531 0.00 12 C012 has 114 38 38 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 0.49 Total of12632 atoms and 4195 groups and 4188 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3425 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1130 Number of atoms = 3425 Number of groups = 1135 Number of bonds = 3418 Number of angles = 1234 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1132 Number of HB donors = 2242 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1130 Number of atoms = 3425 Number of groups = 1135 Number of bonds = 3418 Number of angles = 1234 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1132 Number of HB donors = 2242 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.33" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1130" Evaluating: 1130-7 Parameter: NUMWAT <- "1123" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1123" Comparing "1081" and "1123". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.33" Parameter: BOX -> "32.33" Parameter: BOX -> "32.33" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.33000 B = 32.33000 C = 32.33000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6193 2 1 -1 0 -1 1.3182 3 1 -1 1 -1 5.1127 4 1 0 -1 -1 4.4867 5 1 0 0 -1 0.6146 6 1 0 1 -1 1.2549 7 1 -1 -1 0 4.3630 8 1 -1 0 0 0.7742 9 1 -1 1 0 5.1921 10 1 0 -1 0 0.4273 11 1 0 1 0 0.4273 12 1 -1 -1 1 4.9374 13 1 -1 0 1 1.2995 14 1 -1 1 1 5.5694 15 1 0 -1 1 1.2549 16 1 0 0 1 0.6146 17 1 0 1 1 4.4867 18 1 1 1 1 5.6193 19 1 1 0 1 1.3182 20 1 1 -1 1 5.1127 21 1 1 1 0 4.3630 22 1 1 0 0 0.7742 23 1 1 -1 0 5.1921 24 1 1 1 -1 4.9374 25 1 1 0 -1 1.2995 26 1 1 -1 -1 5.5694 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3351 atoms have been selected out of 3425 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 428 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 759 253 253 0.00 3 C003 has 114 38 38 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1701 558 556 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 114 38 38 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 0.49 Total of12632 atoms and 4195 groups and 4188 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3425 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1129 Number of atoms = 3422 Number of groups = 1134 Number of bonds = 3415 Number of angles = 1233 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1131 Number of HB donors = 2240 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1129 Number of atoms = 3422 Number of groups = 1134 Number of bonds = 3415 Number of angles = 1233 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1131 Number of HB donors = 2240 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.328" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1129" Evaluating: 1129-7 Parameter: NUMWAT <- "1122" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1122" Comparing "1081" and "1122". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.328" Parameter: BOX -> "32.328" Parameter: BOX -> "32.328" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.32800 B = 32.32800 C = 32.32800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6184 2 1 -1 0 -1 1.3159 3 1 -1 1 -1 5.1099 4 1 0 -1 -1 4.4849 5 1 0 0 -1 0.6134 6 1 0 1 -1 1.2526 7 1 -1 -1 0 4.3614 8 1 -1 0 0 0.7730 9 1 -1 1 0 5.1892 10 1 0 -1 0 0.4261 11 1 0 1 0 0.4261 12 1 -1 -1 1 4.9348 13 1 -1 0 1 1.2981 14 1 -1 1 1 5.5666 15 1 0 -1 1 1.2526 16 1 0 0 1 0.6134 17 1 0 1 1 4.4849 18 1 1 1 1 5.6184 19 1 1 0 1 1.3159 20 1 1 -1 1 5.1099 21 1 1 1 0 4.3614 22 1 1 0 0 0.7730 23 1 1 -1 0 5.1892 24 1 1 1 -1 4.9348 25 1 1 0 -1 1.2981 26 1 1 -1 -1 5.5666 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3348 atoms have been selected out of 3422 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 759 253 253 0.00 3 C003 has 114 38 38 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1698 557 555 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 114 38 38 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 0.49 Total of12626 atoms and 4193 groups and 4186 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3422 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1129 Number of atoms = 3422 Number of groups = 1134 Number of bonds = 3415 Number of angles = 1233 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1131 Number of HB donors = 2240 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1129 Number of atoms = 3422 Number of groups = 1134 Number of bonds = 3415 Number of angles = 1233 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1131 Number of HB donors = 2240 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.326" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1129" Evaluating: 1129-7 Parameter: NUMWAT <- "1122" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1122" Comparing "1081" and "1122". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.326" Parameter: BOX -> "32.326" Parameter: BOX -> "32.326" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.32600 B = 32.32600 C = 32.32600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6175 2 1 -1 0 -1 1.3136 3 1 -1 1 -1 5.1070 4 1 0 -1 -1 4.4832 5 1 0 0 -1 0.6123 6 1 0 1 -1 1.2503 7 1 -1 -1 0 4.3598 8 1 -1 0 0 0.7719 9 1 -1 1 0 5.1864 10 1 0 -1 0 0.4248 11 1 0 1 0 0.4248 12 1 -1 -1 1 4.9322 13 1 -1 0 1 1.2967 14 1 -1 1 1 5.5637 15 1 0 -1 1 1.2503 16 1 0 0 1 0.6123 17 1 0 1 1 4.4832 18 1 1 1 1 5.6175 19 1 1 0 1 1.3136 20 1 1 -1 1 5.1070 21 1 1 1 0 4.3598 22 1 1 0 0 0.7719 23 1 1 -1 0 5.1864 24 1 1 1 -1 4.9322 25 1 1 0 -1 1.2967 26 1 1 -1 -1 5.5637 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3348 atoms have been selected out of 3422 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1698 557 555 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 114 38 38 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 0.49 Total of12632 atoms and 4195 groups and 4188 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3422 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1129 Number of atoms = 3422 Number of groups = 1134 Number of bonds = 3415 Number of angles = 1233 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1131 Number of HB donors = 2240 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1129 Number of atoms = 3422 Number of groups = 1134 Number of bonds = 3415 Number of angles = 1233 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1131 Number of HB donors = 2240 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.324" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1129" Evaluating: 1129-7 Parameter: NUMWAT <- "1122" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1122" Comparing "1081" and "1122". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.324" Parameter: BOX -> "32.324" Parameter: BOX -> "32.324" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.32400 B = 32.32400 C = 32.32400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6166 2 1 -1 0 -1 1.3113 3 1 -1 1 -1 5.1042 4 1 0 -1 -1 4.4815 5 1 0 0 -1 0.6112 6 1 0 1 -1 1.2480 7 1 -1 -1 0 4.3582 8 1 -1 0 0 0.7707 9 1 -1 1 0 5.1836 10 1 0 -1 0 0.4236 11 1 0 1 0 0.4236 12 1 -1 -1 1 4.9297 13 1 -1 0 1 1.2953 14 1 -1 1 1 5.5609 15 1 0 -1 1 1.2480 16 1 0 0 1 0.6112 17 1 0 1 1 4.4815 18 1 1 1 1 5.6166 19 1 1 0 1 1.3113 20 1 1 -1 1 5.1042 21 1 1 1 0 4.3582 22 1 1 0 0 0.7707 23 1 1 -1 0 5.1836 24 1 1 1 -1 4.9297 25 1 1 0 -1 1.2953 26 1 1 -1 -1 5.5609 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3348 atoms have been selected out of 3422 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 322 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 651 217 217 0.00 5 C005 has 1509 503 503 0.00 6 C006 has 450 150 150 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1698 557 555 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1590 530 530 0.00 12 C012 has 114 38 38 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 0.48 Total of12638 atoms and 4197 groups and 4190 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3422 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1128 Number of atoms = 3419 Number of groups = 1133 Number of bonds = 3412 Number of angles = 1232 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1130 Number of HB donors = 2238 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1128 Number of atoms = 3419 Number of groups = 1133 Number of bonds = 3412 Number of angles = 1232 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1130 Number of HB donors = 2238 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.322" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1128" Evaluating: 1128-7 Parameter: NUMWAT <- "1121" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1121" Comparing "1081" and "1121". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.322" Parameter: BOX -> "32.322" Parameter: BOX -> "32.322" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.32200 B = 32.32200 C = 32.32200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6158 2 1 -1 0 -1 1.3090 3 1 -1 1 -1 5.1013 4 1 0 -1 -1 4.4798 5 1 0 0 -1 0.6101 6 1 0 1 -1 1.2457 7 1 -1 -1 0 4.3566 8 1 -1 0 0 0.7696 9 1 -1 1 0 5.1808 10 1 0 -1 0 0.4224 11 1 0 1 0 0.4224 12 1 -1 -1 1 4.9271 13 1 -1 0 1 1.2940 14 1 -1 1 1 5.5581 15 1 0 -1 1 1.2457 16 1 0 0 1 0.6101 17 1 0 1 1 4.4798 18 1 1 1 1 5.6158 19 1 1 0 1 1.3090 20 1 1 -1 1 5.1013 21 1 1 1 0 4.3566 22 1 1 0 0 0.7696 23 1 1 -1 0 5.1808 24 1 1 1 -1 4.9271 25 1 1 0 -1 1.2940 26 1 1 -1 -1 5.5581 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3345 atoms have been selected out of 3419 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1698 557 555 0.00 9 C009 has 429 143 143 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 114 38 38 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 0.48 Total of12629 atoms and 4194 groups and 4187 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3419 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1128 Number of atoms = 3419 Number of groups = 1133 Number of bonds = 3412 Number of angles = 1232 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1130 Number of HB donors = 2238 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1128 Number of atoms = 3419 Number of groups = 1133 Number of bonds = 3412 Number of angles = 1232 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1130 Number of HB donors = 2238 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.32" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1128" Evaluating: 1128-7 Parameter: NUMWAT <- "1121" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1121" Comparing "1081" and "1121". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.32" Parameter: BOX -> "32.32" Parameter: BOX -> "32.32" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.32000 B = 32.32000 C = 32.32000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6149 2 1 -1 0 -1 1.3067 3 1 -1 1 -1 5.0985 4 1 0 -1 -1 4.4780 5 1 0 0 -1 0.6089 6 1 0 1 -1 1.2434 7 1 -1 -1 0 4.3551 8 1 -1 0 0 0.7685 9 1 -1 1 0 5.1779 10 1 0 -1 0 0.4211 11 1 0 1 0 0.4211 12 1 -1 -1 1 4.9246 13 1 -1 0 1 1.2926 14 1 -1 1 1 5.5553 15 1 0 -1 1 1.2434 16 1 0 0 1 0.6089 17 1 0 1 1 4.4780 18 1 1 1 1 5.6149 19 1 1 0 1 1.3067 20 1 1 -1 1 5.0985 21 1 1 1 0 4.3551 22 1 1 0 0 0.7685 23 1 1 -1 0 5.1779 24 1 1 1 -1 4.9246 25 1 1 0 -1 1.2926 26 1 1 -1 -1 5.5553 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3345 atoms have been selected out of 3419 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1704 559 557 0.00 9 C009 has 429 143 143 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 114 38 38 0.00 13 C013 has 495 165 165 0.00 14 C014 has 126 42 42 0.48 Total of12638 atoms and 4197 groups and 4190 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3419 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1128 Number of atoms = 3419 Number of groups = 1133 Number of bonds = 3412 Number of angles = 1232 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1130 Number of HB donors = 2238 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1128 Number of atoms = 3419 Number of groups = 1133 Number of bonds = 3412 Number of angles = 1232 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1130 Number of HB donors = 2238 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.318" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1128" Evaluating: 1128-7 Parameter: NUMWAT <- "1121" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1121" Comparing "1081" and "1121". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.318" Parameter: BOX -> "32.318" Parameter: BOX -> "32.318" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.31800 B = 32.31800 C = 32.31800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6140 2 1 -1 0 -1 1.3044 3 1 -1 1 -1 5.0956 4 1 0 -1 -1 4.4763 5 1 0 0 -1 0.6078 6 1 0 1 -1 1.2411 7 1 -1 -1 0 4.3535 8 1 -1 0 0 0.7673 9 1 -1 1 0 5.1751 10 1 0 -1 0 0.4199 11 1 0 1 0 0.4199 12 1 -1 -1 1 4.9220 13 1 -1 0 1 1.2912 14 1 -1 1 1 5.5524 15 1 0 -1 1 1.2411 16 1 0 0 1 0.6078 17 1 0 1 1 4.4763 18 1 1 1 1 5.6140 19 1 1 0 1 1.3044 20 1 1 -1 1 5.0956 21 1 1 1 0 4.3535 22 1 1 0 0 0.7673 23 1 1 -1 0 5.1751 24 1 1 1 -1 4.9220 25 1 1 0 -1 1.2912 26 1 1 -1 -1 5.5524 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3345 atoms have been selected out of 3419 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1704 559 557 0.00 9 C009 has 429 143 143 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 114 38 38 0.00 13 C013 has 495 165 165 0.00 14 C014 has 126 42 42 0.48 Total of12638 atoms and 4197 groups and 4190 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3419 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1128 Number of atoms = 3419 Number of groups = 1133 Number of bonds = 3412 Number of angles = 1232 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1130 Number of HB donors = 2238 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1128 Number of atoms = 3419 Number of groups = 1133 Number of bonds = 3412 Number of angles = 1232 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1130 Number of HB donors = 2238 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.316" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1128" Evaluating: 1128-7 Parameter: NUMWAT <- "1121" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1121" Comparing "1081" and "1121". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.316" Parameter: BOX -> "32.316" Parameter: BOX -> "32.316" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.31600 B = 32.31600 C = 32.31600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6131 2 1 -1 0 -1 1.3021 3 1 -1 1 -1 5.0928 4 1 0 -1 -1 4.4746 5 1 0 0 -1 0.6067 6 1 0 1 -1 1.2389 7 1 -1 -1 0 4.3519 8 1 -1 0 0 0.7662 9 1 -1 1 0 5.1723 10 1 0 -1 0 0.4187 11 1 0 1 0 0.4187 12 1 -1 -1 1 4.9194 13 1 -1 0 1 1.2899 14 1 -1 1 1 5.5496 15 1 0 -1 1 1.2389 16 1 0 0 1 0.6067 17 1 0 1 1 4.4746 18 1 1 1 1 5.6131 19 1 1 0 1 1.3021 20 1 1 -1 1 5.0928 21 1 1 1 0 4.3519 22 1 1 0 0 0.7662 23 1 1 -1 0 5.1723 24 1 1 1 -1 4.9194 25 1 1 0 -1 1.2899 26 1 1 -1 -1 5.5496 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3345 atoms have been selected out of 3419 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1704 559 557 0.00 9 C009 has 429 143 143 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 114 38 38 0.00 13 C013 has 495 165 165 0.00 14 C014 has 126 42 42 0.48 Total of12638 atoms and 4197 groups and 4190 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3419 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1128 Number of atoms = 3419 Number of groups = 1133 Number of bonds = 3412 Number of angles = 1232 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1130 Number of HB donors = 2238 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1128 Number of atoms = 3419 Number of groups = 1133 Number of bonds = 3412 Number of angles = 1232 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1130 Number of HB donors = 2238 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.314" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1128" Evaluating: 1128-7 Parameter: NUMWAT <- "1121" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1121" Comparing "1081" and "1121". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.314" Parameter: BOX -> "32.314" Parameter: BOX -> "32.314" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.31400 B = 32.31400 C = 32.31400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6122 2 1 -1 0 -1 1.2998 3 1 -1 1 -1 5.0899 4 1 0 -1 -1 4.4729 5 1 0 0 -1 0.6056 6 1 0 1 -1 1.2366 7 1 -1 -1 0 4.3503 8 1 -1 0 0 0.7651 9 1 -1 1 0 5.1695 10 1 0 -1 0 0.4175 11 1 0 1 0 0.4175 12 1 -1 -1 1 4.9169 13 1 -1 0 1 1.2885 14 1 -1 1 1 5.5468 15 1 0 -1 1 1.2366 16 1 0 0 1 0.6056 17 1 0 1 1 4.4729 18 1 1 1 1 5.6122 19 1 1 0 1 1.2998 20 1 1 -1 1 5.0899 21 1 1 1 0 4.3503 22 1 1 0 0 0.7651 23 1 1 -1 0 5.1695 24 1 1 1 -1 4.9169 25 1 1 0 -1 1.2885 26 1 1 -1 -1 5.5468 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3345 atoms have been selected out of 3419 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 450 150 150 0.00 7 C007 has 798 266 266 0.00 8 C008 has 1704 559 557 0.00 9 C009 has 429 143 143 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 114 38 38 0.00 13 C013 has 495 165 165 0.00 14 C014 has 126 42 42 0.47 Total of12638 atoms and 4197 groups and 4190 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3419 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1128 Number of atoms = 3419 Number of groups = 1133 Number of bonds = 3412 Number of angles = 1232 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1130 Number of HB donors = 2238 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1128 Number of atoms = 3419 Number of groups = 1133 Number of bonds = 3412 Number of angles = 1232 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1130 Number of HB donors = 2238 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.312" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1128" Evaluating: 1128-7 Parameter: NUMWAT <- "1121" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1121" Comparing "1081" and "1121". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.312" Parameter: BOX -> "32.312" Parameter: BOX -> "32.312" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.31200 B = 32.31200 C = 32.31200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 5.6113 2 1 -1 0 -1 1.2975 3 1 -1 1 -1 5.0871 4 1 0 -1 -1 4.4711 5 1 0 0 -1 0.6045 6 1 0 1 -1 1.2343 7 1 -1 -1 0 4.3487 8 1 -1 0 0 0.7640 9 1 -1 1 0 5.1667 10 1 0 -1 0 0.4163 11 1 0 1 0 0.4163 12 1 -1 -1 1 4.9143 13 1 -1 0 1 1.2871 14 1 -1 1 1 5.5440 15 1 0 -1 1 1.2343 16 1 0 0 1 0.6045 17 1 0 1 1 4.4711 18 1 1 1 1 5.6113 19 1 1 0 1 1.2975 20 1 1 -1 1 5.0871 21 1 1 1 0 4.3487 22 1 1 0 0 0.7640 23 1 1 -1 0 5.1667 24 1 1 1 -1 4.9143 25 1 1 0 -1 1.2871 26 1 1 -1 -1 5.5440 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3345 atoms have been selected out of 3419 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 475 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1055 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 774 258 258 0.00 3 C003 has 132 44 44 0.00 4 C004 has 648 216 216 0.00 5 C005 has 1506 502 502 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1701 558 556 0.00 9 C009 has 441 147 147 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 111 37 37 0.00 13 C013 has 507 169 169 0.00 14 C014 has 138 46 46 0.47 Total of12680 atoms and 4211 groups and 4204 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3419 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1126 Number of atoms = 3413 Number of groups = 1131 Number of bonds = 3406 Number of angles = 1230 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1128 Number of HB donors = 2234 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1126 Number of atoms = 3413 Number of groups = 1131 Number of bonds = 3406 Number of angles = 1230 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1128 Number of HB donors = 2234 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.31" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1126" Evaluating: 1126-7 Parameter: NUMWAT <- "1119" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1119" Comparing "1081" and "1119". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.31" Parameter: BOX -> "32.31" Parameter: BOX -> "32.31" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.31000 B = 32.31000 C = 32.31000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8667 2 1 -1 0 -1 3.6957 3 1 -1 1 -1 5.0842 4 1 0 -1 -1 4.0064 5 1 0 0 -1 0.6034 6 1 0 1 -1 5.4398 7 1 -1 -1 0 4.1451 8 1 -1 0 0 2.8773 9 1 -1 1 0 5.1638 10 1 0 -1 0 0.4151 11 1 0 1 0 0.4151 12 1 -1 -1 1 7.7388 13 1 -1 0 1 3.0092 14 1 -1 1 1 5.5411 15 1 0 -1 1 5.4398 16 1 0 0 1 0.6034 17 1 0 1 1 4.0064 18 1 1 1 1 6.8667 19 1 1 0 1 3.6957 20 1 1 -1 1 5.0842 21 1 1 1 0 4.1451 22 1 1 0 0 2.8773 23 1 1 -1 0 5.1638 24 1 1 1 -1 7.7388 25 1 1 0 -1 3.0092 26 1 1 -1 -1 5.5411 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3339 atoms have been selected out of 3413 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 145 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 645 215 215 0.00 5 C005 has 1503 501 501 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1698 557 555 0.00 9 C009 has 429 143 143 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 0.47 Total of12596 atoms and 4183 groups and 4176 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3413 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1125 Number of atoms = 3410 Number of groups = 1130 Number of bonds = 3403 Number of angles = 1229 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1127 Number of HB donors = 2232 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1125 Number of atoms = 3410 Number of groups = 1130 Number of bonds = 3403 Number of angles = 1229 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1127 Number of HB donors = 2232 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.308" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1125" Evaluating: 1125-7 Parameter: NUMWAT <- "1118" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1118" Comparing "1081" and "1118". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.308" Parameter: BOX -> "32.308" Parameter: BOX -> "32.308" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.30800 B = 32.30800 C = 32.30800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8639 2 1 -1 0 -1 3.6929 3 1 -1 1 -1 5.0814 4 1 0 -1 -1 4.0037 5 1 0 0 -1 0.6023 6 1 0 1 -1 5.4371 7 1 -1 -1 0 4.1459 8 1 -1 0 0 2.8765 9 1 -1 1 0 5.1610 10 1 0 -1 0 0.4139 11 1 0 1 0 0.4139 12 1 -1 -1 1 7.7360 13 1 -1 0 1 3.0067 14 1 -1 1 1 5.5383 15 1 0 -1 1 5.4371 16 1 0 0 1 0.6023 17 1 0 1 1 4.0037 18 1 1 1 1 6.8639 19 1 1 0 1 3.6929 20 1 1 -1 1 5.0814 21 1 1 1 0 4.1459 22 1 1 0 0 2.8765 23 1 1 -1 0 5.1610 24 1 1 1 -1 7.7360 25 1 1 0 -1 3.0067 26 1 1 -1 -1 5.5383 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3336 atoms have been selected out of 3410 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 645 215 215 0.00 5 C005 has 1503 501 501 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1698 557 555 0.00 9 C009 has 429 143 143 0.00 10 C010 has 1581 527 527 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 0.47 Total of12590 atoms and 4181 groups and 4174 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3410 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1125 Number of atoms = 3410 Number of groups = 1130 Number of bonds = 3403 Number of angles = 1229 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1127 Number of HB donors = 2232 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1125 Number of atoms = 3410 Number of groups = 1130 Number of bonds = 3403 Number of angles = 1229 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1127 Number of HB donors = 2232 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.306" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1125" Evaluating: 1125-7 Parameter: NUMWAT <- "1118" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1118" Comparing "1081" and "1118". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.306" Parameter: BOX -> "32.306" Parameter: BOX -> "32.306" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.30600 B = 32.30600 C = 32.30600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8611 2 1 -1 0 -1 3.6901 3 1 -1 1 -1 5.0785 4 1 0 -1 -1 4.0010 5 1 0 0 -1 0.6012 6 1 0 1 -1 5.4344 7 1 -1 -1 0 4.1468 8 1 -1 0 0 2.8758 9 1 -1 1 0 5.1582 10 1 0 -1 0 0.4127 11 1 0 1 0 0.4127 12 1 -1 -1 1 7.7331 13 1 -1 0 1 3.0041 14 1 -1 1 1 5.5355 15 1 0 -1 1 5.4344 16 1 0 0 1 0.6012 17 1 0 1 1 4.0010 18 1 1 1 1 6.8611 19 1 1 0 1 3.6901 20 1 1 -1 1 5.0785 21 1 1 1 0 4.1468 22 1 1 0 0 2.8758 23 1 1 -1 0 5.1582 24 1 1 1 -1 7.7331 25 1 1 0 -1 3.0041 26 1 1 -1 -1 5.5355 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3336 atoms have been selected out of 3410 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 645 215 215 0.00 5 C005 has 1503 501 501 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1698 557 555 0.00 9 C009 has 432 144 144 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 0.47 Total of12596 atoms and 4183 groups and 4176 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3410 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1125 Number of atoms = 3410 Number of groups = 1130 Number of bonds = 3403 Number of angles = 1229 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1127 Number of HB donors = 2232 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1125 Number of atoms = 3410 Number of groups = 1130 Number of bonds = 3403 Number of angles = 1229 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1127 Number of HB donors = 2232 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.304" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1125" Evaluating: 1125-7 Parameter: NUMWAT <- "1118" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1118" Comparing "1081" and "1118". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.304" Parameter: BOX -> "32.304" Parameter: BOX -> "32.304" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.30400 B = 32.30400 C = 32.30400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8584 2 1 -1 0 -1 3.6873 3 1 -1 1 -1 5.0757 4 1 0 -1 -1 3.9983 5 1 0 0 -1 0.6002 6 1 0 1 -1 5.4317 7 1 -1 -1 0 4.1476 8 1 -1 0 0 2.8750 9 1 -1 1 0 5.1554 10 1 0 -1 0 0.4116 11 1 0 1 0 0.4116 12 1 -1 -1 1 7.7303 13 1 -1 0 1 3.0016 14 1 -1 1 1 5.5327 15 1 0 -1 1 5.4317 16 1 0 0 1 0.6002 17 1 0 1 1 3.9983 18 1 1 1 1 6.8584 19 1 1 0 1 3.6873 20 1 1 -1 1 5.0757 21 1 1 1 0 4.1476 22 1 1 0 0 2.8750 23 1 1 -1 0 5.1554 24 1 1 1 -1 7.7303 25 1 1 0 -1 3.0016 26 1 1 -1 -1 5.5327 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3336 atoms have been selected out of 3410 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 645 215 215 0.00 5 C005 has 1503 501 501 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1698 557 555 0.00 9 C009 has 432 144 144 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 111 37 37 0.00 13 C013 has 495 165 165 0.00 14 C014 has 126 42 42 0.46 Total of12599 atoms and 4184 groups and 4177 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3410 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1125 Number of atoms = 3410 Number of groups = 1130 Number of bonds = 3403 Number of angles = 1229 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1127 Number of HB donors = 2232 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1125 Number of atoms = 3410 Number of groups = 1130 Number of bonds = 3403 Number of angles = 1229 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1127 Number of HB donors = 2232 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.302" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1125" Evaluating: 1125-7 Parameter: NUMWAT <- "1118" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1118" Comparing "1081" and "1118". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.302" Parameter: BOX -> "32.302" Parameter: BOX -> "32.302" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.30200 B = 32.30200 C = 32.30200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8556 2 1 -1 0 -1 3.6845 3 1 -1 1 -1 5.0728 4 1 0 -1 -1 3.9956 5 1 0 0 -1 0.5991 6 1 0 1 -1 5.4290 7 1 -1 -1 0 4.1485 8 1 -1 0 0 2.8743 9 1 -1 1 0 5.1525 10 1 0 -1 0 0.4104 11 1 0 1 0 0.4104 12 1 -1 -1 1 7.7274 13 1 -1 0 1 2.9991 14 1 -1 1 1 5.5298 15 1 0 -1 1 5.4290 16 1 0 0 1 0.5991 17 1 0 1 1 3.9956 18 1 1 1 1 6.8556 19 1 1 0 1 3.6845 20 1 1 -1 1 5.0728 21 1 1 1 0 4.1485 22 1 1 0 0 2.8743 23 1 1 -1 0 5.1525 24 1 1 1 -1 7.7274 25 1 1 0 -1 2.9991 26 1 1 -1 -1 5.5298 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3336 atoms have been selected out of 3410 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 233 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 768 256 256 0.00 3 C003 has 117 39 39 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1503 501 501 0.00 6 C006 has 447 149 149 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1698 557 555 0.00 9 C009 has 432 144 144 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 123 41 41 1.07 Total of12584 atoms and 4179 groups and 4172 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3410 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1124 Number of atoms = 3407 Number of groups = 1129 Number of bonds = 3400 Number of angles = 1228 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1126 Number of HB donors = 2230 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1124 Number of atoms = 3407 Number of groups = 1129 Number of bonds = 3400 Number of angles = 1228 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1126 Number of HB donors = 2230 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.3" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1124" Evaluating: 1124-7 Parameter: NUMWAT <- "1117" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1117" Comparing "1081" and "1117". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.3" Parameter: BOX -> "32.3" Parameter: BOX -> "32.3" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.30000 B = 32.30000 C = 32.30000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8528 2 1 -1 0 -1 3.6817 3 1 -1 1 -1 5.0700 4 1 0 -1 -1 3.9929 5 1 0 0 -1 0.5980 6 1 0 1 -1 5.4263 7 1 -1 -1 0 4.1493 8 1 -1 0 0 2.8735 9 1 -1 1 0 5.1497 10 1 0 -1 0 0.4092 11 1 0 1 0 0.4092 12 1 -1 -1 1 7.7246 13 1 -1 0 1 2.9965 14 1 -1 1 1 5.5270 15 1 0 -1 1 5.4263 16 1 0 0 1 0.5980 17 1 0 1 1 3.9929 18 1 1 1 1 6.8528 19 1 1 0 1 3.6817 20 1 1 -1 1 5.0700 21 1 1 1 0 4.1493 22 1 1 0 0 2.8735 23 1 1 -1 0 5.1497 24 1 1 1 -1 7.7246 25 1 1 0 -1 2.9965 26 1 1 -1 -1 5.5270 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3333 atoms have been selected out of 3407 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1500 500 500 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 429 143 143 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 123 41 41 1.07 Total of12563 atoms and 4172 groups and 4165 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3407 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1124 Number of atoms = 3407 Number of groups = 1129 Number of bonds = 3400 Number of angles = 1228 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1126 Number of HB donors = 2230 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1124 Number of atoms = 3407 Number of groups = 1129 Number of bonds = 3400 Number of angles = 1228 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1126 Number of HB donors = 2230 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.298" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1124" Evaluating: 1124-7 Parameter: NUMWAT <- "1117" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1117" Comparing "1081" and "1117". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.298" Parameter: BOX -> "32.298" Parameter: BOX -> "32.298" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.29800 B = 32.29800 C = 32.29800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8501 2 1 -1 0 -1 3.6789 3 1 -1 1 -1 5.0672 4 1 0 -1 -1 3.9902 5 1 0 0 -1 0.5969 6 1 0 1 -1 5.4236 7 1 -1 -1 0 4.1502 8 1 -1 0 0 2.8728 9 1 -1 1 0 5.1469 10 1 0 -1 0 0.4081 11 1 0 1 0 0.4081 12 1 -1 -1 1 7.7217 13 1 -1 0 1 2.9940 14 1 -1 1 1 5.5242 15 1 0 -1 1 5.4236 16 1 0 0 1 0.5969 17 1 0 1 1 3.9902 18 1 1 1 1 6.8501 19 1 1 0 1 3.6789 20 1 1 -1 1 5.0672 21 1 1 1 0 4.1502 22 1 1 0 0 2.8728 23 1 1 -1 0 5.1469 24 1 1 1 -1 7.7217 25 1 1 0 -1 2.9940 26 1 1 -1 -1 5.5242 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3333 atoms have been selected out of 3407 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1500 500 500 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 429 143 143 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 1.07 Total of12569 atoms and 4174 groups and 4167 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3407 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1124 Number of atoms = 3407 Number of groups = 1129 Number of bonds = 3400 Number of angles = 1228 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1126 Number of HB donors = 2230 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1124 Number of atoms = 3407 Number of groups = 1129 Number of bonds = 3400 Number of angles = 1228 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1126 Number of HB donors = 2230 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.296" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1124" Evaluating: 1124-7 Parameter: NUMWAT <- "1117" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1117" Comparing "1081" and "1117". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.296" Parameter: BOX -> "32.296" Parameter: BOX -> "32.296" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.29600 B = 32.29600 C = 32.29600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8473 2 1 -1 0 -1 3.6761 3 1 -1 1 -1 5.0643 4 1 0 -1 -1 3.9874 5 1 0 0 -1 0.5959 6 1 0 1 -1 5.4209 7 1 -1 -1 0 4.1511 8 1 -1 0 0 2.8721 9 1 -1 1 0 5.1441 10 1 0 -1 0 0.4069 11 1 0 1 0 0.4069 12 1 -1 -1 1 7.7189 13 1 -1 0 1 2.9915 14 1 -1 1 1 5.5214 15 1 0 -1 1 5.4209 16 1 0 0 1 0.5959 17 1 0 1 1 3.9874 18 1 1 1 1 6.8473 19 1 1 0 1 3.6761 20 1 1 -1 1 5.0643 21 1 1 1 0 4.1511 22 1 1 0 0 2.8721 23 1 1 -1 0 5.1441 24 1 1 1 -1 7.7189 25 1 1 0 -1 2.9915 26 1 1 -1 -1 5.5214 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3333 atoms have been selected out of 3407 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1500 500 500 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 429 143 143 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 1.07 Total of12572 atoms and 4175 groups and 4168 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3407 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1124 Number of atoms = 3407 Number of groups = 1129 Number of bonds = 3400 Number of angles = 1228 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1126 Number of HB donors = 2230 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1124 Number of atoms = 3407 Number of groups = 1129 Number of bonds = 3400 Number of angles = 1228 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1126 Number of HB donors = 2230 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.294" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1124" Evaluating: 1124-7 Parameter: NUMWAT <- "1117" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1117" Comparing "1081" and "1117". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.294" Parameter: BOX -> "32.294" Parameter: BOX -> "32.294" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.29400 B = 32.29400 C = 32.29400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8445 2 1 -1 0 -1 3.6733 3 1 -1 1 -1 5.0615 4 1 0 -1 -1 3.9847 5 1 0 0 -1 0.5948 6 1 0 1 -1 5.4182 7 1 -1 -1 0 4.1519 8 1 -1 0 0 2.8713 9 1 -1 1 0 5.1413 10 1 0 -1 0 0.4058 11 1 0 1 0 0.4058 12 1 -1 -1 1 7.7160 13 1 -1 0 1 2.9889 14 1 -1 1 1 5.5186 15 1 0 -1 1 5.4182 16 1 0 0 1 0.5948 17 1 0 1 1 3.9847 18 1 1 1 1 6.8445 19 1 1 0 1 3.6733 20 1 1 -1 1 5.0615 21 1 1 1 0 4.1519 22 1 1 0 0 2.8713 23 1 1 -1 0 5.1413 24 1 1 1 -1 7.7160 25 1 1 0 -1 2.9889 26 1 1 -1 -1 5.5186 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3333 atoms have been selected out of 3407 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1500 500 500 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 429 143 143 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 1.06 Total of12572 atoms and 4175 groups and 4168 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3407 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1124 Number of atoms = 3407 Number of groups = 1129 Number of bonds = 3400 Number of angles = 1228 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1126 Number of HB donors = 2230 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1124 Number of atoms = 3407 Number of groups = 1129 Number of bonds = 3400 Number of angles = 1228 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1126 Number of HB donors = 2230 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.292" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1124" Evaluating: 1124-7 Parameter: NUMWAT <- "1117" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1117" Comparing "1081" and "1117". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.292" Parameter: BOX -> "32.292" Parameter: BOX -> "32.292" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.29200 B = 32.29200 C = 32.29200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8418 2 1 -1 0 -1 3.6705 3 1 -1 1 -1 5.0586 4 1 0 -1 -1 3.9820 5 1 0 0 -1 0.5938 6 1 0 1 -1 5.4155 7 1 -1 -1 0 4.1528 8 1 -1 0 0 2.8706 9 1 -1 1 0 5.1384 10 1 0 -1 0 0.4047 11 1 0 1 0 0.4047 12 1 -1 -1 1 7.7132 13 1 -1 0 1 2.9864 14 1 -1 1 1 5.5158 15 1 0 -1 1 5.4155 16 1 0 0 1 0.5938 17 1 0 1 1 3.9820 18 1 1 1 1 6.8418 19 1 1 0 1 3.6705 20 1 1 -1 1 5.0586 21 1 1 1 0 4.1528 22 1 1 0 0 2.8706 23 1 1 -1 0 5.1384 24 1 1 1 -1 7.7132 25 1 1 0 -1 2.9864 26 1 1 -1 -1 5.5158 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3333 atoms have been selected out of 3407 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 768 256 256 0.00 3 C003 has 114 38 38 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1500 500 500 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 429 143 143 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 1.06 Total of12575 atoms and 4176 groups and 4169 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3407 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1124 Number of atoms = 3407 Number of groups = 1129 Number of bonds = 3400 Number of angles = 1228 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1126 Number of HB donors = 2230 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1124 Number of atoms = 3407 Number of groups = 1129 Number of bonds = 3400 Number of angles = 1228 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1126 Number of HB donors = 2230 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.29" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1124" Evaluating: 1124-7 Parameter: NUMWAT <- "1117" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1117" Comparing "1081" and "1117". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.29" Parameter: BOX -> "32.29" Parameter: BOX -> "32.29" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.29000 B = 32.29000 C = 32.29000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8390 2 1 -1 0 -1 3.6677 3 1 -1 1 -1 5.0558 4 1 0 -1 -1 3.9793 5 1 0 0 -1 0.5927 6 1 0 1 -1 5.4128 7 1 -1 -1 0 4.1536 8 1 -1 0 0 2.8698 9 1 -1 1 0 5.1356 10 1 0 -1 0 0.4035 11 1 0 1 0 0.4035 12 1 -1 -1 1 7.7103 13 1 -1 0 1 2.9839 14 1 -1 1 1 5.5129 15 1 0 -1 1 5.4128 16 1 0 0 1 0.5927 17 1 0 1 1 3.9793 18 1 1 1 1 6.8390 19 1 1 0 1 3.6677 20 1 1 -1 1 5.0558 21 1 1 1 0 4.1536 22 1 1 0 0 2.8698 23 1 1 -1 0 5.1356 24 1 1 1 -1 7.7103 25 1 1 0 -1 2.9839 26 1 1 -1 -1 5.5129 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3333 atoms have been selected out of 3407 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 768 256 256 0.00 3 C003 has 114 38 38 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1500 500 500 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 429 143 143 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 1.06 Total of12575 atoms and 4176 groups and 4169 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3407 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1124 Number of atoms = 3407 Number of groups = 1129 Number of bonds = 3400 Number of angles = 1228 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1126 Number of HB donors = 2230 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1124 Number of atoms = 3407 Number of groups = 1129 Number of bonds = 3400 Number of angles = 1228 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1126 Number of HB donors = 2230 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.288" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1124" Evaluating: 1124-7 Parameter: NUMWAT <- "1117" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1117" Comparing "1081" and "1117". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.288" Parameter: BOX -> "32.288" Parameter: BOX -> "32.288" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.28800 B = 32.28800 C = 32.28800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8362 2 1 -1 0 -1 3.6649 3 1 -1 1 -1 5.0530 4 1 0 -1 -1 3.9766 5 1 0 0 -1 0.5917 6 1 0 1 -1 5.4101 7 1 -1 -1 0 4.1545 8 1 -1 0 0 2.8691 9 1 -1 1 0 5.1328 10 1 0 -1 0 0.4024 11 1 0 1 0 0.4024 12 1 -1 -1 1 7.7075 13 1 -1 0 1 2.9814 14 1 -1 1 1 5.5101 15 1 0 -1 1 5.4101 16 1 0 0 1 0.5917 17 1 0 1 1 3.9766 18 1 1 1 1 6.8362 19 1 1 0 1 3.6649 20 1 1 -1 1 5.0530 21 1 1 1 0 4.1545 22 1 1 0 0 2.8691 23 1 1 -1 0 5.1328 24 1 1 1 -1 7.7075 25 1 1 0 -1 2.9814 26 1 1 -1 -1 5.5101 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3333 atoms have been selected out of 3407 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 768 256 256 0.00 3 C003 has 114 38 38 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1500 500 500 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 429 143 143 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 1.06 Total of12578 atoms and 4177 groups and 4170 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3407 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1124 Number of atoms = 3407 Number of groups = 1129 Number of bonds = 3400 Number of angles = 1228 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1126 Number of HB donors = 2230 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1124 Number of atoms = 3407 Number of groups = 1129 Number of bonds = 3400 Number of angles = 1228 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1126 Number of HB donors = 2230 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.286" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1124" Evaluating: 1124-7 Parameter: NUMWAT <- "1117" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1117" Comparing "1081" and "1117". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.286" Parameter: BOX -> "32.286" Parameter: BOX -> "32.286" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.28600 B = 32.28600 C = 32.28600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8335 2 1 -1 0 -1 3.6621 3 1 -1 1 -1 5.0501 4 1 0 -1 -1 3.9739 5 1 0 0 -1 0.5906 6 1 0 1 -1 5.4074 7 1 -1 -1 0 4.1554 8 1 -1 0 0 2.8684 9 1 -1 1 0 5.1300 10 1 0 -1 0 0.4013 11 1 0 1 0 0.4013 12 1 -1 -1 1 7.7047 13 1 -1 0 1 2.9788 14 1 -1 1 1 5.5073 15 1 0 -1 1 5.4074 16 1 0 0 1 0.5906 17 1 0 1 1 3.9739 18 1 1 1 1 6.8335 19 1 1 0 1 3.6621 20 1 1 -1 1 5.0501 21 1 1 1 0 4.1554 22 1 1 0 0 2.8684 23 1 1 -1 0 5.1300 24 1 1 1 -1 7.7047 25 1 1 0 -1 2.9788 26 1 1 -1 -1 5.5073 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3333 atoms have been selected out of 3407 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 768 256 256 0.00 3 C003 has 114 38 38 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1500 500 500 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 429 143 143 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 1.06 Total of12581 atoms and 4178 groups and 4171 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3407 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1124 Number of atoms = 3407 Number of groups = 1129 Number of bonds = 3400 Number of angles = 1228 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1126 Number of HB donors = 2230 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1124 Number of atoms = 3407 Number of groups = 1129 Number of bonds = 3400 Number of angles = 1228 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1126 Number of HB donors = 2230 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.284" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1124" Evaluating: 1124-7 Parameter: NUMWAT <- "1117" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1117" Comparing "1081" and "1117". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.284" Parameter: BOX -> "32.284" Parameter: BOX -> "32.284" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.28400 B = 32.28400 C = 32.28400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8307 2 1 -1 0 -1 3.6593 3 1 -1 1 -1 5.0473 4 1 0 -1 -1 3.9712 5 1 0 0 -1 0.5896 6 1 0 1 -1 5.4047 7 1 -1 -1 0 4.1562 8 1 -1 0 0 2.8676 9 1 -1 1 0 5.1271 10 1 0 -1 0 0.4002 11 1 0 1 0 0.4002 12 1 -1 -1 1 7.7018 13 1 -1 0 1 2.9763 14 1 -1 1 1 5.5045 15 1 0 -1 1 5.4047 16 1 0 0 1 0.5896 17 1 0 1 1 3.9712 18 1 1 1 1 6.8307 19 1 1 0 1 3.6593 20 1 1 -1 1 5.0473 21 1 1 1 0 4.1562 22 1 1 0 0 2.8676 23 1 1 -1 0 5.1271 24 1 1 1 -1 7.7018 25 1 1 0 -1 2.9763 26 1 1 -1 -1 5.5045 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3333 atoms have been selected out of 3407 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 348 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 768 256 256 0.00 3 C003 has 117 39 39 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1500 500 500 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 429 143 143 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 129 43 43 1.05 Total of12590 atoms and 4181 groups and 4174 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3407 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1123 Number of atoms = 3404 Number of groups = 1128 Number of bonds = 3397 Number of angles = 1227 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1125 Number of HB donors = 2228 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1123 Number of atoms = 3404 Number of groups = 1128 Number of bonds = 3397 Number of angles = 1227 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1125 Number of HB donors = 2228 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.282" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1123" Evaluating: 1123-7 Parameter: NUMWAT <- "1116" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1116" Comparing "1081" and "1116". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.282" Parameter: BOX -> "32.282" Parameter: BOX -> "32.282" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.28200 B = 32.28200 C = 32.28200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8279 2 1 -1 0 -1 3.6565 3 1 -1 1 -1 5.0445 4 1 0 -1 -1 3.9685 5 1 0 0 -1 0.5886 6 1 0 1 -1 5.4020 7 1 -1 -1 0 4.1571 8 1 -1 0 0 2.8669 9 1 -1 1 0 5.1243 10 1 0 -1 0 0.3991 11 1 0 1 0 0.3991 12 1 -1 -1 1 7.6990 13 1 -1 0 1 2.9738 14 1 -1 1 1 5.5017 15 1 0 -1 1 5.4020 16 1 0 0 1 0.5886 17 1 0 1 1 3.9685 18 1 1 1 1 6.8279 19 1 1 0 1 3.6565 20 1 1 -1 1 5.0445 21 1 1 1 0 4.1571 22 1 1 0 0 2.8669 23 1 1 -1 0 5.1243 24 1 1 1 -1 7.6990 25 1 1 0 -1 2.9738 26 1 1 -1 -1 5.5017 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3330 atoms have been selected out of 3404 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 768 256 256 0.00 3 C003 has 117 39 39 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1500 500 500 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 429 143 143 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 129 43 43 1.05 Total of12578 atoms and 4177 groups and 4170 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3404 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1123 Number of atoms = 3404 Number of groups = 1128 Number of bonds = 3397 Number of angles = 1227 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1125 Number of HB donors = 2228 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1123 Number of atoms = 3404 Number of groups = 1128 Number of bonds = 3397 Number of angles = 1227 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1125 Number of HB donors = 2228 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.28" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1123" Evaluating: 1123-7 Parameter: NUMWAT <- "1116" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1116" Comparing "1081" and "1116". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.28" Parameter: BOX -> "32.28" Parameter: BOX -> "32.28" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.28000 B = 32.28000 C = 32.28000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8252 2 1 -1 0 -1 3.6537 3 1 -1 1 -1 5.0416 4 1 0 -1 -1 3.9658 5 1 0 0 -1 0.5876 6 1 0 1 -1 5.3993 7 1 -1 -1 0 4.1580 8 1 -1 0 0 2.8662 9 1 -1 1 0 5.1215 10 1 0 -1 0 0.3980 11 1 0 1 0 0.3980 12 1 -1 -1 1 7.6961 13 1 -1 0 1 2.9712 14 1 -1 1 1 5.4989 15 1 0 -1 1 5.3993 16 1 0 0 1 0.5876 17 1 0 1 1 3.9658 18 1 1 1 1 6.8252 19 1 1 0 1 3.6537 20 1 1 -1 1 5.0416 21 1 1 1 0 4.1580 22 1 1 0 0 2.8662 23 1 1 -1 0 5.1215 24 1 1 1 -1 7.6961 25 1 1 0 -1 2.9712 26 1 1 -1 -1 5.4989 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3330 atoms have been selected out of 3404 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 749 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 768 256 256 0.00 3 C003 has 114 38 38 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1500 500 500 0.00 6 C006 has 441 147 147 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1587 529 529 0.00 12 C012 has 111 37 37 0.00 13 C013 has 495 165 165 0.00 14 C014 has 129 43 43 1.05 Total of12587 atoms and 4180 groups and 4173 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3404 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1122 Number of atoms = 3401 Number of groups = 1127 Number of bonds = 3394 Number of angles = 1226 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2226 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1122 Number of atoms = 3401 Number of groups = 1127 Number of bonds = 3394 Number of angles = 1226 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2226 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.278" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1122" Evaluating: 1122-7 Parameter: NUMWAT <- "1115" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1115" Comparing "1081" and "1115". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.278" Parameter: BOX -> "32.278" Parameter: BOX -> "32.278" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.27800 B = 32.27800 C = 32.27800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8224 2 1 -1 0 -1 3.6509 3 1 -1 1 -1 5.0388 4 1 0 -1 -1 3.9631 5 1 0 0 -1 0.5865 6 1 0 1 -1 5.3966 7 1 -1 -1 0 4.1588 8 1 -1 0 0 2.8654 9 1 -1 1 0 5.1187 10 1 0 -1 0 0.3969 11 1 0 1 0 0.3969 12 1 -1 -1 1 7.6933 13 1 -1 0 1 2.9687 14 1 -1 1 1 5.4961 15 1 0 -1 1 5.3966 16 1 0 0 1 0.5865 17 1 0 1 1 3.9631 18 1 1 1 1 6.8224 19 1 1 0 1 3.6509 20 1 1 -1 1 5.0388 21 1 1 1 0 4.1588 22 1 1 0 0 2.8654 23 1 1 -1 0 5.1187 24 1 1 1 -1 7.6933 25 1 1 0 -1 2.9687 26 1 1 -1 -1 5.4961 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3327 atoms have been selected out of 3401 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1497 499 499 0.00 6 C006 has 441 147 147 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 111 37 37 0.00 13 C013 has 495 165 165 0.00 14 C014 has 129 43 43 1.05 Total of12566 atoms and 4173 groups and 4166 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3401 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1122 Number of atoms = 3401 Number of groups = 1127 Number of bonds = 3394 Number of angles = 1226 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2226 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1122 Number of atoms = 3401 Number of groups = 1127 Number of bonds = 3394 Number of angles = 1226 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2226 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.276" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1122" Evaluating: 1122-7 Parameter: NUMWAT <- "1115" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1115" Comparing "1081" and "1115". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.276" Parameter: BOX -> "32.276" Parameter: BOX -> "32.276" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.27600 B = 32.27600 C = 32.27600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8196 2 1 -1 0 -1 3.6481 3 1 -1 1 -1 5.0360 4 1 0 -1 -1 3.9604 5 1 0 0 -1 0.5855 6 1 0 1 -1 5.3939 7 1 -1 -1 0 4.1597 8 1 -1 0 0 2.8647 9 1 -1 1 0 5.1159 10 1 0 -1 0 0.3958 11 1 0 1 0 0.3958 12 1 -1 -1 1 7.6904 13 1 -1 0 1 2.9662 14 1 -1 1 1 5.4932 15 1 0 -1 1 5.3939 16 1 0 0 1 0.5855 17 1 0 1 1 3.9604 18 1 1 1 1 6.8196 19 1 1 0 1 3.6481 20 1 1 -1 1 5.0360 21 1 1 1 0 4.1597 22 1 1 0 0 2.8647 23 1 1 -1 0 5.1159 24 1 1 1 -1 7.6904 25 1 1 0 -1 2.9662 26 1 1 -1 -1 5.4932 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3327 atoms have been selected out of 3401 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1497 499 499 0.00 6 C006 has 441 147 147 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 111 37 37 0.00 13 C013 has 495 165 165 0.00 14 C014 has 129 43 43 1.05 Total of12569 atoms and 4174 groups and 4167 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3401 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1122 Number of atoms = 3401 Number of groups = 1127 Number of bonds = 3394 Number of angles = 1226 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2226 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1122 Number of atoms = 3401 Number of groups = 1127 Number of bonds = 3394 Number of angles = 1226 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2226 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.274" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1122" Evaluating: 1122-7 Parameter: NUMWAT <- "1115" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1115" Comparing "1081" and "1115". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.274" Parameter: BOX -> "32.274" Parameter: BOX -> "32.274" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.27400 B = 32.27400 C = 32.27400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8169 2 1 -1 0 -1 3.6453 3 1 -1 1 -1 5.0331 4 1 0 -1 -1 3.9577 5 1 0 0 -1 0.5845 6 1 0 1 -1 5.3912 7 1 -1 -1 0 4.1606 8 1 -1 0 0 2.8640 9 1 -1 1 0 5.1130 10 1 0 -1 0 0.3948 11 1 0 1 0 0.3948 12 1 -1 -1 1 7.6876 13 1 -1 0 1 2.9637 14 1 -1 1 1 5.4904 15 1 0 -1 1 5.3912 16 1 0 0 1 0.5845 17 1 0 1 1 3.9577 18 1 1 1 1 6.8169 19 1 1 0 1 3.6453 20 1 1 -1 1 5.0331 21 1 1 1 0 4.1606 22 1 1 0 0 2.8640 23 1 1 -1 0 5.1130 24 1 1 1 -1 7.6876 25 1 1 0 -1 2.9637 26 1 1 -1 -1 5.4904 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3327 atoms have been selected out of 3401 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1497 499 499 0.00 6 C006 has 441 147 147 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 111 37 37 0.00 13 C013 has 495 165 165 0.00 14 C014 has 129 43 43 1.04 Total of12569 atoms and 4174 groups and 4167 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3401 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1122 Number of atoms = 3401 Number of groups = 1127 Number of bonds = 3394 Number of angles = 1226 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2226 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1122 Number of atoms = 3401 Number of groups = 1127 Number of bonds = 3394 Number of angles = 1226 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2226 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.272" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1122" Evaluating: 1122-7 Parameter: NUMWAT <- "1115" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1115" Comparing "1081" and "1115". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.272" Parameter: BOX -> "32.272" Parameter: BOX -> "32.272" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.27200 B = 32.27200 C = 32.27200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8141 2 1 -1 0 -1 3.6425 3 1 -1 1 -1 5.0303 4 1 0 -1 -1 3.9550 5 1 0 0 -1 0.5835 6 1 0 1 -1 5.3885 7 1 -1 -1 0 4.1615 8 1 -1 0 0 2.8633 9 1 -1 1 0 5.1102 10 1 0 -1 0 0.3937 11 1 0 1 0 0.3937 12 1 -1 -1 1 7.6847 13 1 -1 0 1 2.9611 14 1 -1 1 1 5.4876 15 1 0 -1 1 5.3885 16 1 0 0 1 0.5835 17 1 0 1 1 3.9550 18 1 1 1 1 6.8141 19 1 1 0 1 3.6425 20 1 1 -1 1 5.0303 21 1 1 1 0 4.1615 22 1 1 0 0 2.8633 23 1 1 -1 0 5.1102 24 1 1 1 -1 7.6847 25 1 1 0 -1 2.9611 26 1 1 -1 -1 5.4876 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3327 atoms have been selected out of 3401 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1497 499 499 0.00 6 C006 has 441 147 147 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 111 37 37 0.00 13 C013 has 495 165 165 0.00 14 C014 has 129 43 43 1.04 Total of12569 atoms and 4174 groups and 4167 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3401 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1122 Number of atoms = 3401 Number of groups = 1127 Number of bonds = 3394 Number of angles = 1226 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2226 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1122 Number of atoms = 3401 Number of groups = 1127 Number of bonds = 3394 Number of angles = 1226 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2226 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.27" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1122" Evaluating: 1122-7 Parameter: NUMWAT <- "1115" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1115" Comparing "1081" and "1115". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.27" Parameter: BOX -> "32.27" Parameter: BOX -> "32.27" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.27000 B = 32.27000 C = 32.27000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8114 2 1 -1 0 -1 3.6397 3 1 -1 1 -1 5.0275 4 1 0 -1 -1 3.9523 5 1 0 0 -1 0.5825 6 1 0 1 -1 5.3858 7 1 -1 -1 0 4.1623 8 1 -1 0 0 2.8625 9 1 -1 1 0 5.1074 10 1 0 -1 0 0.3926 11 1 0 1 0 0.3926 12 1 -1 -1 1 7.6819 13 1 -1 0 1 2.9586 14 1 -1 1 1 5.4848 15 1 0 -1 1 5.3858 16 1 0 0 1 0.5825 17 1 0 1 1 3.9523 18 1 1 1 1 6.8114 19 1 1 0 1 3.6397 20 1 1 -1 1 5.0275 21 1 1 1 0 4.1623 22 1 1 0 0 2.8625 23 1 1 -1 0 5.1074 24 1 1 1 -1 7.6819 25 1 1 0 -1 2.9586 26 1 1 -1 -1 5.4848 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3327 atoms have been selected out of 3401 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1497 499 499 0.00 6 C006 has 441 147 147 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 111 37 37 0.00 13 C013 has 495 165 165 0.00 14 C014 has 129 43 43 1.04 Total of12569 atoms and 4174 groups and 4167 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3401 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1122 Number of atoms = 3401 Number of groups = 1127 Number of bonds = 3394 Number of angles = 1226 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2226 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1122 Number of atoms = 3401 Number of groups = 1127 Number of bonds = 3394 Number of angles = 1226 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2226 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.268" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1122" Evaluating: 1122-7 Parameter: NUMWAT <- "1115" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1115" Comparing "1081" and "1115". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.268" Parameter: BOX -> "32.268" Parameter: BOX -> "32.268" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.26800 B = 32.26800 C = 32.26800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8086 2 1 -1 0 -1 3.6369 3 1 -1 1 -1 5.0246 4 1 0 -1 -1 3.9496 5 1 0 0 -1 0.5815 6 1 0 1 -1 5.3831 7 1 -1 -1 0 4.1632 8 1 -1 0 0 2.8618 9 1 -1 1 0 5.1046 10 1 0 -1 0 0.3916 11 1 0 1 0 0.3916 12 1 -1 -1 1 7.6791 13 1 -1 0 1 2.9561 14 1 -1 1 1 5.4820 15 1 0 -1 1 5.3831 16 1 0 0 1 0.5815 17 1 0 1 1 3.9496 18 1 1 1 1 6.8086 19 1 1 0 1 3.6369 20 1 1 -1 1 5.0246 21 1 1 1 0 4.1632 22 1 1 0 0 2.8618 23 1 1 -1 0 5.1046 24 1 1 1 -1 7.6791 25 1 1 0 -1 2.9561 26 1 1 -1 -1 5.4820 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3327 atoms have been selected out of 3401 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1497 499 499 0.00 6 C006 has 441 147 147 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 111 37 37 0.00 13 C013 has 495 165 165 0.00 14 C014 has 129 43 43 1.04 Total of12569 atoms and 4174 groups and 4167 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3401 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1122 Number of atoms = 3401 Number of groups = 1127 Number of bonds = 3394 Number of angles = 1226 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2226 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1122 Number of atoms = 3401 Number of groups = 1127 Number of bonds = 3394 Number of angles = 1226 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2226 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.266" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1122" Evaluating: 1122-7 Parameter: NUMWAT <- "1115" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1115" Comparing "1081" and "1115". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.266" Parameter: BOX -> "32.266" Parameter: BOX -> "32.266" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.26600 B = 32.26600 C = 32.26600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8058 2 1 -1 0 -1 3.6341 3 1 -1 1 -1 5.0218 4 1 0 -1 -1 3.9469 5 1 0 0 -1 0.5805 6 1 0 1 -1 5.3804 7 1 -1 -1 0 4.1641 8 1 -1 0 0 2.8611 9 1 -1 1 0 5.1017 10 1 0 -1 0 0.3905 11 1 0 1 0 0.3905 12 1 -1 -1 1 7.6762 13 1 -1 0 1 2.9536 14 1 -1 1 1 5.4792 15 1 0 -1 1 5.3804 16 1 0 0 1 0.5805 17 1 0 1 1 3.9469 18 1 1 1 1 6.8058 19 1 1 0 1 3.6341 20 1 1 -1 1 5.0218 21 1 1 1 0 4.1641 22 1 1 0 0 2.8611 23 1 1 -1 0 5.1017 24 1 1 1 -1 7.6762 25 1 1 0 -1 2.9536 26 1 1 -1 -1 5.4792 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3327 atoms have been selected out of 3401 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1497 499 499 0.00 6 C006 has 441 147 147 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 111 37 37 0.00 13 C013 has 495 165 165 0.00 14 C014 has 129 43 43 1.04 Total of12569 atoms and 4174 groups and 4167 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3401 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1122 Number of atoms = 3401 Number of groups = 1127 Number of bonds = 3394 Number of angles = 1226 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2226 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1122 Number of atoms = 3401 Number of groups = 1127 Number of bonds = 3394 Number of angles = 1226 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2226 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.264" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1122" Evaluating: 1122-7 Parameter: NUMWAT <- "1115" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1115" Comparing "1081" and "1115". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.264" Parameter: BOX -> "32.264" Parameter: BOX -> "32.264" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.26400 B = 32.26400 C = 32.26400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8031 2 1 -1 0 -1 3.6313 3 1 -1 1 -1 5.0190 4 1 0 -1 -1 3.9441 5 1 0 0 -1 0.5796 6 1 0 1 -1 5.3777 7 1 -1 -1 0 4.1650 8 1 -1 0 0 2.8604 9 1 -1 1 0 5.0989 10 1 0 -1 0 0.3895 11 1 0 1 0 0.3895 12 1 -1 -1 1 7.6734 13 1 -1 0 1 2.9511 14 1 -1 1 1 5.4764 15 1 0 -1 1 5.3777 16 1 0 0 1 0.5796 17 1 0 1 1 3.9441 18 1 1 1 1 6.8031 19 1 1 0 1 3.6313 20 1 1 -1 1 5.0190 21 1 1 1 0 4.1650 22 1 1 0 0 2.8604 23 1 1 -1 0 5.0989 24 1 1 1 -1 7.6734 25 1 1 0 -1 2.9511 26 1 1 -1 -1 5.4764 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3327 atoms have been selected out of 3401 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 765 255 255 0.00 3 C003 has 114 38 38 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1497 499 499 0.00 6 C006 has 441 147 147 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 111 37 37 0.00 13 C013 has 495 165 165 0.00 14 C014 has 129 43 43 1.03 Total of12569 atoms and 4174 groups and 4167 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3401 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1122 Number of atoms = 3401 Number of groups = 1127 Number of bonds = 3394 Number of angles = 1226 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2226 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1122 Number of atoms = 3401 Number of groups = 1127 Number of bonds = 3394 Number of angles = 1226 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2226 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.262" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1122" Evaluating: 1122-7 Parameter: NUMWAT <- "1115" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1115" Comparing "1081" and "1115". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.262" Parameter: BOX -> "32.262" Parameter: BOX -> "32.262" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.26200 B = 32.26200 C = 32.26200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.8003 2 1 -1 0 -1 3.6285 3 1 -1 1 -1 5.0162 4 1 0 -1 -1 3.9414 5 1 0 0 -1 0.5786 6 1 0 1 -1 5.3750 7 1 -1 -1 0 4.1659 8 1 -1 0 0 2.8597 9 1 -1 1 0 5.0961 10 1 0 -1 0 0.3885 11 1 0 1 0 0.3885 12 1 -1 -1 1 7.6705 13 1 -1 0 1 2.9485 14 1 -1 1 1 5.4736 15 1 0 -1 1 5.3750 16 1 0 0 1 0.5786 17 1 0 1 1 3.9414 18 1 1 1 1 6.8003 19 1 1 0 1 3.6285 20 1 1 -1 1 5.0162 21 1 1 1 0 4.1659 22 1 1 0 0 2.8597 23 1 1 -1 0 5.0961 24 1 1 1 -1 7.6705 25 1 1 0 -1 2.9485 26 1 1 -1 -1 5.4736 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3327 atoms have been selected out of 3401 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 517 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1016 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 768 256 256 0.00 3 C003 has 117 39 39 0.05 4 C004 has 627 209 209 0.00 5 C005 has 1497 499 499 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1698 557 555 0.00 9 C009 has 429 143 143 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 129 43 43 1.22 Total of12575 atoms and 4176 groups and 4169 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3401 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.26" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1120" Evaluating: 1120-7 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1113" Comparing "1081" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.26" Parameter: BOX -> "32.26" Parameter: BOX -> "32.26" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.26000 B = 32.26000 C = 32.26000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7976 2 1 -1 0 -1 3.6257 3 1 -1 1 -1 5.0133 4 1 0 -1 -1 3.9387 5 1 0 0 -1 0.5776 6 1 0 1 -1 5.3723 7 1 -1 -1 0 4.1668 8 1 -1 0 0 2.8589 9 1 -1 1 0 5.0933 10 1 0 -1 0 0.3875 11 1 0 1 0 0.3875 12 1 -1 -1 1 7.6677 13 1 -1 0 1 2.9460 14 1 -1 1 1 5.4708 15 1 0 -1 1 5.3723 16 1 0 0 1 0.5776 17 1 0 1 1 3.9387 18 1 1 1 1 6.7976 19 1 1 0 1 3.6257 20 1 1 -1 1 5.0133 21 1 1 1 0 4.1668 22 1 1 0 0 2.8589 23 1 1 -1 0 5.0933 24 1 1 1 -1 7.6677 25 1 1 0 -1 2.9460 26 1 1 -1 -1 5.4708 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3321 atoms have been selected out of 3395 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.05 4 C004 has 627 209 209 0.00 5 C005 has 1491 497 497 0.00 6 C006 has 441 147 147 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1581 527 527 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 129 43 43 1.21 Total of12536 atoms and 4163 groups and 4156 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3395 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.258" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1120" Evaluating: 1120-7 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1113" Comparing "1081" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.258" Parameter: BOX -> "32.258" Parameter: BOX -> "32.258" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.25800 B = 32.25800 C = 32.25800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7948 2 1 -1 0 -1 3.6229 3 1 -1 1 -1 5.0105 4 1 0 -1 -1 3.9360 5 1 0 0 -1 0.5766 6 1 0 1 -1 5.3696 7 1 -1 -1 0 4.1677 8 1 -1 0 0 2.8582 9 1 -1 1 0 5.0905 10 1 0 -1 0 0.3865 11 1 0 1 0 0.3865 12 1 -1 -1 1 7.6649 13 1 -1 0 1 2.9435 14 1 -1 1 1 5.4680 15 1 0 -1 1 5.3696 16 1 0 0 1 0.5766 17 1 0 1 1 3.9360 18 1 1 1 1 6.7948 19 1 1 0 1 3.6229 20 1 1 -1 1 5.0105 21 1 1 1 0 4.1677 22 1 1 0 0 2.8582 23 1 1 -1 0 5.0905 24 1 1 1 -1 7.6649 25 1 1 0 -1 2.9435 26 1 1 -1 -1 5.4680 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3321 atoms have been selected out of 3395 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.05 4 C004 has 627 209 209 0.00 5 C005 has 1491 497 497 0.00 6 C006 has 441 147 147 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1581 527 527 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 129 43 43 1.21 Total of12536 atoms and 4163 groups and 4156 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3395 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.256" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1120" Evaluating: 1120-7 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1113" Comparing "1081" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.256" Parameter: BOX -> "32.256" Parameter: BOX -> "32.256" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.25600 B = 32.25600 C = 32.25600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7921 2 1 -1 0 -1 3.6201 3 1 -1 1 -1 5.0077 4 1 0 -1 -1 3.9333 5 1 0 0 -1 0.5757 6 1 0 1 -1 5.3669 7 1 -1 -1 0 4.1685 8 1 -1 0 0 2.8575 9 1 -1 1 0 5.0876 10 1 0 -1 0 0.3854 11 1 0 1 0 0.3854 12 1 -1 -1 1 7.6620 13 1 -1 0 1 2.9410 14 1 -1 1 1 5.4652 15 1 0 -1 1 5.3669 16 1 0 0 1 0.5757 17 1 0 1 1 3.9333 18 1 1 1 1 6.7921 19 1 1 0 1 3.6201 20 1 1 -1 1 5.0077 21 1 1 1 0 4.1685 22 1 1 0 0 2.8575 23 1 1 -1 0 5.0876 24 1 1 1 -1 7.6620 25 1 1 0 -1 2.9410 26 1 1 -1 -1 5.4652 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3321 atoms have been selected out of 3395 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.05 4 C004 has 630 210 210 0.00 5 C005 has 1491 497 497 0.00 6 C006 has 441 147 147 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1581 527 527 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 129 43 43 1.21 Total of12539 atoms and 4164 groups and 4157 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3395 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.254" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1120" Evaluating: 1120-7 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1113" Comparing "1081" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.254" Parameter: BOX -> "32.254" Parameter: BOX -> "32.254" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.25400 B = 32.25400 C = 32.25400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7893 2 1 -1 0 -1 3.6173 3 1 -1 1 -1 5.0049 4 1 0 -1 -1 3.9306 5 1 0 0 -1 0.5747 6 1 0 1 -1 5.3642 7 1 -1 -1 0 4.1694 8 1 -1 0 0 2.8568 9 1 -1 1 0 5.0848 10 1 0 -1 0 0.3845 11 1 0 1 0 0.3845 12 1 -1 -1 1 7.6592 13 1 -1 0 1 2.9385 14 1 -1 1 1 5.4624 15 1 0 -1 1 5.3642 16 1 0 0 1 0.5747 17 1 0 1 1 3.9306 18 1 1 1 1 6.7893 19 1 1 0 1 3.6173 20 1 1 -1 1 5.0049 21 1 1 1 0 4.1694 22 1 1 0 0 2.8568 23 1 1 -1 0 5.0848 24 1 1 1 -1 7.6592 25 1 1 0 -1 2.9385 26 1 1 -1 -1 5.4624 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3321 atoms have been selected out of 3395 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.04 4 C004 has 630 210 210 0.00 5 C005 has 1491 497 497 0.00 6 C006 has 441 147 147 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1581 527 527 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 129 43 43 1.21 Total of12539 atoms and 4164 groups and 4157 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3395 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.252" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1120" Evaluating: 1120-7 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1113" Comparing "1081" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.252" Parameter: BOX -> "32.252" Parameter: BOX -> "32.252" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.25200 B = 32.25200 C = 32.25200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7865 2 1 -1 0 -1 3.6146 3 1 -1 1 -1 5.0020 4 1 0 -1 -1 3.9279 5 1 0 0 -1 0.5738 6 1 0 1 -1 5.3615 7 1 -1 -1 0 4.1703 8 1 -1 0 0 2.8561 9 1 -1 1 0 5.0820 10 1 0 -1 0 0.3835 11 1 0 1 0 0.3835 12 1 -1 -1 1 7.6563 13 1 -1 0 1 2.9359 14 1 -1 1 1 5.4596 15 1 0 -1 1 5.3615 16 1 0 0 1 0.5738 17 1 0 1 1 3.9279 18 1 1 1 1 6.7865 19 1 1 0 1 3.6146 20 1 1 -1 1 5.0020 21 1 1 1 0 4.1703 22 1 1 0 0 2.8561 23 1 1 -1 0 5.0820 24 1 1 1 -1 7.6563 25 1 1 0 -1 2.9359 26 1 1 -1 -1 5.4596 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3321 atoms have been selected out of 3395 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.04 4 C004 has 630 210 210 0.00 5 C005 has 1491 497 497 0.00 6 C006 has 441 147 147 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1581 527 527 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 129 43 43 1.21 Total of12539 atoms and 4164 groups and 4157 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3395 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.25" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1120" Evaluating: 1120-7 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1113" Comparing "1081" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.25" Parameter: BOX -> "32.25" Parameter: BOX -> "32.25" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.25000 B = 32.25000 C = 32.25000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7838 2 1 -1 0 -1 3.6118 3 1 -1 1 -1 4.9992 4 1 0 -1 -1 3.9252 5 1 0 0 -1 0.5728 6 1 0 1 -1 5.3588 7 1 -1 -1 0 4.1712 8 1 -1 0 0 2.8554 9 1 -1 1 0 5.0792 10 1 0 -1 0 0.3825 11 1 0 1 0 0.3825 12 1 -1 -1 1 7.6535 13 1 -1 0 1 2.9334 14 1 -1 1 1 5.4568 15 1 0 -1 1 5.3588 16 1 0 0 1 0.5728 17 1 0 1 1 3.9252 18 1 1 1 1 6.7838 19 1 1 0 1 3.6118 20 1 1 -1 1 4.9992 21 1 1 1 0 4.1712 22 1 1 0 0 2.8554 23 1 1 -1 0 5.0792 24 1 1 1 -1 7.6535 25 1 1 0 -1 2.9334 26 1 1 -1 -1 5.4568 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3321 atoms have been selected out of 3395 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.04 4 C004 has 630 210 210 0.00 5 C005 has 1494 498 498 0.00 6 C006 has 441 147 147 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1581 527 527 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 129 43 43 1.20 Total of12542 atoms and 4165 groups and 4158 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3395 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.248" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1120" Evaluating: 1120-7 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1113" Comparing "1081" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.248" Parameter: BOX -> "32.248" Parameter: BOX -> "32.248" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.24800 B = 32.24800 C = 32.24800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7810 2 1 -1 0 -1 3.6090 3 1 -1 1 -1 4.9964 4 1 0 -1 -1 3.9225 5 1 0 0 -1 0.5719 6 1 0 1 -1 5.3561 7 1 -1 -1 0 4.1721 8 1 -1 0 0 2.8547 9 1 -1 1 0 5.0763 10 1 0 -1 0 0.3815 11 1 0 1 0 0.3815 12 1 -1 -1 1 7.6507 13 1 -1 0 1 2.9309 14 1 -1 1 1 5.4540 15 1 0 -1 1 5.3561 16 1 0 0 1 0.5719 17 1 0 1 1 3.9225 18 1 1 1 1 6.7810 19 1 1 0 1 3.6090 20 1 1 -1 1 4.9964 21 1 1 1 0 4.1721 22 1 1 0 0 2.8547 23 1 1 -1 0 5.0763 24 1 1 1 -1 7.6507 25 1 1 0 -1 2.9309 26 1 1 -1 -1 5.4540 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3321 atoms have been selected out of 3395 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.04 4 C004 has 630 210 210 0.00 5 C005 has 1494 498 498 0.00 6 C006 has 441 147 147 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1581 527 527 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 129 43 43 1.20 Total of12542 atoms and 4165 groups and 4158 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3395 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.246" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1120" Evaluating: 1120-7 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1113" Comparing "1081" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.246" Parameter: BOX -> "32.246" Parameter: BOX -> "32.246" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.24600 B = 32.24600 C = 32.24600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7783 2 1 -1 0 -1 3.6062 3 1 -1 1 -1 4.9936 4 1 0 -1 -1 3.9198 5 1 0 0 -1 0.5709 6 1 0 1 -1 5.3534 7 1 -1 -1 0 4.1730 8 1 -1 0 0 2.8539 9 1 -1 1 0 5.0735 10 1 0 -1 0 0.3805 11 1 0 1 0 0.3805 12 1 -1 -1 1 7.6478 13 1 -1 0 1 2.9284 14 1 -1 1 1 5.4512 15 1 0 -1 1 5.3534 16 1 0 0 1 0.5709 17 1 0 1 1 3.9198 18 1 1 1 1 6.7783 19 1 1 0 1 3.6062 20 1 1 -1 1 4.9936 21 1 1 1 0 4.1730 22 1 1 0 0 2.8539 23 1 1 -1 0 5.0735 24 1 1 1 -1 7.6478 25 1 1 0 -1 2.9284 26 1 1 -1 -1 5.4512 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3321 atoms have been selected out of 3395 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.04 4 C004 has 630 210 210 0.00 5 C005 has 1494 498 498 0.00 6 C006 has 441 147 147 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1581 527 527 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 129 43 43 1.20 Total of12542 atoms and 4165 groups and 4158 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3395 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.244" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1120" Evaluating: 1120-7 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1113" Comparing "1081" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.244" Parameter: BOX -> "32.244" Parameter: BOX -> "32.244" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.24400 B = 32.24400 C = 32.24400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7755 2 1 -1 0 -1 3.6034 3 1 -1 1 -1 4.9908 4 1 0 -1 -1 3.9171 5 1 0 0 -1 0.5700 6 1 0 1 -1 5.3507 7 1 -1 -1 0 4.1739 8 1 -1 0 0 2.8532 9 1 -1 1 0 5.0707 10 1 0 -1 0 0.3796 11 1 0 1 0 0.3796 12 1 -1 -1 1 7.6450 13 1 -1 0 1 2.9259 14 1 -1 1 1 5.4484 15 1 0 -1 1 5.3507 16 1 0 0 1 0.5700 17 1 0 1 1 3.9171 18 1 1 1 1 6.7755 19 1 1 0 1 3.6034 20 1 1 -1 1 4.9908 21 1 1 1 0 4.1739 22 1 1 0 0 2.8532 23 1 1 -1 0 5.0707 24 1 1 1 -1 7.6450 25 1 1 0 -1 2.9259 26 1 1 -1 -1 5.4484 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3321 atoms have been selected out of 3395 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.03 4 C004 has 633 211 211 0.00 5 C005 has 1494 498 498 0.00 6 C006 has 441 147 147 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1581 527 527 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 129 43 43 1.20 Total of12545 atoms and 4166 groups and 4159 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3395 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.242" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1120" Evaluating: 1120-7 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1113" Comparing "1081" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.242" Parameter: BOX -> "32.242" Parameter: BOX -> "32.242" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.24200 B = 32.24200 C = 32.24200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7728 2 1 -1 0 -1 3.6006 3 1 -1 1 -1 4.9879 4 1 0 -1 -1 3.9144 5 1 0 0 -1 0.5691 6 1 0 1 -1 5.3480 7 1 -1 -1 0 4.1748 8 1 -1 0 0 2.8525 9 1 -1 1 0 5.0679 10 1 0 -1 0 0.3786 11 1 0 1 0 0.3786 12 1 -1 -1 1 7.6422 13 1 -1 0 1 2.9234 14 1 -1 1 1 5.4456 15 1 0 -1 1 5.3480 16 1 0 0 1 0.5691 17 1 0 1 1 3.9144 18 1 1 1 1 6.7728 19 1 1 0 1 3.6006 20 1 1 -1 1 4.9879 21 1 1 1 0 4.1748 22 1 1 0 0 2.8525 23 1 1 -1 0 5.0679 24 1 1 1 -1 7.6422 25 1 1 0 -1 2.9234 26 1 1 -1 -1 5.4456 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3321 atoms have been selected out of 3395 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.03 4 C004 has 633 211 211 0.00 5 C005 has 1494 498 498 0.00 6 C006 has 441 147 147 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1581 527 527 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 129 43 43 1.20 Total of12545 atoms and 4166 groups and 4159 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3395 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.24" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1120" Evaluating: 1120-7 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1113" Comparing "1081" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.24" Parameter: BOX -> "32.24" Parameter: BOX -> "32.24" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.24000 B = 32.24000 C = 32.24000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7700 2 1 -1 0 -1 3.5978 3 1 -1 1 -1 4.9851 4 1 0 -1 -1 3.9117 5 1 0 0 -1 0.5682 6 1 0 1 -1 5.3453 7 1 -1 -1 0 4.1757 8 1 -1 0 0 2.8518 9 1 -1 1 0 5.0651 10 1 0 -1 0 0.3777 11 1 0 1 0 0.3777 12 1 -1 -1 1 7.6393 13 1 -1 0 1 2.9208 14 1 -1 1 1 5.4428 15 1 0 -1 1 5.3453 16 1 0 0 1 0.5682 17 1 0 1 1 3.9117 18 1 1 1 1 6.7700 19 1 1 0 1 3.5978 20 1 1 -1 1 4.9851 21 1 1 1 0 4.1757 22 1 1 0 0 2.8518 23 1 1 -1 0 5.0651 24 1 1 1 -1 7.6393 25 1 1 0 -1 2.9208 26 1 1 -1 -1 5.4428 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3321 atoms have been selected out of 3395 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.03 4 C004 has 633 211 211 0.00 5 C005 has 1494 498 498 0.00 6 C006 has 441 147 147 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1581 527 527 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 129 43 43 1.19 Total of12545 atoms and 4166 groups and 4159 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3395 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.238" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1120" Evaluating: 1120-7 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1113" Comparing "1081" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.238" Parameter: BOX -> "32.238" Parameter: BOX -> "32.238" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.23800 B = 32.23800 C = 32.23800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7673 2 1 -1 0 -1 3.5950 3 1 -1 1 -1 4.9823 4 1 0 -1 -1 3.9090 5 1 0 0 -1 0.5673 6 1 0 1 -1 5.3426 7 1 -1 -1 0 4.1766 8 1 -1 0 0 2.8511 9 1 -1 1 0 5.0622 10 1 0 -1 0 0.3768 11 1 0 1 0 0.3768 12 1 -1 -1 1 7.6365 13 1 -1 0 1 2.9183 14 1 -1 1 1 5.4400 15 1 0 -1 1 5.3426 16 1 0 0 1 0.5673 17 1 0 1 1 3.9090 18 1 1 1 1 6.7673 19 1 1 0 1 3.5950 20 1 1 -1 1 4.9823 21 1 1 1 0 4.1766 22 1 1 0 0 2.8511 23 1 1 -1 0 5.0622 24 1 1 1 -1 7.6365 25 1 1 0 -1 2.9183 26 1 1 -1 -1 5.4400 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3321 atoms have been selected out of 3395 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.03 4 C004 has 636 212 212 0.00 5 C005 has 1494 498 498 0.00 6 C006 has 441 147 147 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1581 527 527 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 129 43 43 1.19 Total of12548 atoms and 4167 groups and 4160 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3395 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.236" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1120" Evaluating: 1120-7 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1113" Comparing "1081" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.236" Parameter: BOX -> "32.236" Parameter: BOX -> "32.236" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.23600 B = 32.23600 C = 32.23600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7645 2 1 -1 0 -1 3.5922 3 1 -1 1 -1 4.9795 4 1 0 -1 -1 3.9063 5 1 0 0 -1 0.5664 6 1 0 1 -1 5.3399 7 1 -1 -1 0 4.1775 8 1 -1 0 0 2.8504 9 1 -1 1 0 5.0594 10 1 0 -1 0 0.3758 11 1 0 1 0 0.3758 12 1 -1 -1 1 7.6337 13 1 -1 0 1 2.9158 14 1 -1 1 1 5.4372 15 1 0 -1 1 5.3399 16 1 0 0 1 0.5664 17 1 0 1 1 3.9063 18 1 1 1 1 6.7645 19 1 1 0 1 3.5922 20 1 1 -1 1 4.9795 21 1 1 1 0 4.1775 22 1 1 0 0 2.8504 23 1 1 -1 0 5.0594 24 1 1 1 -1 7.6337 25 1 1 0 -1 2.9158 26 1 1 -1 -1 5.4372 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3321 atoms have been selected out of 3395 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.03 4 C004 has 636 212 212 0.00 5 C005 has 1494 498 498 0.00 6 C006 has 441 147 147 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1581 527 527 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 129 43 43 1.19 Total of12551 atoms and 4168 groups and 4161 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3395 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.234" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1120" Evaluating: 1120-7 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1113" Comparing "1081" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.234" Parameter: BOX -> "32.234" Parameter: BOX -> "32.234" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.23400 B = 32.23400 C = 32.23400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7618 2 1 -1 0 -1 3.5894 3 1 -1 1 -1 4.9767 4 1 0 -1 -1 3.9036 5 1 0 0 -1 0.5655 6 1 0 1 -1 5.3372 7 1 -1 -1 0 4.1785 8 1 -1 0 0 2.8497 9 1 -1 1 0 5.0566 10 1 0 -1 0 0.3749 11 1 0 1 0 0.3749 12 1 -1 -1 1 7.6308 13 1 -1 0 1 2.9133 14 1 -1 1 1 5.4344 15 1 0 -1 1 5.3372 16 1 0 0 1 0.5655 17 1 0 1 1 3.9036 18 1 1 1 1 6.7618 19 1 1 0 1 3.5894 20 1 1 -1 1 4.9767 21 1 1 1 0 4.1785 22 1 1 0 0 2.8497 23 1 1 -1 0 5.0566 24 1 1 1 -1 7.6308 25 1 1 0 -1 2.9133 26 1 1 -1 -1 5.4344 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3321 atoms have been selected out of 3395 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.02 4 C004 has 636 212 212 0.00 5 C005 has 1494 498 498 0.00 6 C006 has 441 147 147 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1581 527 527 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 129 43 43 1.19 Total of12551 atoms and 4168 groups and 4161 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3395 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.232" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1120" Evaluating: 1120-7 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1113" Comparing "1081" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.232" Parameter: BOX -> "32.232" Parameter: BOX -> "32.232" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.23200 B = 32.23200 C = 32.23200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7590 2 1 -1 0 -1 3.5866 3 1 -1 1 -1 4.9739 4 1 0 -1 -1 3.9009 5 1 0 0 -1 0.5646 6 1 0 1 -1 5.3345 7 1 -1 -1 0 4.1794 8 1 -1 0 0 2.8490 9 1 -1 1 0 5.0538 10 1 0 -1 0 0.3740 11 1 0 1 0 0.3740 12 1 -1 -1 1 7.6280 13 1 -1 0 1 2.9108 14 1 -1 1 1 5.4316 15 1 0 -1 1 5.3345 16 1 0 0 1 0.5646 17 1 0 1 1 3.9009 18 1 1 1 1 6.7590 19 1 1 0 1 3.5866 20 1 1 -1 1 4.9739 21 1 1 1 0 4.1794 22 1 1 0 0 2.8490 23 1 1 -1 0 5.0538 24 1 1 1 -1 7.6280 25 1 1 0 -1 2.9108 26 1 1 -1 -1 5.4316 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3321 atoms have been selected out of 3395 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.02 4 C004 has 636 212 212 0.00 5 C005 has 1494 498 498 0.00 6 C006 has 441 147 147 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1581 527 527 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 129 43 43 1.19 Total of12554 atoms and 4169 groups and 4162 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3395 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.23" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1120" Evaluating: 1120-7 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1113" Comparing "1081" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.23" Parameter: BOX -> "32.23" Parameter: BOX -> "32.23" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.23000 B = 32.23000 C = 32.23000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7563 2 1 -1 0 -1 3.5838 3 1 -1 1 -1 4.9711 4 1 0 -1 -1 3.8982 5 1 0 0 -1 0.5637 6 1 0 1 -1 5.3319 7 1 -1 -1 0 4.1803 8 1 -1 0 0 2.8483 9 1 -1 1 0 5.0510 10 1 0 -1 0 0.3731 11 1 0 1 0 0.3731 12 1 -1 -1 1 7.6252 13 1 -1 0 1 2.9083 14 1 -1 1 1 5.4288 15 1 0 -1 1 5.3319 16 1 0 0 1 0.5637 17 1 0 1 1 3.8982 18 1 1 1 1 6.7563 19 1 1 0 1 3.5838 20 1 1 -1 1 4.9711 21 1 1 1 0 4.1803 22 1 1 0 0 2.8483 23 1 1 -1 0 5.0510 24 1 1 1 -1 7.6252 25 1 1 0 -1 2.9083 26 1 1 -1 -1 5.4288 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3321 atoms have been selected out of 3395 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.02 4 C004 has 636 212 212 0.00 5 C005 has 1494 498 498 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1581 527 527 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 129 43 43 1.18 Total of12557 atoms and 4170 groups and 4163 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3395 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.228" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1120" Evaluating: 1120-7 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1113" Comparing "1081" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.228" Parameter: BOX -> "32.228" Parameter: BOX -> "32.228" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.22800 B = 32.22800 C = 32.22800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7535 2 1 -1 0 -1 3.5810 3 1 -1 1 -1 4.9682 4 1 0 -1 -1 3.8955 5 1 0 0 -1 0.5628 6 1 0 1 -1 5.3292 7 1 -1 -1 0 4.1812 8 1 -1 0 0 2.8476 9 1 -1 1 0 5.0481 10 1 0 -1 0 0.3722 11 1 0 1 0 0.3722 12 1 -1 -1 1 7.6223 13 1 -1 0 1 2.9058 14 1 -1 1 1 5.4260 15 1 0 -1 1 5.3292 16 1 0 0 1 0.5628 17 1 0 1 1 3.8955 18 1 1 1 1 6.7535 19 1 1 0 1 3.5810 20 1 1 -1 1 4.9682 21 1 1 1 0 4.1812 22 1 1 0 0 2.8476 23 1 1 -1 0 5.0481 24 1 1 1 -1 7.6223 25 1 1 0 -1 2.9058 26 1 1 -1 -1 5.4260 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3321 atoms have been selected out of 3395 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.02 4 C004 has 636 212 212 0.00 5 C005 has 1494 498 498 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 429 143 143 0.00 10 C010 has 1581 527 527 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 129 43 43 1.18 Total of12560 atoms and 4171 groups and 4164 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3395 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.226" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1120" Evaluating: 1120-7 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1113" Comparing "1081" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.226" Parameter: BOX -> "32.226" Parameter: BOX -> "32.226" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.22600 B = 32.22600 C = 32.22600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7508 2 1 -1 0 -1 3.5782 3 1 -1 1 -1 4.9654 4 1 0 -1 -1 3.8928 5 1 0 0 -1 0.5619 6 1 0 1 -1 5.3265 7 1 -1 -1 0 4.1821 8 1 -1 0 0 2.8469 9 1 -1 1 0 5.0453 10 1 0 -1 0 0.3713 11 1 0 1 0 0.3713 12 1 -1 -1 1 7.6195 13 1 -1 0 1 2.9033 14 1 -1 1 1 5.4232 15 1 0 -1 1 5.3265 16 1 0 0 1 0.5619 17 1 0 1 1 3.8928 18 1 1 1 1 6.7508 19 1 1 0 1 3.5782 20 1 1 -1 1 4.9654 21 1 1 1 0 4.1821 22 1 1 0 0 2.8469 23 1 1 -1 0 5.0453 24 1 1 1 -1 7.6195 25 1 1 0 -1 2.9033 26 1 1 -1 -1 5.4232 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3321 atoms have been selected out of 3395 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 762 254 254 0.00 3 C003 has 114 38 38 0.02 4 C004 has 636 212 212 0.00 5 C005 has 1494 498 498 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 429 143 143 0.00 10 C010 has 1581 527 527 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 129 43 43 1.18 Total of12560 atoms and 4171 groups and 4164 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3395 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1120 Number of atoms = 3395 Number of groups = 1125 Number of bonds = 3388 Number of angles = 1224 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2222 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.224" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1120" Evaluating: 1120-7 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1113" Comparing "1081" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.224" Parameter: BOX -> "32.224" Parameter: BOX -> "32.224" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.22400 B = 32.22400 C = 32.22400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7481 2 1 -1 0 -1 3.5754 3 1 -1 1 -1 4.9626 4 1 0 -1 -1 3.8901 5 1 0 0 -1 0.5610 6 1 0 1 -1 5.3238 7 1 -1 -1 0 4.1830 8 1 -1 0 0 2.8462 9 1 -1 1 0 5.0425 10 1 0 -1 0 0.3705 11 1 0 1 0 0.3705 12 1 -1 -1 1 7.6167 13 1 -1 0 1 2.9008 14 1 -1 1 1 5.4204 15 1 0 -1 1 5.3238 16 1 0 0 1 0.5610 17 1 0 1 1 3.8901 18 1 1 1 1 6.7481 19 1 1 0 1 3.5754 20 1 1 -1 1 4.9626 21 1 1 1 0 4.1830 22 1 1 0 0 2.8462 23 1 1 -1 0 5.0425 24 1 1 1 -1 7.6167 25 1 1 0 -1 2.9008 26 1 1 -1 -1 5.4204 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3321 atoms have been selected out of 3395 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 204 OPERATED ON BY TRANSFORMATION C008 RESIDUE 756 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.01 4 C004 has 636 212 212 0.00 5 C005 has 1491 497 497 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1581 527 527 0.00 12 C012 has 111 37 37 0.00 13 C013 has 504 168 168 0.00 14 C014 has 126 42 42 1.18 Total of12554 atoms and 4169 groups and 4162 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3395 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1118 Number of atoms = 3389 Number of groups = 1123 Number of bonds = 3382 Number of angles = 1222 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2218 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1118 Number of atoms = 3389 Number of groups = 1123 Number of bonds = 3382 Number of angles = 1222 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2218 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.222" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1118" Evaluating: 1118-7 Parameter: NUMWAT <- "1111" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1111" Comparing "1081" and "1111". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.222" Parameter: BOX -> "32.222" Parameter: BOX -> "32.222" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.22200 B = 32.22200 C = 32.22200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7453 2 1 -1 0 -1 3.5726 3 1 -1 1 -1 4.9598 4 1 0 -1 -1 3.8874 5 1 0 0 -1 0.5602 6 1 0 1 -1 5.3211 7 1 -1 -1 0 4.1839 8 1 -1 0 0 2.8455 9 1 -1 1 0 5.0397 10 1 0 -1 0 0.3696 11 1 0 1 0 0.3696 12 1 -1 -1 1 7.6138 13 1 -1 0 1 2.8982 14 1 -1 1 1 5.4176 15 1 0 -1 1 5.3211 16 1 0 0 1 0.5602 17 1 0 1 1 3.8874 18 1 1 1 1 6.7453 19 1 1 0 1 3.5726 20 1 1 -1 1 4.9598 21 1 1 1 0 4.1839 22 1 1 0 0 2.8455 23 1 1 -1 0 5.0397 24 1 1 1 -1 7.6138 25 1 1 0 -1 2.8982 26 1 1 -1 -1 5.4176 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3315 atoms have been selected out of 3389 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.01 4 C004 has 636 212 212 0.00 5 C005 has 1488 496 496 0.00 6 C006 has 441 147 147 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1581 527 527 0.00 12 C012 has 111 37 37 0.00 13 C013 has 489 163 163 0.00 14 C014 has 126 42 42 1.18 Total of12524 atoms and 4159 groups and 4152 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3389 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1118 Number of atoms = 3389 Number of groups = 1123 Number of bonds = 3382 Number of angles = 1222 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2218 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1118 Number of atoms = 3389 Number of groups = 1123 Number of bonds = 3382 Number of angles = 1222 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2218 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.22" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1118" Evaluating: 1118-7 Parameter: NUMWAT <- "1111" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1111" Comparing "1081" and "1111". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.22" Parameter: BOX -> "32.22" Parameter: BOX -> "32.22" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.22000 B = 32.22000 C = 32.22000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7426 2 1 -1 0 -1 3.5698 3 1 -1 1 -1 4.9570 4 1 0 -1 -1 3.8847 5 1 0 0 -1 0.5593 6 1 0 1 -1 5.3184 7 1 -1 -1 0 4.1849 8 1 -1 0 0 2.8448 9 1 -1 1 0 5.0368 10 1 0 -1 0 0.3688 11 1 0 1 0 0.3688 12 1 -1 -1 1 7.6110 13 1 -1 0 1 2.8957 14 1 -1 1 1 5.4149 15 1 0 -1 1 5.3184 16 1 0 0 1 0.5593 17 1 0 1 1 3.8847 18 1 1 1 1 6.7426 19 1 1 0 1 3.5698 20 1 1 -1 1 4.9570 21 1 1 1 0 4.1849 22 1 1 0 0 2.8448 23 1 1 -1 0 5.0368 24 1 1 1 -1 7.6110 25 1 1 0 -1 2.8957 26 1 1 -1 -1 5.4149 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3315 atoms have been selected out of 3389 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.01 4 C004 has 636 212 212 0.00 5 C005 has 1488 496 496 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1581 527 527 0.00 12 C012 has 111 37 37 0.00 13 C013 has 489 163 163 0.00 14 C014 has 126 42 42 1.17 Total of12527 atoms and 4160 groups and 4153 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3389 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1118 Number of atoms = 3389 Number of groups = 1123 Number of bonds = 3382 Number of angles = 1222 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2218 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1118 Number of atoms = 3389 Number of groups = 1123 Number of bonds = 3382 Number of angles = 1222 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2218 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.218" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1118" Evaluating: 1118-7 Parameter: NUMWAT <- "1111" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1111" Comparing "1081" and "1111". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.218" Parameter: BOX -> "32.218" Parameter: BOX -> "32.218" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.21800 B = 32.21800 C = 32.21800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7398 2 1 -1 0 -1 3.5670 3 1 -1 1 -1 4.9542 4 1 0 -1 -1 3.8820 5 1 0 0 -1 0.5585 6 1 0 1 -1 5.3157 7 1 -1 -1 0 4.1858 8 1 -1 0 0 2.8441 9 1 -1 1 0 5.0340 10 1 0 -1 0 0.3679 11 1 0 1 0 0.3679 12 1 -1 -1 1 7.6082 13 1 -1 0 1 2.8932 14 1 -1 1 1 5.4121 15 1 0 -1 1 5.3157 16 1 0 0 1 0.5585 17 1 0 1 1 3.8820 18 1 1 1 1 6.7398 19 1 1 0 1 3.5670 20 1 1 -1 1 4.9542 21 1 1 1 0 4.1858 22 1 1 0 0 2.8441 23 1 1 -1 0 5.0340 24 1 1 1 -1 7.6082 25 1 1 0 -1 2.8932 26 1 1 -1 -1 5.4121 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3315 atoms have been selected out of 3389 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.01 4 C004 has 636 212 212 0.00 5 C005 has 1488 496 496 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1581 527 527 0.00 12 C012 has 111 37 37 0.00 13 C013 has 489 163 163 0.00 14 C014 has 126 42 42 1.17 Total of12530 atoms and 4161 groups and 4154 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3389 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1118 Number of atoms = 3389 Number of groups = 1123 Number of bonds = 3382 Number of angles = 1222 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2218 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1118 Number of atoms = 3389 Number of groups = 1123 Number of bonds = 3382 Number of angles = 1222 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2218 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.216" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1118" Evaluating: 1118-7 Parameter: NUMWAT <- "1111" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1111" Comparing "1081" and "1111". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.216" Parameter: BOX -> "32.216" Parameter: BOX -> "32.216" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.21600 B = 32.21600 C = 32.21600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7371 2 1 -1 0 -1 3.5642 3 1 -1 1 -1 4.9514 4 1 0 -1 -1 3.8793 5 1 0 0 -1 0.5576 6 1 0 1 -1 5.3130 7 1 -1 -1 0 4.1867 8 1 -1 0 0 2.8434 9 1 -1 1 0 5.0312 10 1 0 -1 0 0.3671 11 1 0 1 0 0.3671 12 1 -1 -1 1 7.6054 13 1 -1 0 1 2.8907 14 1 -1 1 1 5.4093 15 1 0 -1 1 5.3130 16 1 0 0 1 0.5576 17 1 0 1 1 3.8793 18 1 1 1 1 6.7371 19 1 1 0 1 3.5642 20 1 1 -1 1 4.9514 21 1 1 1 0 4.1867 22 1 1 0 0 2.8434 23 1 1 -1 0 5.0312 24 1 1 1 -1 7.6054 25 1 1 0 -1 2.8907 26 1 1 -1 -1 5.4093 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3315 atoms have been selected out of 3389 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.01 4 C004 has 636 212 212 0.00 5 C005 has 1488 496 496 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1581 527 527 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 1.17 Total of12533 atoms and 4162 groups and 4155 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3389 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1118 Number of atoms = 3389 Number of groups = 1123 Number of bonds = 3382 Number of angles = 1222 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2218 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1118 Number of atoms = 3389 Number of groups = 1123 Number of bonds = 3382 Number of angles = 1222 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2218 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.214" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1118" Evaluating: 1118-7 Parameter: NUMWAT <- "1111" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1111" Comparing "1081" and "1111". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.214" Parameter: BOX -> "32.214" Parameter: BOX -> "32.214" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.21400 B = 32.21400 C = 32.21400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7343 2 1 -1 0 -1 3.5614 3 1 -1 1 -1 4.9486 4 1 0 -1 -1 3.8766 5 1 0 0 -1 0.5568 6 1 0 1 -1 5.3103 7 1 -1 -1 0 4.1876 8 1 -1 0 0 2.8428 9 1 -1 1 0 5.0284 10 1 0 -1 0 0.3662 11 1 0 1 0 0.3662 12 1 -1 -1 1 7.6025 13 1 -1 0 1 2.8882 14 1 -1 1 1 5.4065 15 1 0 -1 1 5.3103 16 1 0 0 1 0.5568 17 1 0 1 1 3.8766 18 1 1 1 1 6.7343 19 1 1 0 1 3.5614 20 1 1 -1 1 4.9486 21 1 1 1 0 4.1876 22 1 1 0 0 2.8428 23 1 1 -1 0 5.0284 24 1 1 1 -1 7.6025 25 1 1 0 -1 2.8882 26 1 1 -1 -1 5.4065 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3315 atoms have been selected out of 3389 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1488 496 496 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 114 38 38 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 1.17 Total of12539 atoms and 4164 groups and 4157 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3389 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1118 Number of atoms = 3389 Number of groups = 1123 Number of bonds = 3382 Number of angles = 1222 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2218 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1118 Number of atoms = 3389 Number of groups = 1123 Number of bonds = 3382 Number of angles = 1222 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2218 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.212" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1118" Evaluating: 1118-7 Parameter: NUMWAT <- "1111" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1111" Comparing "1081" and "1111". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.212" Parameter: BOX -> "32.212" Parameter: BOX -> "32.212" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.21200 B = 32.21200 C = 32.21200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7316 2 1 -1 0 -1 3.5586 3 1 -1 1 -1 4.9458 4 1 0 -1 -1 3.8739 5 1 0 0 -1 0.5559 6 1 0 1 -1 5.3076 7 1 -1 -1 0 4.1886 8 1 -1 0 0 2.8421 9 1 -1 1 0 5.0256 10 1 0 -1 0 0.3654 11 1 0 1 0 0.3654 12 1 -1 -1 1 7.5997 13 1 -1 0 1 2.8857 14 1 -1 1 1 5.4037 15 1 0 -1 1 5.3076 16 1 0 0 1 0.5559 17 1 0 1 1 3.8739 18 1 1 1 1 6.7316 19 1 1 0 1 3.5586 20 1 1 -1 1 4.9458 21 1 1 1 0 4.1886 22 1 1 0 0 2.8421 23 1 1 -1 0 5.0256 24 1 1 1 -1 7.5997 25 1 1 0 -1 2.8857 26 1 1 -1 -1 5.4037 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3315 atoms have been selected out of 3389 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 636 212 212 0.00 5 C005 has 1488 496 496 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 114 38 38 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 1.17 Total of12539 atoms and 4164 groups and 4157 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3389 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1118 Number of atoms = 3389 Number of groups = 1123 Number of bonds = 3382 Number of angles = 1222 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2218 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1118 Number of atoms = 3389 Number of groups = 1123 Number of bonds = 3382 Number of angles = 1222 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2218 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.21" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1118" Evaluating: 1118-7 Parameter: NUMWAT <- "1111" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1111" Comparing "1081" and "1111". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.21" Parameter: BOX -> "32.21" Parameter: BOX -> "32.21" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.21000 B = 32.21000 C = 32.21000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7289 2 1 -1 0 -1 3.5558 3 1 -1 1 -1 4.9430 4 1 0 -1 -1 3.8712 5 1 0 0 -1 0.5551 6 1 0 1 -1 5.3049 7 1 -1 -1 0 4.1895 8 1 -1 0 0 2.8414 9 1 -1 1 0 5.0227 10 1 0 -1 0 0.3646 11 1 0 1 0 0.3646 12 1 -1 -1 1 7.5969 13 1 -1 0 1 2.8832 14 1 -1 1 1 5.4009 15 1 0 -1 1 5.3049 16 1 0 0 1 0.5551 17 1 0 1 1 3.8712 18 1 1 1 1 6.7289 19 1 1 0 1 3.5558 20 1 1 -1 1 4.9430 21 1 1 1 0 4.1895 22 1 1 0 0 2.8414 23 1 1 -1 0 5.0227 24 1 1 1 -1 7.5969 25 1 1 0 -1 2.8832 26 1 1 -1 -1 5.4009 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3315 atoms have been selected out of 3389 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 855 OPERATED ON BY TRANSFORMATION C010 RESIDUE 883 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 759 253 253 0.00 3 C003 has 111 37 37 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1488 496 496 0.00 6 C006 has 447 149 149 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1584 528 528 0.00 12 C012 has 114 38 38 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 1.16 Total of12536 atoms and 4163 groups and 4156 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3389 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1116 Number of atoms = 3383 Number of groups = 1121 Number of bonds = 3376 Number of angles = 1220 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1118 Number of HB donors = 2214 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1116 Number of atoms = 3383 Number of groups = 1121 Number of bonds = 3376 Number of angles = 1220 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1118 Number of HB donors = 2214 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.208" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1116" Evaluating: 1116-7 Parameter: NUMWAT <- "1109" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1109" Comparing "1081" and "1109". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.208" Parameter: BOX -> "32.208" Parameter: BOX -> "32.208" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.20800 B = 32.20800 C = 32.20800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7261 2 1 -1 0 -1 3.5530 3 1 -1 1 -1 4.9402 4 1 0 -1 -1 3.8685 5 1 0 0 -1 0.5543 6 1 0 1 -1 5.3022 7 1 -1 -1 0 4.1904 8 1 -1 0 0 2.8407 9 1 -1 1 0 5.0199 10 1 0 -1 0 0.3638 11 1 0 1 0 0.3638 12 1 -1 -1 1 7.5940 13 1 -1 0 1 2.8807 14 1 -1 1 1 5.3981 15 1 0 -1 1 5.3022 16 1 0 0 1 0.5543 17 1 0 1 1 3.8685 18 1 1 1 1 6.7261 19 1 1 0 1 3.5530 20 1 1 -1 1 4.9402 21 1 1 1 0 4.1904 22 1 1 0 0 2.8407 23 1 1 -1 0 5.0199 24 1 1 1 -1 7.5940 25 1 1 0 -1 2.8807 26 1 1 -1 -1 5.3981 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3309 atoms have been selected out of 3383 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 761 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1479 493 493 0.00 6 C006 has 441 147 147 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1578 526 526 0.00 12 C012 has 114 38 38 0.00 13 C013 has 495 165 165 0.00 14 C014 has 126 42 42 1.16 Total of12509 atoms and 4154 groups and 4147 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3383 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1115 Number of atoms = 3380 Number of groups = 1120 Number of bonds = 3373 Number of angles = 1219 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1117 Number of HB donors = 2212 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1115 Number of atoms = 3380 Number of groups = 1120 Number of bonds = 3373 Number of angles = 1219 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1117 Number of HB donors = 2212 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.206" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1115" Evaluating: 1115-7 Parameter: NUMWAT <- "1108" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1108" Comparing "1081" and "1108". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.206" Parameter: BOX -> "32.206" Parameter: BOX -> "32.206" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.20600 B = 32.20600 C = 32.20600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7234 2 1 -1 0 -1 3.5502 3 1 -1 1 -1 4.9374 4 1 0 -1 -1 3.8658 5 1 0 0 -1 0.5535 6 1 0 1 -1 5.2995 7 1 -1 -1 0 4.1914 8 1 -1 0 0 2.8400 9 1 -1 1 0 5.0171 10 1 0 -1 0 0.3630 11 1 0 1 0 0.3630 12 1 -1 -1 1 7.5912 13 1 -1 0 1 2.8782 14 1 -1 1 1 5.3954 15 1 0 -1 1 5.2995 16 1 0 0 1 0.5535 17 1 0 1 1 3.8658 18 1 1 1 1 6.7234 19 1 1 0 1 3.5502 20 1 1 -1 1 4.9374 21 1 1 1 0 4.1914 22 1 1 0 0 2.8400 23 1 1 -1 0 5.0171 24 1 1 1 -1 7.5912 25 1 1 0 -1 2.8782 26 1 1 -1 -1 5.3954 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3306 atoms have been selected out of 3380 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1479 493 493 0.00 6 C006 has 441 147 147 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1578 526 526 0.00 12 C012 has 114 38 38 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 1.16 Total of12500 atoms and 4151 groups and 4144 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3380 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1115 Number of atoms = 3380 Number of groups = 1120 Number of bonds = 3373 Number of angles = 1219 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1117 Number of HB donors = 2212 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1115 Number of atoms = 3380 Number of groups = 1120 Number of bonds = 3373 Number of angles = 1219 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1117 Number of HB donors = 2212 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.204" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1115" Evaluating: 1115-7 Parameter: NUMWAT <- "1108" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1108" Comparing "1081" and "1108". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.204" Parameter: BOX -> "32.204" Parameter: BOX -> "32.204" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.20400 B = 32.20400 C = 32.20400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7206 2 1 -1 0 -1 3.5474 3 1 -1 1 -1 4.9346 4 1 0 -1 -1 3.8631 5 1 0 0 -1 0.5526 6 1 0 1 -1 5.2968 7 1 -1 -1 0 4.1923 8 1 -1 0 0 2.8393 9 1 -1 1 0 5.0143 10 1 0 -1 0 0.3622 11 1 0 1 0 0.3622 12 1 -1 -1 1 7.5884 13 1 -1 0 1 2.8757 14 1 -1 1 1 5.3926 15 1 0 -1 1 5.2968 16 1 0 0 1 0.5526 17 1 0 1 1 3.8631 18 1 1 1 1 6.7206 19 1 1 0 1 3.5474 20 1 1 -1 1 4.9346 21 1 1 1 0 4.1923 22 1 1 0 0 2.8393 23 1 1 -1 0 5.0143 24 1 1 1 -1 7.5884 25 1 1 0 -1 2.8757 26 1 1 -1 -1 5.3926 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3306 atoms have been selected out of 3380 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1479 493 493 0.00 6 C006 has 441 147 147 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1578 526 526 0.00 12 C012 has 114 38 38 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 1.16 Total of12500 atoms and 4151 groups and 4144 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3380 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1115 Number of atoms = 3380 Number of groups = 1120 Number of bonds = 3373 Number of angles = 1219 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1117 Number of HB donors = 2212 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1115 Number of atoms = 3380 Number of groups = 1120 Number of bonds = 3373 Number of angles = 1219 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1117 Number of HB donors = 2212 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.202" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1115" Evaluating: 1115-7 Parameter: NUMWAT <- "1108" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1108" Comparing "1081" and "1108". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.202" Parameter: BOX -> "32.202" Parameter: BOX -> "32.202" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.20200 B = 32.20200 C = 32.20200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7179 2 1 -1 0 -1 3.5446 3 1 -1 1 -1 4.9318 4 1 0 -1 -1 3.8604 5 1 0 0 -1 0.5518 6 1 0 1 -1 5.2941 7 1 -1 -1 0 4.1932 8 1 -1 0 0 2.8386 9 1 -1 1 0 5.0114 10 1 0 -1 0 0.3615 11 1 0 1 0 0.3615 12 1 -1 -1 1 7.5856 13 1 -1 0 1 2.8732 14 1 -1 1 1 5.3898 15 1 0 -1 1 5.2941 16 1 0 0 1 0.5518 17 1 0 1 1 3.8604 18 1 1 1 1 6.7179 19 1 1 0 1 3.5446 20 1 1 -1 1 4.9318 21 1 1 1 0 4.1932 22 1 1 0 0 2.8386 23 1 1 -1 0 5.0114 24 1 1 1 -1 7.5856 25 1 1 0 -1 2.8732 26 1 1 -1 -1 5.3898 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3306 atoms have been selected out of 3380 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1479 493 493 0.00 6 C006 has 441 147 147 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1578 526 526 0.00 12 C012 has 114 38 38 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 1.16 Total of12503 atoms and 4152 groups and 4145 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3380 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1115 Number of atoms = 3380 Number of groups = 1120 Number of bonds = 3373 Number of angles = 1219 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1117 Number of HB donors = 2212 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1115 Number of atoms = 3380 Number of groups = 1120 Number of bonds = 3373 Number of angles = 1219 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1117 Number of HB donors = 2212 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.2" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1115" Evaluating: 1115-7 Parameter: NUMWAT <- "1108" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1108" Comparing "1081" and "1108". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.2" Parameter: BOX -> "32.2" Parameter: BOX -> "32.2" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.20000 B = 32.20000 C = 32.20000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7152 2 1 -1 0 -1 3.5418 3 1 -1 1 -1 4.9290 4 1 0 -1 -1 3.8577 5 1 0 0 -1 0.5510 6 1 0 1 -1 5.2914 7 1 -1 -1 0 4.1942 8 1 -1 0 0 2.8380 9 1 -1 1 0 5.0086 10 1 0 -1 0 0.3607 11 1 0 1 0 0.3607 12 1 -1 -1 1 7.5827 13 1 -1 0 1 2.8707 14 1 -1 1 1 5.3870 15 1 0 -1 1 5.2914 16 1 0 0 1 0.5510 17 1 0 1 1 3.8577 18 1 1 1 1 6.7152 19 1 1 0 1 3.5418 20 1 1 -1 1 4.9290 21 1 1 1 0 4.1942 22 1 1 0 0 2.8380 23 1 1 -1 0 5.0086 24 1 1 1 -1 7.5827 25 1 1 0 -1 2.8707 26 1 1 -1 -1 5.3870 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3306 atoms have been selected out of 3380 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1047 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1479 493 493 0.00 6 C006 has 441 147 147 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1578 526 526 0.00 12 C012 has 114 38 38 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 1.15 Total of12503 atoms and 4152 groups and 4145 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3380 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1114 Number of atoms = 3377 Number of groups = 1119 Number of bonds = 3370 Number of angles = 1218 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1116 Number of HB donors = 2210 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1114 Number of atoms = 3377 Number of groups = 1119 Number of bonds = 3370 Number of angles = 1218 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1116 Number of HB donors = 2210 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.198" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1114" Evaluating: 1114-7 Parameter: NUMWAT <- "1107" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1107" Comparing "1081" and "1107". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.198" Parameter: BOX -> "32.198" Parameter: BOX -> "32.198" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.19800 B = 32.19800 C = 32.19800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7124 2 1 -1 0 -1 3.5391 3 1 -1 1 -1 4.9262 4 1 0 -1 -1 3.8550 5 1 0 0 -1 0.5502 6 1 0 1 -1 5.2887 7 1 -1 -1 0 4.1951 8 1 -1 0 0 2.8373 9 1 -1 1 0 5.0058 10 1 0 -1 0 0.3599 11 1 0 1 0 0.3599 12 1 -1 -1 1 7.5799 13 1 -1 0 1 2.8682 14 1 -1 1 1 5.3842 15 1 0 -1 1 5.2887 16 1 0 0 1 0.5502 17 1 0 1 1 3.8550 18 1 1 1 1 6.7124 19 1 1 0 1 3.5391 20 1 1 -1 1 4.9262 21 1 1 1 0 4.1951 22 1 1 0 0 2.8373 23 1 1 -1 0 5.0058 24 1 1 1 -1 7.5799 25 1 1 0 -1 2.8682 26 1 1 -1 -1 5.3842 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3303 atoms have been selected out of 3377 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1476 492 492 0.00 6 C006 has 441 147 147 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1578 526 526 0.00 12 C012 has 114 38 38 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 1.15 Total of12491 atoms and 4148 groups and 4141 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3377 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1114 Number of atoms = 3377 Number of groups = 1119 Number of bonds = 3370 Number of angles = 1218 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1116 Number of HB donors = 2210 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1114 Number of atoms = 3377 Number of groups = 1119 Number of bonds = 3370 Number of angles = 1218 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1116 Number of HB donors = 2210 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.196" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1114" Evaluating: 1114-7 Parameter: NUMWAT <- "1107" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1107" Comparing "1081" and "1107". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.196" Parameter: BOX -> "32.196" Parameter: BOX -> "32.196" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.19600 B = 32.19600 C = 32.19600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7097 2 1 -1 0 -1 3.5363 3 1 -1 1 -1 4.9234 4 1 0 -1 -1 3.8523 5 1 0 0 -1 0.5494 6 1 0 1 -1 5.2860 7 1 -1 -1 0 4.1961 8 1 -1 0 0 2.8366 9 1 -1 1 0 5.0030 10 1 0 -1 0 0.3592 11 1 0 1 0 0.3592 12 1 -1 -1 1 7.5771 13 1 -1 0 1 2.8657 14 1 -1 1 1 5.3814 15 1 0 -1 1 5.2860 16 1 0 0 1 0.5494 17 1 0 1 1 3.8523 18 1 1 1 1 6.7097 19 1 1 0 1 3.5363 20 1 1 -1 1 4.9234 21 1 1 1 0 4.1961 22 1 1 0 0 2.8366 23 1 1 -1 0 5.0030 24 1 1 1 -1 7.5771 25 1 1 0 -1 2.8657 26 1 1 -1 -1 5.3814 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3303 atoms have been selected out of 3377 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1476 492 492 0.00 6 C006 has 441 147 147 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1578 526 526 0.00 12 C012 has 114 38 38 0.00 13 C013 has 495 165 165 0.00 14 C014 has 126 42 42 1.15 Total of12497 atoms and 4150 groups and 4143 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3377 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1114 Number of atoms = 3377 Number of groups = 1119 Number of bonds = 3370 Number of angles = 1218 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1116 Number of HB donors = 2210 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1114 Number of atoms = 3377 Number of groups = 1119 Number of bonds = 3370 Number of angles = 1218 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1116 Number of HB donors = 2210 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.194" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1114" Evaluating: 1114-7 Parameter: NUMWAT <- "1107" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1107" Comparing "1081" and "1107". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.194" Parameter: BOX -> "32.194" Parameter: BOX -> "32.194" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.19400 B = 32.19400 C = 32.19400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7069 2 1 -1 0 -1 3.5335 3 1 -1 1 -1 4.9206 4 1 0 -1 -1 3.8496 5 1 0 0 -1 0.5487 6 1 0 1 -1 5.2833 7 1 -1 -1 0 4.1970 8 1 -1 0 0 2.8359 9 1 -1 1 0 5.0002 10 1 0 -1 0 0.3585 11 1 0 1 0 0.3585 12 1 -1 -1 1 7.5743 13 1 -1 0 1 2.8632 14 1 -1 1 1 5.3787 15 1 0 -1 1 5.2833 16 1 0 0 1 0.5487 17 1 0 1 1 3.8496 18 1 1 1 1 6.7069 19 1 1 0 1 3.5335 20 1 1 -1 1 4.9206 21 1 1 1 0 4.1970 22 1 1 0 0 2.8359 23 1 1 -1 0 5.0002 24 1 1 1 -1 7.5743 25 1 1 0 -1 2.8632 26 1 1 -1 -1 5.3787 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3303 atoms have been selected out of 3377 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1479 493 493 0.00 6 C006 has 441 147 147 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1578 526 526 0.00 12 C012 has 114 38 38 0.00 13 C013 has 495 165 165 0.00 14 C014 has 126 42 42 1.15 Total of12500 atoms and 4151 groups and 4144 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3377 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1114 Number of atoms = 3377 Number of groups = 1119 Number of bonds = 3370 Number of angles = 1218 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1116 Number of HB donors = 2210 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1114 Number of atoms = 3377 Number of groups = 1119 Number of bonds = 3370 Number of angles = 1218 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1116 Number of HB donors = 2210 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.192" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1114" Evaluating: 1114-7 Parameter: NUMWAT <- "1107" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1107" Comparing "1081" and "1107". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.192" Parameter: BOX -> "32.192" Parameter: BOX -> "32.192" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.19200 B = 32.19200 C = 32.19200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7042 2 1 -1 0 -1 3.5307 3 1 -1 1 -1 4.9178 4 1 0 -1 -1 3.8469 5 1 0 0 -1 0.5479 6 1 0 1 -1 5.2806 7 1 -1 -1 0 4.1980 8 1 -1 0 0 2.8352 9 1 -1 1 0 4.9973 10 1 0 -1 0 0.3577 11 1 0 1 0 0.3577 12 1 -1 -1 1 7.5715 13 1 -1 0 1 2.8607 14 1 -1 1 1 5.3759 15 1 0 -1 1 5.2806 16 1 0 0 1 0.5479 17 1 0 1 1 3.8469 18 1 1 1 1 6.7042 19 1 1 0 1 3.5307 20 1 1 -1 1 4.9178 21 1 1 1 0 4.1980 22 1 1 0 0 2.8352 23 1 1 -1 0 4.9973 24 1 1 1 -1 7.5715 25 1 1 0 -1 2.8607 26 1 1 -1 -1 5.3759 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3303 atoms have been selected out of 3377 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1479 493 493 0.00 6 C006 has 441 147 147 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1578 526 526 0.00 12 C012 has 114 38 38 0.00 13 C013 has 495 165 165 0.00 14 C014 has 126 42 42 1.15 Total of12500 atoms and 4151 groups and 4144 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3377 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1114 Number of atoms = 3377 Number of groups = 1119 Number of bonds = 3370 Number of angles = 1218 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1116 Number of HB donors = 2210 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1114 Number of atoms = 3377 Number of groups = 1119 Number of bonds = 3370 Number of angles = 1218 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1116 Number of HB donors = 2210 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.19" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1114" Evaluating: 1114-7 Parameter: NUMWAT <- "1107" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1107" Comparing "1081" and "1107". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.19" Parameter: BOX -> "32.19" Parameter: BOX -> "32.19" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.19000 B = 32.19000 C = 32.19000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.7015 2 1 -1 0 -1 3.5279 3 1 -1 1 -1 4.9150 4 1 0 -1 -1 3.8442 5 1 0 0 -1 0.5471 6 1 0 1 -1 5.2779 7 1 -1 -1 0 4.1989 8 1 -1 0 0 2.8346 9 1 -1 1 0 4.9945 10 1 0 -1 0 0.3570 11 1 0 1 0 0.3570 12 1 -1 -1 1 7.5686 13 1 -1 0 1 2.8582 14 1 -1 1 1 5.3731 15 1 0 -1 1 5.2779 16 1 0 0 1 0.5471 17 1 0 1 1 3.8442 18 1 1 1 1 6.7015 19 1 1 0 1 3.5279 20 1 1 -1 1 4.9150 21 1 1 1 0 4.1989 22 1 1 0 0 2.8346 23 1 1 -1 0 4.9945 24 1 1 1 -1 7.5686 25 1 1 0 -1 2.8582 26 1 1 -1 -1 5.3731 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3303 atoms have been selected out of 3377 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 56 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1479 493 493 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1581 527 527 0.00 12 C012 has 114 38 38 0.00 13 C013 has 495 165 165 0.00 14 C014 has 126 42 42 1.14 Total of12506 atoms and 4153 groups and 4146 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3377 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1113 Number of atoms = 3374 Number of groups = 1118 Number of bonds = 3367 Number of angles = 1217 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1115 Number of HB donors = 2208 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1113 Number of atoms = 3374 Number of groups = 1118 Number of bonds = 3367 Number of angles = 1217 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1115 Number of HB donors = 2208 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.188" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1113" Evaluating: 1113-7 Parameter: NUMWAT <- "1106" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1106" Comparing "1081" and "1106". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.188" Parameter: BOX -> "32.188" Parameter: BOX -> "32.188" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.18800 B = 32.18800 C = 32.18800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6987 2 1 -1 0 -1 3.5251 3 1 -1 1 -1 4.9122 4 1 0 -1 -1 3.8415 5 1 0 0 -1 0.5464 6 1 0 1 -1 5.2753 7 1 -1 -1 0 4.1998 8 1 -1 0 0 2.8339 9 1 -1 1 0 4.9917 10 1 0 -1 0 0.3563 11 1 0 1 0 0.3563 12 1 -1 -1 1 7.5658 13 1 -1 0 1 2.8557 14 1 -1 1 1 5.3703 15 1 0 -1 1 5.2753 16 1 0 0 1 0.5464 17 1 0 1 1 3.8415 18 1 1 1 1 6.6987 19 1 1 0 1 3.5251 20 1 1 -1 1 4.9122 21 1 1 1 0 4.1998 22 1 1 0 0 2.8339 23 1 1 -1 0 4.9917 24 1 1 1 -1 7.5658 25 1 1 0 -1 2.8557 26 1 1 -1 -1 5.3703 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3300 atoms have been selected out of 3374 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 753 251 251 0.00 3 C003 has 111 37 37 0.00 4 C004 has 633 211 211 0.00 5 C005 has 1479 493 493 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1578 526 526 0.00 12 C012 has 114 38 38 0.00 13 C013 has 495 165 165 0.00 14 C014 has 126 42 42 1.14 Total of12503 atoms and 4152 groups and 4145 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3374 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1113 Number of atoms = 3374 Number of groups = 1118 Number of bonds = 3367 Number of angles = 1217 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1115 Number of HB donors = 2208 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1113 Number of atoms = 3374 Number of groups = 1118 Number of bonds = 3367 Number of angles = 1217 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1115 Number of HB donors = 2208 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.186" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1113" Evaluating: 1113-7 Parameter: NUMWAT <- "1106" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1106" Comparing "1081" and "1106". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.186" Parameter: BOX -> "32.186" Parameter: BOX -> "32.186" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.18600 B = 32.18600 C = 32.18600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6960 2 1 -1 0 -1 3.5223 3 1 -1 1 -1 4.9094 4 1 0 -1 -1 3.8388 5 1 0 0 -1 0.5456 6 1 0 1 -1 5.2726 7 1 -1 -1 0 4.2008 8 1 -1 0 0 2.8332 9 1 -1 1 0 4.9889 10 1 0 -1 0 0.3556 11 1 0 1 0 0.3556 12 1 -1 -1 1 7.5630 13 1 -1 0 1 2.8532 14 1 -1 1 1 5.3676 15 1 0 -1 1 5.2726 16 1 0 0 1 0.5456 17 1 0 1 1 3.8388 18 1 1 1 1 6.6960 19 1 1 0 1 3.5223 20 1 1 -1 1 4.9094 21 1 1 1 0 4.2008 22 1 1 0 0 2.8332 23 1 1 -1 0 4.9889 24 1 1 1 -1 7.5630 25 1 1 0 -1 2.8532 26 1 1 -1 -1 5.3676 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3300 atoms have been selected out of 3374 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 899 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1044 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 756 252 252 0.00 3 C003 has 111 37 37 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1473 491 491 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1578 526 526 0.00 12 C012 has 117 39 39 0.00 13 C013 has 483 161 161 0.00 14 C014 has 126 42 42 1.14 Total of12479 atoms and 4144 groups and 4137 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3374 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1111 Number of atoms = 3368 Number of groups = 1116 Number of bonds = 3361 Number of angles = 1215 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1113 Number of HB donors = 2204 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1111 Number of atoms = 3368 Number of groups = 1116 Number of bonds = 3361 Number of angles = 1215 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1113 Number of HB donors = 2204 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.184" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1111" Evaluating: 1111-7 Parameter: NUMWAT <- "1104" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1104" Comparing "1081" and "1104". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.184" Parameter: BOX -> "32.184" Parameter: BOX -> "32.184" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.18400 B = 32.18400 C = 32.18400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6933 2 1 -1 0 -1 3.5195 3 1 -1 1 -1 4.9066 4 1 0 -1 -1 3.8361 5 1 0 0 -1 0.5448 6 1 0 1 -1 5.2699 7 1 -1 -1 0 4.2191 8 1 -1 0 0 3.2210 9 1 -1 1 0 4.9860 10 1 0 -1 0 0.3549 11 1 0 1 0 0.3549 12 1 -1 -1 1 7.2210 13 1 -1 0 1 3.4797 14 1 -1 1 1 5.3648 15 1 0 -1 1 5.2699 16 1 0 0 1 0.5448 17 1 0 1 1 3.8361 18 1 1 1 1 6.6933 19 1 1 0 1 3.5195 20 1 1 -1 1 4.9066 21 1 1 1 0 4.2191 22 1 1 0 0 3.2210 23 1 1 -1 0 4.9860 24 1 1 1 -1 7.2210 25 1 1 0 -1 3.4797 26 1 1 -1 -1 5.3648 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3294 atoms have been selected out of 3368 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1473 491 491 0.00 6 C006 has 447 149 149 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1689 554 552 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1572 524 524 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.14 Total of12452 atoms and 4135 groups and 4128 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3368 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1111 Number of atoms = 3368 Number of groups = 1116 Number of bonds = 3361 Number of angles = 1215 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1113 Number of HB donors = 2204 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1111 Number of atoms = 3368 Number of groups = 1116 Number of bonds = 3361 Number of angles = 1215 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1113 Number of HB donors = 2204 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.182" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1111" Evaluating: 1111-7 Parameter: NUMWAT <- "1104" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1104" Comparing "1081" and "1104". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.182" Parameter: BOX -> "32.182" Parameter: BOX -> "32.182" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.18200 B = 32.18200 C = 32.18200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6906 2 1 -1 0 -1 3.5167 3 1 -1 1 -1 4.9038 4 1 0 -1 -1 3.8334 5 1 0 0 -1 0.5441 6 1 0 1 -1 5.2672 7 1 -1 -1 0 4.2165 8 1 -1 0 0 3.2199 9 1 -1 1 0 4.9832 10 1 0 -1 0 0.3543 11 1 0 1 0 0.3543 12 1 -1 -1 1 7.2178 13 1 -1 0 1 3.4779 14 1 -1 1 1 5.3620 15 1 0 -1 1 5.2672 16 1 0 0 1 0.5441 17 1 0 1 1 3.8334 18 1 1 1 1 6.6906 19 1 1 0 1 3.5167 20 1 1 -1 1 4.9038 21 1 1 1 0 4.2165 22 1 1 0 0 3.2199 23 1 1 -1 0 4.9832 24 1 1 1 -1 7.2178 25 1 1 0 -1 3.4779 26 1 1 -1 -1 5.3620 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3294 atoms have been selected out of 3368 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 528 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1473 491 491 0.00 6 C006 has 447 149 149 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1569 523 523 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.14 Total of12452 atoms and 4135 groups and 4128 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3368 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1110 Number of atoms = 3365 Number of groups = 1115 Number of bonds = 3358 Number of angles = 1214 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1112 Number of HB donors = 2202 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1110 Number of atoms = 3365 Number of groups = 1115 Number of bonds = 3358 Number of angles = 1214 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1112 Number of HB donors = 2202 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.18" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1110" Evaluating: 1110-7 Parameter: NUMWAT <- "1103" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1103" Comparing "1081" and "1103". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.18" Parameter: BOX -> "32.18" Parameter: BOX -> "32.18" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.18000 B = 32.18000 C = 32.18000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6878 2 1 -1 0 -1 3.5139 3 1 -1 1 -1 4.9010 4 1 0 -1 -1 3.8307 5 1 0 0 -1 0.5434 6 1 0 1 -1 5.2645 7 1 -1 -1 0 4.2139 8 1 -1 0 0 3.2187 9 1 -1 1 0 4.9804 10 1 0 -1 0 0.3536 11 1 0 1 0 0.3536 12 1 -1 -1 1 7.2146 13 1 -1 0 1 3.4762 14 1 -1 1 1 5.3592 15 1 0 -1 1 5.2645 16 1 0 0 1 0.5434 17 1 0 1 1 3.8307 18 1 1 1 1 6.6878 19 1 1 0 1 3.5139 20 1 1 -1 1 4.9010 21 1 1 1 0 4.2139 22 1 1 0 0 3.2187 23 1 1 -1 0 4.9804 24 1 1 1 -1 7.2146 25 1 1 0 -1 3.4762 26 1 1 -1 -1 5.3592 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3291 atoms have been selected out of 3365 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1473 491 491 0.00 6 C006 has 447 149 149 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1569 523 523 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.13 Total of12446 atoms and 4133 groups and 4126 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3365 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1110 Number of atoms = 3365 Number of groups = 1115 Number of bonds = 3358 Number of angles = 1214 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1112 Number of HB donors = 2202 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1110 Number of atoms = 3365 Number of groups = 1115 Number of bonds = 3358 Number of angles = 1214 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1112 Number of HB donors = 2202 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.178" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1110" Evaluating: 1110-7 Parameter: NUMWAT <- "1103" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1103" Comparing "1081" and "1103". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.178" Parameter: BOX -> "32.178" Parameter: BOX -> "32.178" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.17800 B = 32.17800 C = 32.17800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6851 2 1 -1 0 -1 3.5111 3 1 -1 1 -1 4.8982 4 1 0 -1 -1 3.8280 5 1 0 0 -1 0.5426 6 1 0 1 -1 5.2618 7 1 -1 -1 0 4.2113 8 1 -1 0 0 3.2176 9 1 -1 1 0 4.9776 10 1 0 -1 0 0.3529 11 1 0 1 0 0.3529 12 1 -1 -1 1 7.2114 13 1 -1 0 1 3.4744 14 1 -1 1 1 5.3565 15 1 0 -1 1 5.2618 16 1 0 0 1 0.5426 17 1 0 1 1 3.8280 18 1 1 1 1 6.6851 19 1 1 0 1 3.5111 20 1 1 -1 1 4.8982 21 1 1 1 0 4.2113 22 1 1 0 0 3.2176 23 1 1 -1 0 4.9776 24 1 1 1 -1 7.2114 25 1 1 0 -1 3.4744 26 1 1 -1 -1 5.3565 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3291 atoms have been selected out of 3365 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1473 491 491 0.00 6 C006 has 447 149 149 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1569 523 523 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.13 Total of12446 atoms and 4133 groups and 4126 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3365 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1110 Number of atoms = 3365 Number of groups = 1115 Number of bonds = 3358 Number of angles = 1214 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1112 Number of HB donors = 2202 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1110 Number of atoms = 3365 Number of groups = 1115 Number of bonds = 3358 Number of angles = 1214 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1112 Number of HB donors = 2202 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.176" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1110" Evaluating: 1110-7 Parameter: NUMWAT <- "1103" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1103" Comparing "1081" and "1103". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.176" Parameter: BOX -> "32.176" Parameter: BOX -> "32.176" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.17600 B = 32.17600 C = 32.17600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6824 2 1 -1 0 -1 3.5083 3 1 -1 1 -1 4.8954 4 1 0 -1 -1 3.8253 5 1 0 0 -1 0.5419 6 1 0 1 -1 5.2591 7 1 -1 -1 0 4.2088 8 1 -1 0 0 3.2165 9 1 -1 1 0 4.9748 10 1 0 -1 0 0.3523 11 1 0 1 0 0.3523 12 1 -1 -1 1 7.2082 13 1 -1 0 1 3.4726 14 1 -1 1 1 5.3537 15 1 0 -1 1 5.2591 16 1 0 0 1 0.5419 17 1 0 1 1 3.8253 18 1 1 1 1 6.6824 19 1 1 0 1 3.5083 20 1 1 -1 1 4.8954 21 1 1 1 0 4.2088 22 1 1 0 0 3.2165 23 1 1 -1 0 4.9748 24 1 1 1 -1 7.2082 25 1 1 0 -1 3.4726 26 1 1 -1 -1 5.3537 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3291 atoms have been selected out of 3365 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 750 250 250 0.00 3 C003 has 111 37 37 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1473 491 491 0.00 6 C006 has 447 149 149 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1569 523 523 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.13 Total of12446 atoms and 4133 groups and 4126 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3365 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1110 Number of atoms = 3365 Number of groups = 1115 Number of bonds = 3358 Number of angles = 1214 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1112 Number of HB donors = 2202 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1110 Number of atoms = 3365 Number of groups = 1115 Number of bonds = 3358 Number of angles = 1214 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1112 Number of HB donors = 2202 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.174" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1110" Evaluating: 1110-7 Parameter: NUMWAT <- "1103" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1103" Comparing "1081" and "1103". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.174" Parameter: BOX -> "32.174" Parameter: BOX -> "32.174" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.17400 B = 32.17400 C = 32.17400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6796 2 1 -1 0 -1 3.5055 3 1 -1 1 -1 4.8926 4 1 0 -1 -1 3.8226 5 1 0 0 -1 0.5412 6 1 0 1 -1 5.2564 7 1 -1 -1 0 4.2062 8 1 -1 0 0 3.2153 9 1 -1 1 0 4.9719 10 1 0 -1 0 0.3517 11 1 0 1 0 0.3517 12 1 -1 -1 1 7.2050 13 1 -1 0 1 3.4709 14 1 -1 1 1 5.3509 15 1 0 -1 1 5.2564 16 1 0 0 1 0.5412 17 1 0 1 1 3.8226 18 1 1 1 1 6.6796 19 1 1 0 1 3.5055 20 1 1 -1 1 4.8926 21 1 1 1 0 4.2062 22 1 1 0 0 3.2153 23 1 1 -1 0 4.9719 24 1 1 1 -1 7.2050 25 1 1 0 -1 3.4709 26 1 1 -1 -1 5.3509 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3291 atoms have been selected out of 3365 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 750 250 250 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1473 491 491 0.00 6 C006 has 447 149 149 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1569 523 523 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.13 Total of12449 atoms and 4134 groups and 4127 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3365 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1110 Number of atoms = 3365 Number of groups = 1115 Number of bonds = 3358 Number of angles = 1214 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1112 Number of HB donors = 2202 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1110 Number of atoms = 3365 Number of groups = 1115 Number of bonds = 3358 Number of angles = 1214 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1112 Number of HB donors = 2202 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.172" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1110" Evaluating: 1110-7 Parameter: NUMWAT <- "1103" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1103" Comparing "1081" and "1103". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.172" Parameter: BOX -> "32.172" Parameter: BOX -> "32.172" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.17200 B = 32.17200 C = 32.17200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6769 2 1 -1 0 -1 3.5027 3 1 -1 1 -1 4.8898 4 1 0 -1 -1 3.8199 5 1 0 0 -1 0.5405 6 1 0 1 -1 5.2537 7 1 -1 -1 0 4.2036 8 1 -1 0 0 3.2142 9 1 -1 1 0 4.9691 10 1 0 -1 0 0.3510 11 1 0 1 0 0.3510 12 1 -1 -1 1 7.2018 13 1 -1 0 1 3.4691 14 1 -1 1 1 5.3482 15 1 0 -1 1 5.2537 16 1 0 0 1 0.5405 17 1 0 1 1 3.8199 18 1 1 1 1 6.6769 19 1 1 0 1 3.5027 20 1 1 -1 1 4.8898 21 1 1 1 0 4.2036 22 1 1 0 0 3.2142 23 1 1 -1 0 4.9691 24 1 1 1 -1 7.2018 25 1 1 0 -1 3.4691 26 1 1 -1 -1 5.3482 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3291 atoms have been selected out of 3365 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 820 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 747 249 249 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1473 491 491 0.00 6 C006 has 444 148 148 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1569 523 523 0.00 12 C012 has 114 38 38 0.00 13 C013 has 483 161 161 0.00 14 C014 has 126 42 42 1.13 Total of12446 atoms and 4133 groups and 4126 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3365 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1109 Number of atoms = 3362 Number of groups = 1114 Number of bonds = 3355 Number of angles = 1213 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1111 Number of HB donors = 2200 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1109 Number of atoms = 3362 Number of groups = 1114 Number of bonds = 3355 Number of angles = 1213 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1111 Number of HB donors = 2200 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.17" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1109" Evaluating: 1109-7 Parameter: NUMWAT <- "1102" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1102" Comparing "1081" and "1102". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.17" Parameter: BOX -> "32.17" Parameter: BOX -> "32.17" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.17000 B = 32.17000 C = 32.17000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6742 2 1 -1 0 -1 3.4999 3 1 -1 1 -1 4.8870 4 1 0 -1 -1 3.8172 5 1 0 0 -1 0.5398 6 1 0 1 -1 5.2510 7 1 -1 -1 0 4.2010 8 1 -1 0 0 3.2131 9 1 -1 1 0 4.9663 10 1 0 -1 0 0.3504 11 1 0 1 0 0.3504 12 1 -1 -1 1 7.1986 13 1 -1 0 1 3.4674 14 1 -1 1 1 5.3454 15 1 0 -1 1 5.2510 16 1 0 0 1 0.5398 17 1 0 1 1 3.8172 18 1 1 1 1 6.6742 19 1 1 0 1 3.4999 20 1 1 -1 1 4.8870 21 1 1 1 0 4.2010 22 1 1 0 0 3.2131 23 1 1 -1 0 4.9663 24 1 1 1 -1 7.1986 25 1 1 0 -1 3.4674 26 1 1 -1 -1 5.3454 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3288 atoms have been selected out of 3362 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 747 249 249 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1470 490 490 0.00 6 C006 has 444 148 148 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1689 554 552 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1569 523 523 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.12 Total of12434 atoms and 4129 groups and 4122 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3362 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1109 Number of atoms = 3362 Number of groups = 1114 Number of bonds = 3355 Number of angles = 1213 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1111 Number of HB donors = 2200 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1109 Number of atoms = 3362 Number of groups = 1114 Number of bonds = 3355 Number of angles = 1213 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1111 Number of HB donors = 2200 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.168" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1109" Evaluating: 1109-7 Parameter: NUMWAT <- "1102" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1102" Comparing "1081" and "1102". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.168" Parameter: BOX -> "32.168" Parameter: BOX -> "32.168" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.16800 B = 32.16800 C = 32.16800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6714 2 1 -1 0 -1 3.4971 3 1 -1 1 -1 4.8843 4 1 0 -1 -1 3.8145 5 1 0 0 -1 0.5391 6 1 0 1 -1 5.2483 7 1 -1 -1 0 4.1984 8 1 -1 0 0 3.2119 9 1 -1 1 0 4.9635 10 1 0 -1 0 0.3498 11 1 0 1 0 0.3498 12 1 -1 -1 1 7.1954 13 1 -1 0 1 3.4656 14 1 -1 1 1 5.3426 15 1 0 -1 1 5.2483 16 1 0 0 1 0.5391 17 1 0 1 1 3.8145 18 1 1 1 1 6.6714 19 1 1 0 1 3.4971 20 1 1 -1 1 4.8843 21 1 1 1 0 4.1984 22 1 1 0 0 3.2119 23 1 1 -1 0 4.9635 24 1 1 1 -1 7.1954 25 1 1 0 -1 3.4656 26 1 1 -1 -1 5.3426 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3288 atoms have been selected out of 3362 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 747 249 249 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1470 490 490 0.00 6 C006 has 444 148 148 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1689 554 552 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1569 523 523 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.12 Total of12434 atoms and 4129 groups and 4122 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3362 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1109 Number of atoms = 3362 Number of groups = 1114 Number of bonds = 3355 Number of angles = 1213 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1111 Number of HB donors = 2200 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1109 Number of atoms = 3362 Number of groups = 1114 Number of bonds = 3355 Number of angles = 1213 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1111 Number of HB donors = 2200 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.166" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1109" Evaluating: 1109-7 Parameter: NUMWAT <- "1102" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1102" Comparing "1081" and "1102". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.166" Parameter: BOX -> "32.166" Parameter: BOX -> "32.166" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.16600 B = 32.16600 C = 32.16600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6687 2 1 -1 0 -1 3.4943 3 1 -1 1 -1 4.8815 4 1 0 -1 -1 3.8118 5 1 0 0 -1 0.5384 6 1 0 1 -1 5.2456 7 1 -1 -1 0 4.1958 8 1 -1 0 0 3.2108 9 1 -1 1 0 4.9607 10 1 0 -1 0 0.3492 11 1 0 1 0 0.3492 12 1 -1 -1 1 7.1921 13 1 -1 0 1 3.4638 14 1 -1 1 1 5.3398 15 1 0 -1 1 5.2456 16 1 0 0 1 0.5384 17 1 0 1 1 3.8118 18 1 1 1 1 6.6687 19 1 1 0 1 3.4943 20 1 1 -1 1 4.8815 21 1 1 1 0 4.1958 22 1 1 0 0 3.2108 23 1 1 -1 0 4.9607 24 1 1 1 -1 7.1921 25 1 1 0 -1 3.4638 26 1 1 -1 -1 5.3398 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3288 atoms have been selected out of 3362 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 747 249 249 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1470 490 490 0.00 6 C006 has 444 148 148 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1569 523 523 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.12 Total of12437 atoms and 4130 groups and 4123 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3362 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1109 Number of atoms = 3362 Number of groups = 1114 Number of bonds = 3355 Number of angles = 1213 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1111 Number of HB donors = 2200 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1109 Number of atoms = 3362 Number of groups = 1114 Number of bonds = 3355 Number of angles = 1213 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1111 Number of HB donors = 2200 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.164" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1109" Evaluating: 1109-7 Parameter: NUMWAT <- "1102" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1102" Comparing "1081" and "1102". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.164" Parameter: BOX -> "32.164" Parameter: BOX -> "32.164" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.16400 B = 32.16400 C = 32.16400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6660 2 1 -1 0 -1 3.4915 3 1 -1 1 -1 4.8787 4 1 0 -1 -1 3.8091 5 1 0 0 -1 0.5377 6 1 0 1 -1 5.2429 7 1 -1 -1 0 4.1932 8 1 -1 0 0 3.2097 9 1 -1 1 0 4.9578 10 1 0 -1 0 0.3486 11 1 0 1 0 0.3486 12 1 -1 -1 1 7.1889 13 1 -1 0 1 3.4621 14 1 -1 1 1 5.3371 15 1 0 -1 1 5.2429 16 1 0 0 1 0.5377 17 1 0 1 1 3.8091 18 1 1 1 1 6.6660 19 1 1 0 1 3.4915 20 1 1 -1 1 4.8787 21 1 1 1 0 4.1932 22 1 1 0 0 3.2097 23 1 1 -1 0 4.9578 24 1 1 1 -1 7.1889 25 1 1 0 -1 3.4621 26 1 1 -1 -1 5.3371 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3288 atoms have been selected out of 3362 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 747 249 249 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1470 490 490 0.00 6 C006 has 444 148 148 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1569 523 523 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.12 Total of12437 atoms and 4130 groups and 4123 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3362 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1109 Number of atoms = 3362 Number of groups = 1114 Number of bonds = 3355 Number of angles = 1213 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1111 Number of HB donors = 2200 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1109 Number of atoms = 3362 Number of groups = 1114 Number of bonds = 3355 Number of angles = 1213 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1111 Number of HB donors = 2200 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.162" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1109" Evaluating: 1109-7 Parameter: NUMWAT <- "1102" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1102" Comparing "1081" and "1102". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.162" Parameter: BOX -> "32.162" Parameter: BOX -> "32.162" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.16200 B = 32.16200 C = 32.16200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6633 2 1 -1 0 -1 3.4887 3 1 -1 1 -1 4.8759 4 1 0 -1 -1 3.8064 5 1 0 0 -1 0.5370 6 1 0 1 -1 5.2402 7 1 -1 -1 0 4.1907 8 1 -1 0 0 3.2085 9 1 -1 1 0 4.9550 10 1 0 -1 0 0.3481 11 1 0 1 0 0.3481 12 1 -1 -1 1 7.1857 13 1 -1 0 1 3.4596 14 1 -1 1 1 5.3343 15 1 0 -1 1 5.2402 16 1 0 0 1 0.5370 17 1 0 1 1 3.8064 18 1 1 1 1 6.6633 19 1 1 0 1 3.4887 20 1 1 -1 1 4.8759 21 1 1 1 0 4.1907 22 1 1 0 0 3.2085 23 1 1 -1 0 4.9550 24 1 1 1 -1 7.1857 25 1 1 0 -1 3.4596 26 1 1 -1 -1 5.3343 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3288 atoms have been selected out of 3362 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 750 250 250 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1473 491 491 0.00 6 C006 has 444 148 148 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1569 523 523 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.12 Total of12443 atoms and 4132 groups and 4125 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3362 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1109 Number of atoms = 3362 Number of groups = 1114 Number of bonds = 3355 Number of angles = 1213 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1111 Number of HB donors = 2200 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1109 Number of atoms = 3362 Number of groups = 1114 Number of bonds = 3355 Number of angles = 1213 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1111 Number of HB donors = 2200 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.16" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1109" Evaluating: 1109-7 Parameter: NUMWAT <- "1102" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1102" Comparing "1081" and "1102". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.16" Parameter: BOX -> "32.16" Parameter: BOX -> "32.16" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.16000 B = 32.16000 C = 32.16000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6605 2 1 -1 0 -1 3.4859 3 1 -1 1 -1 4.8731 4 1 0 -1 -1 3.8038 5 1 0 0 -1 0.5363 6 1 0 1 -1 5.2376 7 1 -1 -1 0 4.1881 8 1 -1 0 0 3.2074 9 1 -1 1 0 4.9522 10 1 0 -1 0 0.3475 11 1 0 1 0 0.3475 12 1 -1 -1 1 7.1825 13 1 -1 0 1 3.4569 14 1 -1 1 1 5.3315 15 1 0 -1 1 5.2376 16 1 0 0 1 0.5363 17 1 0 1 1 3.8038 18 1 1 1 1 6.6605 19 1 1 0 1 3.4859 20 1 1 -1 1 4.8731 21 1 1 1 0 4.1881 22 1 1 0 0 3.2074 23 1 1 -1 0 4.9522 24 1 1 1 -1 7.1825 25 1 1 0 -1 3.4569 26 1 1 -1 -1 5.3315 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3288 atoms have been selected out of 3362 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 750 250 250 0.00 3 C003 has 117 39 39 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1473 491 491 0.00 6 C006 has 444 148 148 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1569 523 523 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.11 Total of12446 atoms and 4133 groups and 4126 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3362 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1109 Number of atoms = 3362 Number of groups = 1114 Number of bonds = 3355 Number of angles = 1213 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1111 Number of HB donors = 2200 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1109 Number of atoms = 3362 Number of groups = 1114 Number of bonds = 3355 Number of angles = 1213 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1111 Number of HB donors = 2200 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.158" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1109" Evaluating: 1109-7 Parameter: NUMWAT <- "1102" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1102" Comparing "1081" and "1102". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.158" Parameter: BOX -> "32.158" Parameter: BOX -> "32.158" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.15800 B = 32.15800 C = 32.15800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6578 2 1 -1 0 -1 3.4832 3 1 -1 1 -1 4.8703 4 1 0 -1 -1 3.8011 5 1 0 0 -1 0.5357 6 1 0 1 -1 5.2349 7 1 -1 -1 0 4.1855 8 1 -1 0 0 3.2063 9 1 -1 1 0 4.9494 10 1 0 -1 0 0.3469 11 1 0 1 0 0.3469 12 1 -1 -1 1 7.1793 13 1 -1 0 1 3.4541 14 1 -1 1 1 5.3288 15 1 0 -1 1 5.2349 16 1 0 0 1 0.5357 17 1 0 1 1 3.8011 18 1 1 1 1 6.6578 19 1 1 0 1 3.4832 20 1 1 -1 1 4.8703 21 1 1 1 0 4.1855 22 1 1 0 0 3.2063 23 1 1 -1 0 4.9494 24 1 1 1 -1 7.1793 25 1 1 0 -1 3.4541 26 1 1 -1 -1 5.3288 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3288 atoms have been selected out of 3362 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 750 250 250 0.00 3 C003 has 117 39 39 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1473 491 491 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1569 523 523 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.11 Total of12449 atoms and 4134 groups and 4127 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3362 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1109 Number of atoms = 3362 Number of groups = 1114 Number of bonds = 3355 Number of angles = 1213 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1111 Number of HB donors = 2200 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1109 Number of atoms = 3362 Number of groups = 1114 Number of bonds = 3355 Number of angles = 1213 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1111 Number of HB donors = 2200 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.156" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1109" Evaluating: 1109-7 Parameter: NUMWAT <- "1102" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1102" Comparing "1081" and "1102". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.156" Parameter: BOX -> "32.156" Parameter: BOX -> "32.156" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.15600 B = 32.15600 C = 32.15600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6551 2 1 -1 0 -1 3.4804 3 1 -1 1 -1 4.8676 4 1 0 -1 -1 3.7984 5 1 0 0 -1 0.5350 6 1 0 1 -1 5.2322 7 1 -1 -1 0 4.1829 8 1 -1 0 0 3.2052 9 1 -1 1 0 4.9465 10 1 0 -1 0 0.3464 11 1 0 1 0 0.3464 12 1 -1 -1 1 7.1761 13 1 -1 0 1 3.4514 14 1 -1 1 1 5.3260 15 1 0 -1 1 5.2322 16 1 0 0 1 0.5350 17 1 0 1 1 3.7984 18 1 1 1 1 6.6551 19 1 1 0 1 3.4804 20 1 1 -1 1 4.8676 21 1 1 1 0 4.1829 22 1 1 0 0 3.2052 23 1 1 -1 0 4.9465 24 1 1 1 -1 7.1761 25 1 1 0 -1 3.4514 26 1 1 -1 -1 5.3260 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3288 atoms have been selected out of 3362 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 750 250 250 0.00 3 C003 has 117 39 39 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1473 491 491 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1572 524 524 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.11 Total of12452 atoms and 4135 groups and 4128 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3362 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1109 Number of atoms = 3362 Number of groups = 1114 Number of bonds = 3355 Number of angles = 1213 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1111 Number of HB donors = 2200 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1109 Number of atoms = 3362 Number of groups = 1114 Number of bonds = 3355 Number of angles = 1213 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1111 Number of HB donors = 2200 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.154" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1109" Evaluating: 1109-7 Parameter: NUMWAT <- "1102" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1102" Comparing "1081" and "1102". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.154" Parameter: BOX -> "32.154" Parameter: BOX -> "32.154" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.15400 B = 32.15400 C = 32.15400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6524 2 1 -1 0 -1 3.4776 3 1 -1 1 -1 4.8648 4 1 0 -1 -1 3.7957 5 1 0 0 -1 0.5343 6 1 0 1 -1 5.2295 7 1 -1 -1 0 4.1803 8 1 -1 0 0 3.2040 9 1 -1 1 0 4.9437 10 1 0 -1 0 0.3459 11 1 0 1 0 0.3459 12 1 -1 -1 1 7.1729 13 1 -1 0 1 3.4486 14 1 -1 1 1 5.3233 15 1 0 -1 1 5.2295 16 1 0 0 1 0.5343 17 1 0 1 1 3.7957 18 1 1 1 1 6.6524 19 1 1 0 1 3.4776 20 1 1 -1 1 4.8648 21 1 1 1 0 4.1803 22 1 1 0 0 3.2040 23 1 1 -1 0 4.9437 24 1 1 1 -1 7.1729 25 1 1 0 -1 3.4486 26 1 1 -1 -1 5.3233 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3288 atoms have been selected out of 3362 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 750 250 250 0.00 3 C003 has 117 39 39 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1476 492 492 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1572 524 524 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.11 Total of12458 atoms and 4137 groups and 4130 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3362 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1109 Number of atoms = 3362 Number of groups = 1114 Number of bonds = 3355 Number of angles = 1213 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1111 Number of HB donors = 2200 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1109 Number of atoms = 3362 Number of groups = 1114 Number of bonds = 3355 Number of angles = 1213 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1111 Number of HB donors = 2200 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.152" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1109" Evaluating: 1109-7 Parameter: NUMWAT <- "1102" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1102" Comparing "1081" and "1102". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.152" Parameter: BOX -> "32.152" Parameter: BOX -> "32.152" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.15200 B = 32.15200 C = 32.15200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6497 2 1 -1 0 -1 3.4748 3 1 -1 1 -1 4.8620 4 1 0 -1 -1 3.7930 5 1 0 0 -1 0.5337 6 1 0 1 -1 5.2268 7 1 -1 -1 0 4.1777 8 1 -1 0 0 3.2029 9 1 -1 1 0 4.9409 10 1 0 -1 0 0.3453 11 1 0 1 0 0.3453 12 1 -1 -1 1 7.1697 13 1 -1 0 1 3.4459 14 1 -1 1 1 5.3205 15 1 0 -1 1 5.2268 16 1 0 0 1 0.5337 17 1 0 1 1 3.7930 18 1 1 1 1 6.6497 19 1 1 0 1 3.4748 20 1 1 -1 1 4.8620 21 1 1 1 0 4.1777 22 1 1 0 0 3.2029 23 1 1 -1 0 4.9409 24 1 1 1 -1 7.1697 25 1 1 0 -1 3.4459 26 1 1 -1 -1 5.3205 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3288 atoms have been selected out of 3362 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 750 250 250 0.00 3 C003 has 117 39 39 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1476 492 492 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1572 524 524 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.11 Total of12461 atoms and 4138 groups and 4131 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3362 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1109 Number of atoms = 3362 Number of groups = 1114 Number of bonds = 3355 Number of angles = 1213 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1111 Number of HB donors = 2200 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1109 Number of atoms = 3362 Number of groups = 1114 Number of bonds = 3355 Number of angles = 1213 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1111 Number of HB donors = 2200 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.15" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1109" Evaluating: 1109-7 Parameter: NUMWAT <- "1102" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1102" Comparing "1081" and "1102". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.15" Parameter: BOX -> "32.15" Parameter: BOX -> "32.15" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.15000 B = 32.15000 C = 32.15000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6469 2 1 -1 0 -1 3.4720 3 1 -1 1 -1 4.8592 4 1 0 -1 -1 3.7903 5 1 0 0 -1 0.5331 6 1 0 1 -1 5.2241 7 1 -1 -1 0 4.1752 8 1 -1 0 0 3.2018 9 1 -1 1 0 4.9381 10 1 0 -1 0 0.3448 11 1 0 1 0 0.3448 12 1 -1 -1 1 7.1665 13 1 -1 0 1 3.4432 14 1 -1 1 1 5.3177 15 1 0 -1 1 5.2241 16 1 0 0 1 0.5331 17 1 0 1 1 3.7903 18 1 1 1 1 6.6469 19 1 1 0 1 3.4720 20 1 1 -1 1 4.8592 21 1 1 1 0 4.1752 22 1 1 0 0 3.2018 23 1 1 -1 0 4.9381 24 1 1 1 -1 7.1665 25 1 1 0 -1 3.4432 26 1 1 -1 -1 5.3177 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3288 atoms have been selected out of 3362 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 750 250 250 0.00 3 C003 has 117 39 39 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1476 492 492 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1572 524 524 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.10 Total of12461 atoms and 4138 groups and 4131 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3362 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1109 Number of atoms = 3362 Number of groups = 1114 Number of bonds = 3355 Number of angles = 1213 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1111 Number of HB donors = 2200 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1109 Number of atoms = 3362 Number of groups = 1114 Number of bonds = 3355 Number of angles = 1213 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1111 Number of HB donors = 2200 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.148" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1109" Evaluating: 1109-7 Parameter: NUMWAT <- "1102" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1102" Comparing "1081" and "1102". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.148" Parameter: BOX -> "32.148" Parameter: BOX -> "32.148" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.14800 B = 32.14800 C = 32.14800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6442 2 1 -1 0 -1 3.4692 3 1 -1 1 -1 4.8564 4 1 0 -1 -1 3.7876 5 1 0 0 -1 0.5324 6 1 0 1 -1 5.2214 7 1 -1 -1 0 4.1726 8 1 -1 0 0 3.2007 9 1 -1 1 0 4.9353 10 1 0 -1 0 0.3443 11 1 0 1 0 0.3443 12 1 -1 -1 1 7.1633 13 1 -1 0 1 3.4404 14 1 -1 1 1 5.3150 15 1 0 -1 1 5.2214 16 1 0 0 1 0.5324 17 1 0 1 1 3.7876 18 1 1 1 1 6.6442 19 1 1 0 1 3.4692 20 1 1 -1 1 4.8564 21 1 1 1 0 4.1726 22 1 1 0 0 3.2007 23 1 1 -1 0 4.9353 24 1 1 1 -1 7.1633 25 1 1 0 -1 3.4404 26 1 1 -1 -1 5.3150 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3288 atoms have been selected out of 3362 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 60 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 750 250 250 0.00 3 C003 has 117 39 39 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1476 492 492 0.00 6 C006 has 456 152 152 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1692 555 553 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1575 525 525 0.00 12 C012 has 114 38 38 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.10 Total of12479 atoms and 4144 groups and 4137 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3362 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1108 Number of atoms = 3359 Number of groups = 1113 Number of bonds = 3352 Number of angles = 1212 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1110 Number of HB donors = 2198 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1108 Number of atoms = 3359 Number of groups = 1113 Number of bonds = 3352 Number of angles = 1212 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1110 Number of HB donors = 2198 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.146" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1108" Evaluating: 1108-7 Parameter: NUMWAT <- "1101" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1101" Comparing "1081" and "1101". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.146" Parameter: BOX -> "32.146" Parameter: BOX -> "32.146" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.14600 B = 32.14600 C = 32.14600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6415 2 1 -1 0 -1 3.4664 3 1 -1 1 -1 4.8537 4 1 0 -1 -1 3.7849 5 1 0 0 -1 0.5318 6 1 0 1 -1 5.2187 7 1 -1 -1 0 4.1700 8 1 -1 0 0 3.1995 9 1 -1 1 0 4.9324 10 1 0 -1 0 0.3439 11 1 0 1 0 0.3439 12 1 -1 -1 1 7.1601 13 1 -1 0 1 3.4377 14 1 -1 1 1 5.3122 15 1 0 -1 1 5.2187 16 1 0 0 1 0.5318 17 1 0 1 1 3.7849 18 1 1 1 1 6.6415 19 1 1 0 1 3.4664 20 1 1 -1 1 4.8537 21 1 1 1 0 4.1700 22 1 1 0 0 3.1995 23 1 1 -1 0 4.9324 24 1 1 1 -1 7.1601 25 1 1 0 -1 3.4377 26 1 1 -1 -1 5.3122 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3285 atoms have been selected out of 3359 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 438 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 750 250 250 0.00 3 C003 has 117 39 39 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1476 492 492 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1695 556 554 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1572 524 524 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 1.10 Total of12455 atoms and 4136 groups and 4129 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3359 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1107 Number of atoms = 3356 Number of groups = 1112 Number of bonds = 3349 Number of angles = 1211 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1109 Number of HB donors = 2196 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1107 Number of atoms = 3356 Number of groups = 1112 Number of bonds = 3349 Number of angles = 1211 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1109 Number of HB donors = 2196 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.144" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1107" Evaluating: 1107-7 Parameter: NUMWAT <- "1100" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1100" Comparing "1081" and "1100". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.144" Parameter: BOX -> "32.144" Parameter: BOX -> "32.144" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.14400 B = 32.14400 C = 32.14400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6388 2 1 -1 0 -1 3.4636 3 1 -1 1 -1 4.8509 4 1 0 -1 -1 3.7822 5 1 0 0 -1 0.5312 6 1 0 1 -1 5.2160 7 1 -1 -1 0 4.1674 8 1 -1 0 0 3.1984 9 1 -1 1 0 4.9296 10 1 0 -1 0 0.3434 11 1 0 1 0 0.3434 12 1 -1 -1 1 7.1569 13 1 -1 0 1 3.4349 14 1 -1 1 1 5.3095 15 1 0 -1 1 5.2160 16 1 0 0 1 0.5312 17 1 0 1 1 3.7822 18 1 1 1 1 6.6388 19 1 1 0 1 3.4636 20 1 1 -1 1 4.8509 21 1 1 1 0 4.1674 22 1 1 0 0 3.1984 23 1 1 -1 0 4.9296 24 1 1 1 -1 7.1569 25 1 1 0 -1 3.4349 26 1 1 -1 -1 5.3095 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3282 atoms have been selected out of 3356 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 840 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 750 250 250 0.00 3 C003 has 117 39 39 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1476 492 492 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1689 554 552 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1569 523 523 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 1.10 Total of12440 atoms and 4131 groups and 4124 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3356 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1106 Number of atoms = 3353 Number of groups = 1111 Number of bonds = 3346 Number of angles = 1210 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1108 Number of HB donors = 2194 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1106 Number of atoms = 3353 Number of groups = 1111 Number of bonds = 3346 Number of angles = 1210 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1108 Number of HB donors = 2194 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.142" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1106" Evaluating: 1106-7 Parameter: NUMWAT <- "1099" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1099" Comparing "1081" and "1099". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.142" Parameter: BOX -> "32.142" Parameter: BOX -> "32.142" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.14200 B = 32.14200 C = 32.14200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6361 2 1 -1 0 -1 3.4608 3 1 -1 1 -1 4.8481 4 1 0 -1 -1 3.7795 5 1 0 0 -1 0.5306 6 1 0 1 -1 5.2133 7 1 -1 -1 0 4.1648 8 1 -1 0 0 3.1973 9 1 -1 1 0 4.9268 10 1 0 -1 0 0.3429 11 1 0 1 0 0.3429 12 1 -1 -1 1 7.1537 13 1 -1 0 1 3.4322 14 1 -1 1 1 5.3067 15 1 0 -1 1 5.2133 16 1 0 0 1 0.5306 17 1 0 1 1 3.7795 18 1 1 1 1 6.6361 19 1 1 0 1 3.4608 20 1 1 -1 1 4.8481 21 1 1 1 0 4.1648 22 1 1 0 0 3.1973 23 1 1 -1 0 4.9268 24 1 1 1 -1 7.1537 25 1 1 0 -1 3.4322 26 1 1 -1 -1 5.3067 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3279 atoms have been selected out of 3353 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 750 250 250 0.00 3 C003 has 117 39 39 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1473 491 491 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1689 554 552 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1566 522 522 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 1.10 Total of12431 atoms and 4128 groups and 4121 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3353 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1106 Number of atoms = 3353 Number of groups = 1111 Number of bonds = 3346 Number of angles = 1210 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1108 Number of HB donors = 2194 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1106 Number of atoms = 3353 Number of groups = 1111 Number of bonds = 3346 Number of angles = 1210 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1108 Number of HB donors = 2194 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.14" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1106" Evaluating: 1106-7 Parameter: NUMWAT <- "1099" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1099" Comparing "1081" and "1099". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.14" Parameter: BOX -> "32.14" Parameter: BOX -> "32.14" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.14000 B = 32.14000 C = 32.14000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6333 2 1 -1 0 -1 3.4580 3 1 -1 1 -1 4.8453 4 1 0 -1 -1 3.7768 5 1 0 0 -1 0.5300 6 1 0 1 -1 5.2106 7 1 -1 -1 0 4.1623 8 1 -1 0 0 3.1962 9 1 -1 1 0 4.9240 10 1 0 -1 0 0.3425 11 1 0 1 0 0.3425 12 1 -1 -1 1 7.1505 13 1 -1 0 1 3.4295 14 1 -1 1 1 5.3039 15 1 0 -1 1 5.2106 16 1 0 0 1 0.5300 17 1 0 1 1 3.7768 18 1 1 1 1 6.6333 19 1 1 0 1 3.4580 20 1 1 -1 1 4.8453 21 1 1 1 0 4.1623 22 1 1 0 0 3.1962 23 1 1 -1 0 4.9240 24 1 1 1 -1 7.1505 25 1 1 0 -1 3.4295 26 1 1 -1 -1 5.3039 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3279 atoms have been selected out of 3353 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 750 250 250 0.00 3 C003 has 117 39 39 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1473 491 491 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1689 554 552 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1566 522 522 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 1.09 Total of12431 atoms and 4128 groups and 4121 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3353 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1106 Number of atoms = 3353 Number of groups = 1111 Number of bonds = 3346 Number of angles = 1210 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1108 Number of HB donors = 2194 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1106 Number of atoms = 3353 Number of groups = 1111 Number of bonds = 3346 Number of angles = 1210 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1108 Number of HB donors = 2194 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.138" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1106" Evaluating: 1106-7 Parameter: NUMWAT <- "1099" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1099" Comparing "1081" and "1099". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.138" Parameter: BOX -> "32.138" Parameter: BOX -> "32.138" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.13800 B = 32.13800 C = 32.13800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6306 2 1 -1 0 -1 3.4552 3 1 -1 1 -1 4.8426 4 1 0 -1 -1 3.7741 5 1 0 0 -1 0.5294 6 1 0 1 -1 5.2080 7 1 -1 -1 0 4.1597 8 1 -1 0 0 3.1951 9 1 -1 1 0 4.9211 10 1 0 -1 0 0.3420 11 1 0 1 0 0.3420 12 1 -1 -1 1 7.1473 13 1 -1 0 1 3.4267 14 1 -1 1 1 5.3012 15 1 0 -1 1 5.2080 16 1 0 0 1 0.5294 17 1 0 1 1 3.7741 18 1 1 1 1 6.6306 19 1 1 0 1 3.4552 20 1 1 -1 1 4.8426 21 1 1 1 0 4.1597 22 1 1 0 0 3.1951 23 1 1 -1 0 4.9211 24 1 1 1 -1 7.1473 25 1 1 0 -1 3.4267 26 1 1 -1 -1 5.3012 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3279 atoms have been selected out of 3353 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 750 250 250 0.00 3 C003 has 117 39 39 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1473 491 491 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1689 554 552 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1566 522 522 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 1.09 Total of12431 atoms and 4128 groups and 4121 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3353 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1106 Number of atoms = 3353 Number of groups = 1111 Number of bonds = 3346 Number of angles = 1210 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1108 Number of HB donors = 2194 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1106 Number of atoms = 3353 Number of groups = 1111 Number of bonds = 3346 Number of angles = 1210 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1108 Number of HB donors = 2194 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.136" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1106" Evaluating: 1106-7 Parameter: NUMWAT <- "1099" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1099" Comparing "1081" and "1099". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.136" Parameter: BOX -> "32.136" Parameter: BOX -> "32.136" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.13600 B = 32.13600 C = 32.13600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6279 2 1 -1 0 -1 3.4524 3 1 -1 1 -1 4.8398 4 1 0 -1 -1 3.7714 5 1 0 0 -1 0.5288 6 1 0 1 -1 5.2053 7 1 -1 -1 0 4.1571 8 1 -1 0 0 3.1939 9 1 -1 1 0 4.9183 10 1 0 -1 0 0.3416 11 1 0 1 0 0.3416 12 1 -1 -1 1 7.1441 13 1 -1 0 1 3.4240 14 1 -1 1 1 5.2984 15 1 0 -1 1 5.2053 16 1 0 0 1 0.5288 17 1 0 1 1 3.7714 18 1 1 1 1 6.6279 19 1 1 0 1 3.4524 20 1 1 -1 1 4.8398 21 1 1 1 0 4.1571 22 1 1 0 0 3.1939 23 1 1 -1 0 4.9183 24 1 1 1 -1 7.1441 25 1 1 0 -1 3.4240 26 1 1 -1 -1 5.2984 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3279 atoms have been selected out of 3353 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 750 250 250 0.00 3 C003 has 117 39 39 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1473 491 491 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1689 554 552 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1566 522 522 0.00 12 C012 has 111 37 37 0.00 13 C013 has 477 159 159 0.00 14 C014 has 126 42 42 1.09 Total of12431 atoms and 4128 groups and 4121 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3353 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1106 Number of atoms = 3353 Number of groups = 1111 Number of bonds = 3346 Number of angles = 1210 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1108 Number of HB donors = 2194 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1106 Number of atoms = 3353 Number of groups = 1111 Number of bonds = 3346 Number of angles = 1210 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1108 Number of HB donors = 2194 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.134" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1106" Evaluating: 1106-7 Parameter: NUMWAT <- "1099" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1099" Comparing "1081" and "1099". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.134" Parameter: BOX -> "32.134" Parameter: BOX -> "32.134" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.13400 B = 32.13400 C = 32.13400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6252 2 1 -1 0 -1 3.4496 3 1 -1 1 -1 4.8370 4 1 0 -1 -1 3.7687 5 1 0 0 -1 0.5282 6 1 0 1 -1 5.2026 7 1 -1 -1 0 4.1545 8 1 -1 0 0 3.1928 9 1 -1 1 0 4.9155 10 1 0 -1 0 0.3412 11 1 0 1 0 0.3412 12 1 -1 -1 1 7.1409 13 1 -1 0 1 3.4212 14 1 -1 1 1 5.2957 15 1 0 -1 1 5.2026 16 1 0 0 1 0.5282 17 1 0 1 1 3.7687 18 1 1 1 1 6.6252 19 1 1 0 1 3.4496 20 1 1 -1 1 4.8370 21 1 1 1 0 4.1545 22 1 1 0 0 3.1928 23 1 1 -1 0 4.9155 24 1 1 1 -1 7.1409 25 1 1 0 -1 3.4212 26 1 1 -1 -1 5.2957 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3279 atoms have been selected out of 3353 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 750 250 250 0.00 3 C003 has 117 39 39 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1473 491 491 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1689 554 552 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1566 522 522 0.00 12 C012 has 111 37 37 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.09 Total of12434 atoms and 4129 groups and 4122 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3353 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1106 Number of atoms = 3353 Number of groups = 1111 Number of bonds = 3346 Number of angles = 1210 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1108 Number of HB donors = 2194 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1106 Number of atoms = 3353 Number of groups = 1111 Number of bonds = 3346 Number of angles = 1210 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1108 Number of HB donors = 2194 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.132" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1106" Evaluating: 1106-7 Parameter: NUMWAT <- "1099" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1099" Comparing "1081" and "1099". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.132" Parameter: BOX -> "32.132" Parameter: BOX -> "32.132" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.13200 B = 32.13200 C = 32.13200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6225 2 1 -1 0 -1 3.4468 3 1 -1 1 -1 4.8342 4 1 0 -1 -1 3.7660 5 1 0 0 -1 0.5276 6 1 0 1 -1 5.1999 7 1 -1 -1 0 4.1519 8 1 -1 0 0 3.1917 9 1 -1 1 0 4.9127 10 1 0 -1 0 0.3407 11 1 0 1 0 0.3407 12 1 -1 -1 1 7.1377 13 1 -1 0 1 3.4185 14 1 -1 1 1 5.2929 15 1 0 -1 1 5.1999 16 1 0 0 1 0.5276 17 1 0 1 1 3.7660 18 1 1 1 1 6.6225 19 1 1 0 1 3.4468 20 1 1 -1 1 4.8342 21 1 1 1 0 4.1519 22 1 1 0 0 3.1917 23 1 1 -1 0 4.9127 24 1 1 1 -1 7.1377 25 1 1 0 -1 3.4185 26 1 1 -1 -1 5.2929 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3279 atoms have been selected out of 3353 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 750 250 250 0.00 3 C003 has 117 39 39 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1473 491 491 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1689 554 552 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1566 522 522 0.00 12 C012 has 111 37 37 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.09 Total of12434 atoms and 4129 groups and 4122 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3353 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1106 Number of atoms = 3353 Number of groups = 1111 Number of bonds = 3346 Number of angles = 1210 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1108 Number of HB donors = 2194 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1106 Number of atoms = 3353 Number of groups = 1111 Number of bonds = 3346 Number of angles = 1210 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1108 Number of HB donors = 2194 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.13" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1106" Evaluating: 1106-7 Parameter: NUMWAT <- "1099" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1099" Comparing "1081" and "1099". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.13" Parameter: BOX -> "32.13" Parameter: BOX -> "32.13" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.13000 B = 32.13000 C = 32.13000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6198 2 1 -1 0 -1 3.4440 3 1 -1 1 -1 4.8315 4 1 0 -1 -1 3.7633 5 1 0 0 -1 0.5270 6 1 0 1 -1 5.1972 7 1 -1 -1 0 4.1494 8 1 -1 0 0 3.1906 9 1 -1 1 0 4.9099 10 1 0 -1 0 0.3403 11 1 0 1 0 0.3403 12 1 -1 -1 1 7.1344 13 1 -1 0 1 3.4158 14 1 -1 1 1 5.2902 15 1 0 -1 1 5.1972 16 1 0 0 1 0.5270 17 1 0 1 1 3.7633 18 1 1 1 1 6.6198 19 1 1 0 1 3.4440 20 1 1 -1 1 4.8315 21 1 1 1 0 4.1494 22 1 1 0 0 3.1906 23 1 1 -1 0 4.9099 24 1 1 1 -1 7.1344 25 1 1 0 -1 3.4158 26 1 1 -1 -1 5.2902 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3279 atoms have been selected out of 3353 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 698 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 747 249 249 0.00 3 C003 has 117 39 39 0.00 4 C004 has 630 210 210 0.00 5 C005 has 1473 491 491 0.00 6 C006 has 441 147 147 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1689 554 552 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1563 521 521 0.00 12 C012 has 111 37 37 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.08 Total of12431 atoms and 4128 groups and 4121 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3353 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1105 Number of atoms = 3350 Number of groups = 1110 Number of bonds = 3343 Number of angles = 1209 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1107 Number of HB donors = 2192 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1105 Number of atoms = 3350 Number of groups = 1110 Number of bonds = 3343 Number of angles = 1209 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1107 Number of HB donors = 2192 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.128" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1105" Evaluating: 1105-7 Parameter: NUMWAT <- "1098" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1098" Comparing "1081" and "1098". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.128" Parameter: BOX -> "32.128" Parameter: BOX -> "32.128" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.12800 B = 32.12800 C = 32.12800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6171 2 1 -1 0 -1 3.4412 3 1 -1 1 -1 4.8287 4 1 0 -1 -1 3.7607 5 1 0 0 -1 0.5265 6 1 0 1 -1 5.1945 7 1 -1 -1 0 4.1468 8 1 -1 0 0 3.1895 9 1 -1 1 0 4.9070 10 1 0 -1 0 0.3400 11 1 0 1 0 0.3400 12 1 -1 -1 1 7.1312 13 1 -1 0 1 3.4130 14 1 -1 1 1 5.2874 15 1 0 -1 1 5.1945 16 1 0 0 1 0.5265 17 1 0 1 1 3.7607 18 1 1 1 1 6.6171 19 1 1 0 1 3.4412 20 1 1 -1 1 4.8287 21 1 1 1 0 4.1468 22 1 1 0 0 3.1895 23 1 1 -1 0 4.9070 24 1 1 1 -1 7.1312 25 1 1 0 -1 3.4130 26 1 1 -1 -1 5.2874 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3276 atoms have been selected out of 3350 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 747 249 249 0.00 3 C003 has 117 39 39 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1470 490 490 0.00 6 C006 has 441 147 147 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1686 553 551 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1560 520 520 0.00 12 C012 has 111 37 37 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.08 Total of12410 atoms and 4121 groups and 4114 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3350 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1105 Number of atoms = 3350 Number of groups = 1110 Number of bonds = 3343 Number of angles = 1209 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1107 Number of HB donors = 2192 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1105 Number of atoms = 3350 Number of groups = 1110 Number of bonds = 3343 Number of angles = 1209 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1107 Number of HB donors = 2192 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.126" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1105" Evaluating: 1105-7 Parameter: NUMWAT <- "1098" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1098" Comparing "1081" and "1098". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.126" Parameter: BOX -> "32.126" Parameter: BOX -> "32.126" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.12600 B = 32.12600 C = 32.12600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6143 2 1 -1 0 -1 3.4384 3 1 -1 1 -1 4.8259 4 1 0 -1 -1 3.7580 5 1 0 0 -1 0.5259 6 1 0 1 -1 5.1918 7 1 -1 -1 0 4.1442 8 1 -1 0 0 3.1884 9 1 -1 1 0 4.9042 10 1 0 -1 0 0.3396 11 1 0 1 0 0.3396 12 1 -1 -1 1 7.1280 13 1 -1 0 1 3.4103 14 1 -1 1 1 5.2847 15 1 0 -1 1 5.1918 16 1 0 0 1 0.5259 17 1 0 1 1 3.7580 18 1 1 1 1 6.6143 19 1 1 0 1 3.4384 20 1 1 -1 1 4.8259 21 1 1 1 0 4.1442 22 1 1 0 0 3.1884 23 1 1 -1 0 4.9042 24 1 1 1 -1 7.1280 25 1 1 0 -1 3.4103 26 1 1 -1 -1 5.2847 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3276 atoms have been selected out of 3350 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 750 250 250 0.00 3 C003 has 117 39 39 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1470 490 490 0.00 6 C006 has 441 147 147 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1686 553 551 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1560 520 520 0.00 12 C012 has 111 37 37 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.08 Total of12413 atoms and 4122 groups and 4115 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3350 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1105 Number of atoms = 3350 Number of groups = 1110 Number of bonds = 3343 Number of angles = 1209 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1107 Number of HB donors = 2192 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1105 Number of atoms = 3350 Number of groups = 1110 Number of bonds = 3343 Number of angles = 1209 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1107 Number of HB donors = 2192 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.124" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1105" Evaluating: 1105-7 Parameter: NUMWAT <- "1098" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1098" Comparing "1081" and "1098". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.124" Parameter: BOX -> "32.124" Parameter: BOX -> "32.124" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.12400 B = 32.12400 C = 32.12400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6116 2 1 -1 0 -1 3.4357 3 1 -1 1 -1 4.8232 4 1 0 -1 -1 3.7553 5 1 0 0 -1 0.5253 6 1 0 1 -1 5.1891 7 1 -1 -1 0 4.1416 8 1 -1 0 0 3.1872 9 1 -1 1 0 4.9014 10 1 0 -1 0 0.3392 11 1 0 1 0 0.3392 12 1 -1 -1 1 7.1248 13 1 -1 0 1 3.4076 14 1 -1 1 1 5.2819 15 1 0 -1 1 5.1891 16 1 0 0 1 0.5253 17 1 0 1 1 3.7553 18 1 1 1 1 6.6116 19 1 1 0 1 3.4357 20 1 1 -1 1 4.8232 21 1 1 1 0 4.1416 22 1 1 0 0 3.1872 23 1 1 -1 0 4.9014 24 1 1 1 -1 7.1248 25 1 1 0 -1 3.4076 26 1 1 -1 -1 5.2819 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3276 atoms have been selected out of 3350 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 750 250 250 0.00 3 C003 has 117 39 39 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1470 490 490 0.00 6 C006 has 441 147 147 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1686 553 551 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1560 520 520 0.00 12 C012 has 111 37 37 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.08 Total of12413 atoms and 4122 groups and 4115 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3350 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1105 Number of atoms = 3350 Number of groups = 1110 Number of bonds = 3343 Number of angles = 1209 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1107 Number of HB donors = 2192 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1105 Number of atoms = 3350 Number of groups = 1110 Number of bonds = 3343 Number of angles = 1209 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1107 Number of HB donors = 2192 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.122" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1105" Evaluating: 1105-7 Parameter: NUMWAT <- "1098" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1098" Comparing "1081" and "1098". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.122" Parameter: BOX -> "32.122" Parameter: BOX -> "32.122" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.12200 B = 32.12200 C = 32.12200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6089 2 1 -1 0 -1 3.4329 3 1 -1 1 -1 4.8204 4 1 0 -1 -1 3.7526 5 1 0 0 -1 0.5248 6 1 0 1 -1 5.1864 7 1 -1 -1 0 4.1390 8 1 -1 0 0 3.1861 9 1 -1 1 0 4.8986 10 1 0 -1 0 0.3389 11 1 0 1 0 0.3389 12 1 -1 -1 1 7.1216 13 1 -1 0 1 3.4048 14 1 -1 1 1 5.2792 15 1 0 -1 1 5.1864 16 1 0 0 1 0.5248 17 1 0 1 1 3.7526 18 1 1 1 1 6.6089 19 1 1 0 1 3.4329 20 1 1 -1 1 4.8204 21 1 1 1 0 4.1390 22 1 1 0 0 3.1861 23 1 1 -1 0 4.8986 24 1 1 1 -1 7.1216 25 1 1 0 -1 3.4048 26 1 1 -1 -1 5.2792 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3276 atoms have been selected out of 3350 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 750 250 250 0.00 3 C003 has 117 39 39 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1470 490 490 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1686 553 551 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1560 520 520 0.00 12 C012 has 111 37 37 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.08 Total of12419 atoms and 4124 groups and 4117 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3350 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1105 Number of atoms = 3350 Number of groups = 1110 Number of bonds = 3343 Number of angles = 1209 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1107 Number of HB donors = 2192 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1105 Number of atoms = 3350 Number of groups = 1110 Number of bonds = 3343 Number of angles = 1209 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1107 Number of HB donors = 2192 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.12" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1105" Evaluating: 1105-7 Parameter: NUMWAT <- "1098" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1098" Comparing "1081" and "1098". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.12" Parameter: BOX -> "32.12" Parameter: BOX -> "32.12" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.12000 B = 32.12000 C = 32.12000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6062 2 1 -1 0 -1 3.4301 3 1 -1 1 -1 4.8176 4 1 0 -1 -1 3.7499 5 1 0 0 -1 0.5243 6 1 0 1 -1 5.1838 7 1 -1 -1 0 4.1365 8 1 -1 0 0 3.1850 9 1 -1 1 0 4.8958 10 1 0 -1 0 0.3385 11 1 0 1 0 0.3385 12 1 -1 -1 1 7.1184 13 1 -1 0 1 3.4021 14 1 -1 1 1 5.2764 15 1 0 -1 1 5.1838 16 1 0 0 1 0.5243 17 1 0 1 1 3.7499 18 1 1 1 1 6.6062 19 1 1 0 1 3.4301 20 1 1 -1 1 4.8176 21 1 1 1 0 4.1365 22 1 1 0 0 3.1850 23 1 1 -1 0 4.8958 24 1 1 1 -1 7.1184 25 1 1 0 -1 3.4021 26 1 1 -1 -1 5.2764 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3276 atoms have been selected out of 3350 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 750 250 250 0.00 3 C003 has 117 39 39 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1470 490 490 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1686 553 551 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1560 520 520 0.00 12 C012 has 111 37 37 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.07 Total of12419 atoms and 4124 groups and 4117 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3350 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1105 Number of atoms = 3350 Number of groups = 1110 Number of bonds = 3343 Number of angles = 1209 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1107 Number of HB donors = 2192 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1105 Number of atoms = 3350 Number of groups = 1110 Number of bonds = 3343 Number of angles = 1209 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1107 Number of HB donors = 2192 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.118" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1105" Evaluating: 1105-7 Parameter: NUMWAT <- "1098" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1098" Comparing "1081" and "1098". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.118" Parameter: BOX -> "32.118" Parameter: BOX -> "32.118" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.11800 B = 32.11800 C = 32.11800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 6.6035 2 1 -1 0 -1 3.4273 3 1 -1 1 -1 4.8149 4 1 0 -1 -1 3.7472 5 1 0 0 -1 0.5237 6 1 0 1 -1 5.1811 7 1 -1 -1 0 4.1339 8 1 -1 0 0 3.1839 9 1 -1 1 0 4.8929 10 1 0 -1 0 0.3382 11 1 0 1 0 0.3382 12 1 -1 -1 1 7.1152 13 1 -1 0 1 3.3994 14 1 -1 1 1 5.2737 15 1 0 -1 1 5.1811 16 1 0 0 1 0.5237 17 1 0 1 1 3.7472 18 1 1 1 1 6.6035 19 1 1 0 1 3.4273 20 1 1 -1 1 4.8149 21 1 1 1 0 4.1339 22 1 1 0 0 3.1839 23 1 1 -1 0 4.8929 24 1 1 1 -1 7.1152 25 1 1 0 -1 3.3994 26 1 1 -1 -1 5.2737 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3276 atoms have been selected out of 3350 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 737 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1002 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 747 249 249 0.00 3 C003 has 117 39 39 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1467 489 489 0.00 6 C006 has 450 150 150 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1689 554 552 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1560 520 520 0.00 12 C012 has 111 37 37 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.07 Total of12422 atoms and 4125 groups and 4118 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3350 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1103 Number of atoms = 3344 Number of groups = 1108 Number of bonds = 3337 Number of angles = 1207 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1105 Number of HB donors = 2188 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1103 Number of atoms = 3344 Number of groups = 1108 Number of bonds = 3337 Number of angles = 1207 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1105 Number of HB donors = 2188 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.116" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1103" Evaluating: 1103-7 Parameter: NUMWAT <- "1096" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1096" Comparing "1081" and "1096". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.116" Parameter: BOX -> "32.116" Parameter: BOX -> "32.116" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.11600 B = 32.11600 C = 32.11600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.1614 2 1 -1 0 -1 3.4245 3 1 -1 1 -1 4.8121 4 1 0 -1 -1 3.7445 5 1 0 0 -1 0.5232 6 1 0 1 -1 4.9345 7 1 -1 -1 0 4.1313 8 1 -1 0 0 3.1828 9 1 -1 1 0 4.8901 10 1 0 -1 0 1.1943 11 1 0 1 0 1.1943 12 1 -1 -1 1 7.1120 13 1 -1 0 1 3.3966 14 1 -1 1 1 5.2709 15 1 0 -1 1 4.9345 16 1 0 0 1 0.5232 17 1 0 1 1 3.7445 18 1 1 1 1 7.1614 19 1 1 0 1 3.4245 20 1 1 -1 1 4.8121 21 1 1 1 0 4.1313 22 1 1 0 0 3.1828 23 1 1 -1 0 4.8901 24 1 1 1 -1 7.1120 25 1 1 0 -1 3.3966 26 1 1 -1 -1 5.2709 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3270 atoms have been selected out of 3344 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 129 OPERATED ON BY TRANSFORMATION C022 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 747 249 249 0.00 3 C003 has 117 39 39 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1464 488 488 0.00 6 C006 has 441 147 147 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1689 554 552 0.00 9 C009 has 429 143 143 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 129 43 43 1.07 Total of12404 atoms and 4119 groups and 4112 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3344 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1102 Number of atoms = 3341 Number of groups = 1107 Number of bonds = 3334 Number of angles = 1206 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1104 Number of HB donors = 2186 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1102 Number of atoms = 3341 Number of groups = 1107 Number of bonds = 3334 Number of angles = 1206 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1104 Number of HB donors = 2186 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.114" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1102" Evaluating: 1102-7 Parameter: NUMWAT <- "1095" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1095" Comparing "1081" and "1095". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.114" Parameter: BOX -> "32.114" Parameter: BOX -> "32.114" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.11400 B = 32.11400 C = 32.11400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.1638 2 1 -1 0 -1 3.4217 3 1 -1 1 -1 4.8093 4 1 0 -1 -1 3.7418 5 1 0 0 -1 0.5227 6 1 0 1 -1 4.9332 7 1 -1 -1 0 4.1287 8 1 -1 0 0 3.1817 9 1 -1 1 0 4.8873 10 1 0 -1 0 1.1943 11 1 0 1 0 1.1943 12 1 -1 -1 1 7.1088 13 1 -1 0 1 3.3939 14 1 -1 1 1 5.2682 15 1 0 -1 1 4.9332 16 1 0 0 1 0.5227 17 1 0 1 1 3.7418 18 1 1 1 1 7.1638 19 1 1 0 1 3.4217 20 1 1 -1 1 4.8093 21 1 1 1 0 4.1287 22 1 1 0 0 3.1817 23 1 1 -1 0 4.8873 24 1 1 1 -1 7.1088 25 1 1 0 -1 3.3939 26 1 1 -1 -1 5.2682 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3267 atoms have been selected out of 3341 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 747 249 249 0.00 3 C003 has 117 39 39 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1464 488 488 0.00 6 C006 has 441 147 147 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1686 553 551 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 111 37 37 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.07 Total of12386 atoms and 4113 groups and 4106 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3341 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1102 Number of atoms = 3341 Number of groups = 1107 Number of bonds = 3334 Number of angles = 1206 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1104 Number of HB donors = 2186 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1102 Number of atoms = 3341 Number of groups = 1107 Number of bonds = 3334 Number of angles = 1206 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1104 Number of HB donors = 2186 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.112" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1102" Evaluating: 1102-7 Parameter: NUMWAT <- "1095" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1095" Comparing "1081" and "1095". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.112" Parameter: BOX -> "32.112" Parameter: BOX -> "32.112" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.11200 B = 32.11200 C = 32.11200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.1661 2 1 -1 0 -1 3.4189 3 1 -1 1 -1 4.8066 4 1 0 -1 -1 3.7391 5 1 0 0 -1 0.5222 6 1 0 1 -1 4.9320 7 1 -1 -1 0 4.1262 8 1 -1 0 0 3.1806 9 1 -1 1 0 4.8845 10 1 0 -1 0 1.1943 11 1 0 1 0 1.1943 12 1 -1 -1 1 7.1056 13 1 -1 0 1 3.3911 14 1 -1 1 1 5.2654 15 1 0 -1 1 4.9320 16 1 0 0 1 0.5222 17 1 0 1 1 3.7391 18 1 1 1 1 7.1661 19 1 1 0 1 3.4189 20 1 1 -1 1 4.8066 21 1 1 1 0 4.1262 22 1 1 0 0 3.1806 23 1 1 -1 0 4.8845 24 1 1 1 -1 7.1056 25 1 1 0 -1 3.3911 26 1 1 -1 -1 5.2654 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3267 atoms have been selected out of 3341 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 747 249 249 0.00 3 C003 has 117 39 39 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1464 488 488 0.00 6 C006 has 441 147 147 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1686 553 551 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 111 37 37 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.07 Total of12389 atoms and 4114 groups and 4107 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3341 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1102 Number of atoms = 3341 Number of groups = 1107 Number of bonds = 3334 Number of angles = 1206 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1104 Number of HB donors = 2186 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1102 Number of atoms = 3341 Number of groups = 1107 Number of bonds = 3334 Number of angles = 1206 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1104 Number of HB donors = 2186 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.11" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1102" Evaluating: 1102-7 Parameter: NUMWAT <- "1095" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1095" Comparing "1081" and "1095". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.11" Parameter: BOX -> "32.11" Parameter: BOX -> "32.11" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.11000 B = 32.11000 C = 32.11000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.1684 2 1 -1 0 -1 3.4161 3 1 -1 1 -1 4.8038 4 1 0 -1 -1 3.7364 5 1 0 0 -1 0.5217 6 1 0 1 -1 4.9308 7 1 -1 -1 0 4.1236 8 1 -1 0 0 3.1795 9 1 -1 1 0 4.8816 10 1 0 -1 0 1.1942 11 1 0 1 0 1.1942 12 1 -1 -1 1 7.1024 13 1 -1 0 1 3.3884 14 1 -1 1 1 5.2627 15 1 0 -1 1 4.9308 16 1 0 0 1 0.5217 17 1 0 1 1 3.7364 18 1 1 1 1 7.1684 19 1 1 0 1 3.4161 20 1 1 -1 1 4.8038 21 1 1 1 0 4.1236 22 1 1 0 0 3.1795 23 1 1 -1 0 4.8816 24 1 1 1 -1 7.1024 25 1 1 0 -1 3.3884 26 1 1 -1 -1 5.2627 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3267 atoms have been selected out of 3341 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 747 249 249 0.00 3 C003 has 117 39 39 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1464 488 488 0.00 6 C006 has 441 147 147 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1686 553 551 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 111 37 37 0.00 13 C013 has 480 160 160 0.00 14 C014 has 126 42 42 1.06 Total of12392 atoms and 4115 groups and 4108 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3341 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1102 Number of atoms = 3341 Number of groups = 1107 Number of bonds = 3334 Number of angles = 1206 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1104 Number of HB donors = 2186 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1102 Number of atoms = 3341 Number of groups = 1107 Number of bonds = 3334 Number of angles = 1206 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1104 Number of HB donors = 2186 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.108" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1102" Evaluating: 1102-7 Parameter: NUMWAT <- "1095" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1095" Comparing "1081" and "1095". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.108" Parameter: BOX -> "32.108" Parameter: BOX -> "32.108" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.10800 B = 32.10800 C = 32.10800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.1708 2 1 -1 0 -1 3.4133 3 1 -1 1 -1 4.8011 4 1 0 -1 -1 3.7337 5 1 0 0 -1 0.5212 6 1 0 1 -1 4.9295 7 1 -1 -1 0 4.1210 8 1 -1 0 0 3.1784 9 1 -1 1 0 4.8788 10 1 0 -1 0 1.1942 11 1 0 1 0 1.1942 12 1 -1 -1 1 7.0992 13 1 -1 0 1 3.3857 14 1 -1 1 1 5.2599 15 1 0 -1 1 4.9295 16 1 0 0 1 0.5212 17 1 0 1 1 3.7337 18 1 1 1 1 7.1708 19 1 1 0 1 3.4133 20 1 1 -1 1 4.8011 21 1 1 1 0 4.1210 22 1 1 0 0 3.1784 23 1 1 -1 0 4.8788 24 1 1 1 -1 7.0992 25 1 1 0 -1 3.3857 26 1 1 -1 -1 5.2599 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3267 atoms have been selected out of 3341 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 747 249 249 0.00 3 C003 has 117 39 39 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1464 488 488 0.00 6 C006 has 441 147 147 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1686 553 551 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 126 42 42 1.06 Total of12395 atoms and 4116 groups and 4109 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3341 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1102 Number of atoms = 3341 Number of groups = 1107 Number of bonds = 3334 Number of angles = 1206 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1104 Number of HB donors = 2186 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1102 Number of atoms = 3341 Number of groups = 1107 Number of bonds = 3334 Number of angles = 1206 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1104 Number of HB donors = 2186 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.106" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1102" Evaluating: 1102-7 Parameter: NUMWAT <- "1095" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1095" Comparing "1081" and "1095". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.106" Parameter: BOX -> "32.106" Parameter: BOX -> "32.106" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.10600 B = 32.10600 C = 32.10600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.1731 2 1 -1 0 -1 3.4105 3 1 -1 1 -1 4.7983 4 1 0 -1 -1 3.7311 5 1 0 0 -1 0.5207 6 1 0 1 -1 4.9283 7 1 -1 -1 0 4.1184 8 1 -1 0 0 3.1773 9 1 -1 1 0 4.8760 10 1 0 -1 0 1.1942 11 1 0 1 0 1.1942 12 1 -1 -1 1 7.0960 13 1 -1 0 1 3.3829 14 1 -1 1 1 5.2572 15 1 0 -1 1 4.9283 16 1 0 0 1 0.5207 17 1 0 1 1 3.7311 18 1 1 1 1 7.1731 19 1 1 0 1 3.4105 20 1 1 -1 1 4.7983 21 1 1 1 0 4.1184 22 1 1 0 0 3.1773 23 1 1 -1 0 4.8760 24 1 1 1 -1 7.0960 25 1 1 0 -1 3.3829 26 1 1 -1 -1 5.2572 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3267 atoms have been selected out of 3341 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 736 OPERATED ON BY TRANSFORMATION C008 RESIDUE 987 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 744 248 248 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1464 488 488 0.00 6 C006 has 441 147 147 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1686 553 551 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1557 519 519 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 126 42 42 1.06 Total of12389 atoms and 4114 groups and 4107 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3341 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1100 Number of atoms = 3335 Number of groups = 1105 Number of bonds = 3328 Number of angles = 1204 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1102 Number of HB donors = 2182 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1100 Number of atoms = 3335 Number of groups = 1105 Number of bonds = 3328 Number of angles = 1204 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1102 Number of HB donors = 2182 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.104" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1100" Evaluating: 1100-7 Parameter: NUMWAT <- "1093" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1093" Comparing "1081" and "1093". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.104" Parameter: BOX -> "32.104" Parameter: BOX -> "32.104" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.10400 B = 32.10400 C = 32.10400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.1755 2 1 -1 0 -1 3.4077 3 1 -1 1 -1 4.7955 4 1 0 -1 -1 3.7284 5 1 0 0 -1 0.5202 6 1 0 1 -1 4.9271 7 1 -1 -1 0 4.1159 8 1 -1 0 0 3.1762 9 1 -1 1 0 4.8732 10 1 0 -1 0 1.1942 11 1 0 1 0 1.1942 12 1 -1 -1 1 7.0928 13 1 -1 0 1 3.3802 14 1 -1 1 1 5.2545 15 1 0 -1 1 4.9271 16 1 0 0 1 0.5202 17 1 0 1 1 3.7284 18 1 1 1 1 7.1755 19 1 1 0 1 3.4077 20 1 1 -1 1 4.7955 21 1 1 1 0 4.1159 22 1 1 0 0 3.1762 23 1 1 -1 0 4.8732 24 1 1 1 -1 7.0928 25 1 1 0 -1 3.3802 26 1 1 -1 -1 5.2545 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3261 atoms have been selected out of 3335 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 84 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 744 248 248 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1464 488 488 0.00 6 C006 has 438 146 146 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1677 550 548 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1557 519 519 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 126 42 42 1.06 Total of12371 atoms and 4108 groups and 4101 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3335 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.102" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1099" Evaluating: 1099-7 Parameter: NUMWAT <- "1092" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1092" Comparing "1081" and "1092". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.102" Parameter: BOX -> "32.102" Parameter: BOX -> "32.102" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.10200 B = 32.10200 C = 32.10200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.1778 2 1 -1 0 -1 3.4049 3 1 -1 1 -1 4.7928 4 1 0 -1 -1 3.7257 5 1 0 0 -1 0.5197 6 1 0 1 -1 4.9258 7 1 -1 -1 0 4.1133 8 1 -1 0 0 3.1751 9 1 -1 1 0 4.8704 10 1 0 -1 0 1.1942 11 1 0 1 0 1.1942 12 1 -1 -1 1 7.0896 13 1 -1 0 1 3.3775 14 1 -1 1 1 5.2517 15 1 0 -1 1 4.9258 16 1 0 0 1 0.5197 17 1 0 1 1 3.7257 18 1 1 1 1 7.1778 19 1 1 0 1 3.4049 20 1 1 -1 1 4.7928 21 1 1 1 0 4.1133 22 1 1 0 0 3.1751 23 1 1 -1 0 4.8704 24 1 1 1 -1 7.0896 25 1 1 0 -1 3.3775 26 1 1 -1 -1 5.2517 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3258 atoms have been selected out of 3332 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 744 248 248 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1464 488 488 0.00 6 C006 has 438 146 146 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1677 550 548 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 126 42 42 1.06 Total of12365 atoms and 4106 groups and 4099 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3332 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.1" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1099" Evaluating: 1099-7 Parameter: NUMWAT <- "1092" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1092" Comparing "1081" and "1092". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.1" Parameter: BOX -> "32.1" Parameter: BOX -> "32.1" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.10000 B = 32.10000 C = 32.10000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.1801 2 1 -1 0 -1 3.4021 3 1 -1 1 -1 4.7900 4 1 0 -1 -1 3.7230 5 1 0 0 -1 0.5193 6 1 0 1 -1 4.9246 7 1 -1 -1 0 4.1107 8 1 -1 0 0 3.1739 9 1 -1 1 0 4.8675 10 1 0 -1 0 1.1942 11 1 0 1 0 1.1942 12 1 -1 -1 1 7.0864 13 1 -1 0 1 3.3747 14 1 -1 1 1 5.2490 15 1 0 -1 1 4.9246 16 1 0 0 1 0.5193 17 1 0 1 1 3.7230 18 1 1 1 1 7.1801 19 1 1 0 1 3.4021 20 1 1 -1 1 4.7900 21 1 1 1 0 4.1107 22 1 1 0 0 3.1739 23 1 1 -1 0 4.8675 24 1 1 1 -1 7.0864 25 1 1 0 -1 3.3747 26 1 1 -1 -1 5.2490 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3258 atoms have been selected out of 3332 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 480 160 160 0.00 2 C002 has 744 248 248 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1464 488 488 0.00 6 C006 has 438 146 146 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1677 550 548 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 126 42 42 1.06 Total of12365 atoms and 4106 groups and 4099 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3332 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.098" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1099" Evaluating: 1099-7 Parameter: NUMWAT <- "1092" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1092" Comparing "1081" and "1092". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.098" Parameter: BOX -> "32.098" Parameter: BOX -> "32.098" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.09800 B = 32.09800 C = 32.09800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.1825 2 1 -1 0 -1 3.3993 3 1 -1 1 -1 4.7873 4 1 0 -1 -1 3.7203 5 1 0 0 -1 0.5188 6 1 0 1 -1 4.9234 7 1 -1 -1 0 4.1081 8 1 -1 0 0 3.1728 9 1 -1 1 0 4.8647 10 1 0 -1 0 1.1942 11 1 0 1 0 1.1942 12 1 -1 -1 1 7.0832 13 1 -1 0 1 3.3720 14 1 -1 1 1 5.2462 15 1 0 -1 1 4.9234 16 1 0 0 1 0.5188 17 1 0 1 1 3.7203 18 1 1 1 1 7.1825 19 1 1 0 1 3.3993 20 1 1 -1 1 4.7873 21 1 1 1 0 4.1081 22 1 1 0 0 3.1728 23 1 1 -1 0 4.8647 24 1 1 1 -1 7.0832 25 1 1 0 -1 3.3720 26 1 1 -1 -1 5.2462 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3258 atoms have been selected out of 3332 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 744 248 248 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1464 488 488 0.00 6 C006 has 438 146 146 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1677 550 548 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 126 42 42 1.06 Total of12371 atoms and 4108 groups and 4101 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3332 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.096" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1099" Evaluating: 1099-7 Parameter: NUMWAT <- "1092" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1092" Comparing "1081" and "1092". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.096" Parameter: BOX -> "32.096" Parameter: BOX -> "32.096" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.09600 B = 32.09600 C = 32.09600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.1848 2 1 -1 0 -1 3.3966 3 1 -1 1 -1 4.7845 4 1 0 -1 -1 3.7176 5 1 0 0 -1 0.5184 6 1 0 1 -1 4.9221 7 1 -1 -1 0 4.1056 8 1 -1 0 0 3.1717 9 1 -1 1 0 4.8619 10 1 0 -1 0 1.1942 11 1 0 1 0 1.1942 12 1 -1 -1 1 7.0800 13 1 -1 0 1 3.3693 14 1 -1 1 1 5.2435 15 1 0 -1 1 4.9221 16 1 0 0 1 0.5184 17 1 0 1 1 3.7176 18 1 1 1 1 7.1848 19 1 1 0 1 3.3966 20 1 1 -1 1 4.7845 21 1 1 1 0 4.1056 22 1 1 0 0 3.1717 23 1 1 -1 0 4.8619 24 1 1 1 -1 7.0800 25 1 1 0 -1 3.3693 26 1 1 -1 -1 5.2435 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3258 atoms have been selected out of 3332 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 744 248 248 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1464 488 488 0.00 6 C006 has 438 146 146 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1680 551 549 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 126 42 42 1.05 Total of12374 atoms and 4109 groups and 4102 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3332 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.094" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1099" Evaluating: 1099-7 Parameter: NUMWAT <- "1092" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1092" Comparing "1081" and "1092". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.094" Parameter: BOX -> "32.094" Parameter: BOX -> "32.094" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.09400 B = 32.09400 C = 32.09400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.1872 2 1 -1 0 -1 3.3938 3 1 -1 1 -1 4.7818 4 1 0 -1 -1 3.7149 5 1 0 0 -1 0.5179 6 1 0 1 -1 4.9209 7 1 -1 -1 0 4.1030 8 1 -1 0 0 3.1706 9 1 -1 1 0 4.8591 10 1 0 -1 0 1.1942 11 1 0 1 0 1.1942 12 1 -1 -1 1 7.0768 13 1 -1 0 1 3.3665 14 1 -1 1 1 5.2408 15 1 0 -1 1 4.9209 16 1 0 0 1 0.5179 17 1 0 1 1 3.7149 18 1 1 1 1 7.1872 19 1 1 0 1 3.3938 20 1 1 -1 1 4.7818 21 1 1 1 0 4.1030 22 1 1 0 0 3.1706 23 1 1 -1 0 4.8591 24 1 1 1 -1 7.0768 25 1 1 0 -1 3.3665 26 1 1 -1 -1 5.2408 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3258 atoms have been selected out of 3332 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 744 248 248 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1464 488 488 0.00 6 C006 has 438 146 146 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1680 551 549 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 126 42 42 1.05 Total of12374 atoms and 4109 groups and 4102 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3332 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.092" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1099" Evaluating: 1099-7 Parameter: NUMWAT <- "1092" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1092" Comparing "1081" and "1092". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.092" Parameter: BOX -> "32.092" Parameter: BOX -> "32.092" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.09200 B = 32.09200 C = 32.09200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.1895 2 1 -1 0 -1 3.3910 3 1 -1 1 -1 4.7790 4 1 0 -1 -1 3.7122 5 1 0 0 -1 0.5175 6 1 0 1 -1 4.9197 7 1 -1 -1 0 4.1004 8 1 -1 0 0 3.1695 9 1 -1 1 0 4.8563 10 1 0 -1 0 1.1942 11 1 0 1 0 1.1942 12 1 -1 -1 1 7.0736 13 1 -1 0 1 3.3638 14 1 -1 1 1 5.2380 15 1 0 -1 1 4.9197 16 1 0 0 1 0.5175 17 1 0 1 1 3.7122 18 1 1 1 1 7.1895 19 1 1 0 1 3.3910 20 1 1 -1 1 4.7790 21 1 1 1 0 4.1004 22 1 1 0 0 3.1695 23 1 1 -1 0 4.8563 24 1 1 1 -1 7.0736 25 1 1 0 -1 3.3638 26 1 1 -1 -1 5.2380 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3258 atoms have been selected out of 3332 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 483 161 161 0.00 2 C002 has 744 248 248 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1464 488 488 0.00 6 C006 has 438 146 146 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1680 551 549 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 126 42 42 1.05 Total of12374 atoms and 4109 groups and 4102 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3332 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.09" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1099" Evaluating: 1099-7 Parameter: NUMWAT <- "1092" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1092" Comparing "1081" and "1092". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.09" Parameter: BOX -> "32.09" Parameter: BOX -> "32.09" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.09000 B = 32.09000 C = 32.09000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.1919 2 1 -1 0 -1 3.3882 3 1 -1 1 -1 4.7762 4 1 0 -1 -1 3.7095 5 1 0 0 -1 0.5171 6 1 0 1 -1 4.9185 7 1 -1 -1 0 4.0978 8 1 -1 0 0 3.1684 9 1 -1 1 0 4.8534 10 1 0 -1 0 1.1942 11 1 0 1 0 1.1942 12 1 -1 -1 1 7.0704 13 1 -1 0 1 3.3610 14 1 -1 1 1 5.2353 15 1 0 -1 1 4.9185 16 1 0 0 1 0.5171 17 1 0 1 1 3.7095 18 1 1 1 1 7.1919 19 1 1 0 1 3.3882 20 1 1 -1 1 4.7762 21 1 1 1 0 4.0978 22 1 1 0 0 3.1684 23 1 1 -1 0 4.8534 24 1 1 1 -1 7.0704 25 1 1 0 -1 3.3610 26 1 1 -1 -1 5.2353 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3258 atoms have been selected out of 3332 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 744 248 248 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1464 488 488 0.00 6 C006 has 438 146 146 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1683 552 550 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 126 42 42 1.05 Total of12380 atoms and 4111 groups and 4104 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3332 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.088" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1099" Evaluating: 1099-7 Parameter: NUMWAT <- "1092" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1092" Comparing "1081" and "1092". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.088" Parameter: BOX -> "32.088" Parameter: BOX -> "32.088" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.08800 B = 32.08800 C = 32.08800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.1942 2 1 -1 0 -1 3.3854 3 1 -1 1 -1 4.7735 4 1 0 -1 -1 3.7069 5 1 0 0 -1 0.5166 6 1 0 1 -1 4.9173 7 1 -1 -1 0 4.0953 8 1 -1 0 0 3.1673 9 1 -1 1 0 4.8506 10 1 0 -1 0 1.1942 11 1 0 1 0 1.1942 12 1 -1 -1 1 7.0672 13 1 -1 0 1 3.3583 14 1 -1 1 1 5.2325 15 1 0 -1 1 4.9173 16 1 0 0 1 0.5166 17 1 0 1 1 3.7069 18 1 1 1 1 7.1942 19 1 1 0 1 3.3854 20 1 1 -1 1 4.7735 21 1 1 1 0 4.0953 22 1 1 0 0 3.1673 23 1 1 -1 0 4.8506 24 1 1 1 -1 7.0672 25 1 1 0 -1 3.3583 26 1 1 -1 -1 5.2325 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3258 atoms have been selected out of 3332 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 744 248 248 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1464 488 488 0.00 6 C006 has 438 146 146 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1683 552 550 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 126 42 42 1.05 Total of12380 atoms and 4111 groups and 4104 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3332 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.086" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1099" Evaluating: 1099-7 Parameter: NUMWAT <- "1092" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1092" Comparing "1081" and "1092". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.086" Parameter: BOX -> "32.086" Parameter: BOX -> "32.086" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.08600 B = 32.08600 C = 32.08600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.1966 2 1 -1 0 -1 3.3826 3 1 -1 1 -1 4.7707 4 1 0 -1 -1 3.7042 5 1 0 0 -1 0.5162 6 1 0 1 -1 4.9160 7 1 -1 -1 0 4.0927 8 1 -1 0 0 3.1663 9 1 -1 1 0 4.8478 10 1 0 -1 0 1.1942 11 1 0 1 0 1.1942 12 1 -1 -1 1 7.0640 13 1 -1 0 1 3.3556 14 1 -1 1 1 5.2298 15 1 0 -1 1 4.9160 16 1 0 0 1 0.5162 17 1 0 1 1 3.7042 18 1 1 1 1 7.1966 19 1 1 0 1 3.3826 20 1 1 -1 1 4.7707 21 1 1 1 0 4.0927 22 1 1 0 0 3.1663 23 1 1 -1 0 4.8478 24 1 1 1 -1 7.0640 25 1 1 0 -1 3.3556 26 1 1 -1 -1 5.2298 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3258 atoms have been selected out of 3332 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 744 248 248 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1464 488 488 0.00 6 C006 has 441 147 147 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1683 552 550 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 126 42 42 1.04 Total of12383 atoms and 4112 groups and 4105 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3332 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.084" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1099" Evaluating: 1099-7 Parameter: NUMWAT <- "1092" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1092" Comparing "1081" and "1092". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.084" Parameter: BOX -> "32.084" Parameter: BOX -> "32.084" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.08400 B = 32.08400 C = 32.08400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.1989 2 1 -1 0 -1 3.3798 3 1 -1 1 -1 4.7680 4 1 0 -1 -1 3.7015 5 1 0 0 -1 0.5158 6 1 0 1 -1 4.9148 7 1 -1 -1 0 4.0901 8 1 -1 0 0 3.1652 9 1 -1 1 0 4.8450 10 1 0 -1 0 1.1942 11 1 0 1 0 1.1942 12 1 -1 -1 1 7.0608 13 1 -1 0 1 3.3528 14 1 -1 1 1 5.2271 15 1 0 -1 1 4.9148 16 1 0 0 1 0.5158 17 1 0 1 1 3.7015 18 1 1 1 1 7.1989 19 1 1 0 1 3.3798 20 1 1 -1 1 4.7680 21 1 1 1 0 4.0901 22 1 1 0 0 3.1652 23 1 1 -1 0 4.8450 24 1 1 1 -1 7.0608 25 1 1 0 -1 3.3528 26 1 1 -1 -1 5.2271 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3258 atoms have been selected out of 3332 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 486 162 162 0.00 2 C002 has 744 248 248 0.00 3 C003 has 117 39 39 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1467 489 489 0.00 6 C006 has 441 147 147 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1683 552 550 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1557 519 519 0.00 12 C012 has 114 38 38 0.00 13 C013 has 483 161 161 0.00 14 C014 has 126 42 42 1.04 Total of12395 atoms and 4116 groups and 4109 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3332 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.082" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1099" Evaluating: 1099-7 Parameter: NUMWAT <- "1092" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1092" Comparing "1081" and "1092". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.082" Parameter: BOX -> "32.082" Parameter: BOX -> "32.082" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.08200 B = 32.08200 C = 32.08200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2013 2 1 -1 0 -1 3.3770 3 1 -1 1 -1 4.7652 4 1 0 -1 -1 3.6988 5 1 0 0 -1 0.5154 6 1 0 1 -1 4.9136 7 1 -1 -1 0 4.0875 8 1 -1 0 0 3.1641 9 1 -1 1 0 4.8421 10 1 0 -1 0 1.1943 11 1 0 1 0 1.1943 12 1 -1 -1 1 7.0576 13 1 -1 0 1 3.3501 14 1 -1 1 1 5.2243 15 1 0 -1 1 4.9136 16 1 0 0 1 0.5154 17 1 0 1 1 3.6988 18 1 1 1 1 7.2013 19 1 1 0 1 3.3770 20 1 1 -1 1 4.7652 21 1 1 1 0 4.0875 22 1 1 0 0 3.1641 23 1 1 -1 0 4.8421 24 1 1 1 -1 7.0576 25 1 1 0 -1 3.3501 26 1 1 -1 -1 5.2243 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3258 atoms have been selected out of 3332 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 744 248 248 0.00 3 C003 has 117 39 39 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1467 489 489 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1683 552 550 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1557 519 519 0.00 12 C012 has 114 38 38 0.00 13 C013 has 483 161 161 0.00 14 C014 has 126 42 42 1.04 Total of12401 atoms and 4118 groups and 4111 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3332 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.08" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1099" Evaluating: 1099-7 Parameter: NUMWAT <- "1092" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1092" Comparing "1081" and "1092". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.08" Parameter: BOX -> "32.08" Parameter: BOX -> "32.08" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.08000 B = 32.08000 C = 32.08000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2036 2 1 -1 0 -1 3.3742 3 1 -1 1 -1 4.7625 4 1 0 -1 -1 3.6961 5 1 0 0 -1 0.5150 6 1 0 1 -1 4.9124 7 1 -1 -1 0 4.0850 8 1 -1 0 0 3.1630 9 1 -1 1 0 4.8393 10 1 0 -1 0 1.1943 11 1 0 1 0 1.1943 12 1 -1 -1 1 7.0544 13 1 -1 0 1 3.3474 14 1 -1 1 1 5.2216 15 1 0 -1 1 4.9124 16 1 0 0 1 0.5150 17 1 0 1 1 3.6961 18 1 1 1 1 7.2036 19 1 1 0 1 3.3742 20 1 1 -1 1 4.7625 21 1 1 1 0 4.0850 22 1 1 0 0 3.1630 23 1 1 -1 0 4.8393 24 1 1 1 -1 7.0544 25 1 1 0 -1 3.3474 26 1 1 -1 -1 5.2216 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3258 atoms have been selected out of 3332 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 744 248 248 0.00 3 C003 has 117 39 39 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1467 489 489 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1683 552 550 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1557 519 519 0.00 12 C012 has 114 38 38 0.00 13 C013 has 483 161 161 0.00 14 C014 has 126 42 42 1.04 Total of12401 atoms and 4118 groups and 4111 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3332 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.078" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1099" Evaluating: 1099-7 Parameter: NUMWAT <- "1092" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1092" Comparing "1081" and "1092". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.078" Parameter: BOX -> "32.078" Parameter: BOX -> "32.078" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.07800 B = 32.07800 C = 32.07800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2060 2 1 -1 0 -1 3.3714 3 1 -1 1 -1 4.7598 4 1 0 -1 -1 3.6934 5 1 0 0 -1 0.5147 6 1 0 1 -1 4.9112 7 1 -1 -1 0 4.0824 8 1 -1 0 0 3.1619 9 1 -1 1 0 4.8365 10 1 0 -1 0 1.1943 11 1 0 1 0 1.1943 12 1 -1 -1 1 7.0512 13 1 -1 0 1 3.3446 14 1 -1 1 1 5.2189 15 1 0 -1 1 4.9112 16 1 0 0 1 0.5147 17 1 0 1 1 3.6934 18 1 1 1 1 7.2060 19 1 1 0 1 3.3714 20 1 1 -1 1 4.7598 21 1 1 1 0 4.0824 22 1 1 0 0 3.1619 23 1 1 -1 0 4.8365 24 1 1 1 -1 7.0512 25 1 1 0 -1 3.3446 26 1 1 -1 -1 5.2189 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3258 atoms have been selected out of 3332 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 744 248 248 0.00 3 C003 has 117 39 39 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1467 489 489 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1683 552 550 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1560 520 520 0.00 12 C012 has 114 38 38 0.00 13 C013 has 483 161 161 0.00 14 C014 has 126 42 42 1.04 Total of12404 atoms and 4119 groups and 4112 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3332 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1099 Number of atoms = 3332 Number of groups = 1104 Number of bonds = 3325 Number of angles = 1203 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1101 Number of HB donors = 2180 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.076" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1099" Evaluating: 1099-7 Parameter: NUMWAT <- "1092" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1092" Comparing "1081" and "1092". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.076" Parameter: BOX -> "32.076" Parameter: BOX -> "32.076" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.07600 B = 32.07600 C = 32.07600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2083 2 1 -1 0 -1 3.3686 3 1 -1 1 -1 4.7570 4 1 0 -1 -1 3.6907 5 1 0 0 -1 0.5143 6 1 0 1 -1 4.9100 7 1 -1 -1 0 4.0798 8 1 -1 0 0 3.1608 9 1 -1 1 0 4.8337 10 1 0 -1 0 1.1943 11 1 0 1 0 1.1943 12 1 -1 -1 1 7.0481 13 1 -1 0 1 3.3419 14 1 -1 1 1 5.2162 15 1 0 -1 1 4.9100 16 1 0 0 1 0.5143 17 1 0 1 1 3.6907 18 1 1 1 1 7.2083 19 1 1 0 1 3.3686 20 1 1 -1 1 4.7570 21 1 1 1 0 4.0798 22 1 1 0 0 3.1608 23 1 1 -1 0 4.8337 24 1 1 1 -1 7.0481 25 1 1 0 -1 3.3419 26 1 1 -1 -1 5.2162 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3258 atoms have been selected out of 3332 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 702 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 741 247 247 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1467 489 489 0.00 6 C006 has 444 148 148 0.00 7 C007 has 795 265 265 0.00 8 C008 has 1683 552 550 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1563 521 521 0.00 12 C012 has 114 38 38 0.00 13 C013 has 486 162 162 0.00 14 C014 has 129 43 43 1.03 Total of12410 atoms and 4121 groups and 4114 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3332 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1098 Number of atoms = 3329 Number of groups = 1103 Number of bonds = 3322 Number of angles = 1202 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1100 Number of HB donors = 2178 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1098 Number of atoms = 3329 Number of groups = 1103 Number of bonds = 3322 Number of angles = 1202 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1100 Number of HB donors = 2178 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.074" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1098" Evaluating: 1098-7 Parameter: NUMWAT <- "1091" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1091" Comparing "1081" and "1091". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.074" Parameter: BOX -> "32.074" Parameter: BOX -> "32.074" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.07400 B = 32.07400 C = 32.07400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2107 2 1 -1 0 -1 3.3658 3 1 -1 1 -1 4.7543 4 1 0 -1 -1 3.6880 5 1 0 0 -1 0.5139 6 1 0 1 -1 4.9088 7 1 -1 -1 0 4.0773 8 1 -1 0 0 2.5441 9 1 -1 1 0 4.8309 10 1 0 -1 0 1.1944 11 1 0 1 0 1.1944 12 1 -1 -1 1 7.0449 13 1 -1 0 1 3.3392 14 1 -1 1 1 5.2134 15 1 0 -1 1 4.9088 16 1 0 0 1 0.5139 17 1 0 1 1 3.6880 18 1 1 1 1 7.2107 19 1 1 0 1 3.3658 20 1 1 -1 1 4.7543 21 1 1 1 0 4.0773 22 1 1 0 0 2.5441 23 1 1 -1 0 4.8309 24 1 1 1 -1 7.0449 25 1 1 0 -1 3.3392 26 1 1 -1 -1 5.2134 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3255 atoms have been selected out of 3329 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 741 247 247 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1464 488 488 0.00 6 C006 has 444 148 148 0.00 7 C007 has 792 264 264 0.00 8 C008 has 1680 551 549 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1566 522 522 0.00 12 C012 has 114 38 38 0.00 13 C013 has 486 162 162 0.00 14 C014 has 126 42 42 1.03 Total of12395 atoms and 4116 groups and 4109 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3329 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1098 Number of atoms = 3329 Number of groups = 1103 Number of bonds = 3322 Number of angles = 1202 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1100 Number of HB donors = 2178 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1098 Number of atoms = 3329 Number of groups = 1103 Number of bonds = 3322 Number of angles = 1202 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1100 Number of HB donors = 2178 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.072" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1098" Evaluating: 1098-7 Parameter: NUMWAT <- "1091" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1091" Comparing "1081" and "1091". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.072" Parameter: BOX -> "32.072" Parameter: BOX -> "32.072" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.07200 B = 32.07200 C = 32.07200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2130 2 1 -1 0 -1 3.3630 3 1 -1 1 -1 4.7515 4 1 0 -1 -1 3.6854 5 1 0 0 -1 0.5135 6 1 0 1 -1 4.9075 7 1 -1 -1 0 4.0747 8 1 -1 0 0 2.5427 9 1 -1 1 0 4.8280 10 1 0 -1 0 1.1944 11 1 0 1 0 1.1944 12 1 -1 -1 1 7.0417 13 1 -1 0 1 3.3364 14 1 -1 1 1 5.2107 15 1 0 -1 1 4.9075 16 1 0 0 1 0.5135 17 1 0 1 1 3.6854 18 1 1 1 1 7.2130 19 1 1 0 1 3.3630 20 1 1 -1 1 4.7515 21 1 1 1 0 4.0747 22 1 1 0 0 2.5427 23 1 1 -1 0 4.8280 24 1 1 1 -1 7.0417 25 1 1 0 -1 3.3364 26 1 1 -1 -1 5.2107 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3255 atoms have been selected out of 3329 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 478 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 741 247 247 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1464 488 488 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1680 551 549 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1566 522 522 0.00 12 C012 has 111 37 37 0.00 13 C013 has 486 162 162 0.00 14 C014 has 129 43 43 1.03 Total of12395 atoms and 4116 groups and 4109 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3329 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1097 Number of atoms = 3326 Number of groups = 1102 Number of bonds = 3319 Number of angles = 1201 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2176 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1097 Number of atoms = 3326 Number of groups = 1102 Number of bonds = 3319 Number of angles = 1201 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2176 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.07" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1097" Evaluating: 1097-7 Parameter: NUMWAT <- "1090" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1090" Comparing "1081" and "1090". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.07" Parameter: BOX -> "32.07" Parameter: BOX -> "32.07" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.07000 B = 32.07000 C = 32.07000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2154 2 1 -1 0 -1 3.3603 3 1 -1 1 -1 4.7488 4 1 0 -1 -1 3.6827 5 1 0 0 -1 0.5132 6 1 0 1 -1 4.9063 7 1 -1 -1 0 4.0721 8 1 -1 0 0 2.5412 9 1 -1 1 0 4.8252 10 1 0 -1 0 1.1945 11 1 0 1 0 1.1945 12 1 -1 -1 1 7.0385 13 1 -1 0 1 3.3337 14 1 -1 1 1 5.2080 15 1 0 -1 1 4.9063 16 1 0 0 1 0.5132 17 1 0 1 1 3.6827 18 1 1 1 1 7.2154 19 1 1 0 1 3.3603 20 1 1 -1 1 4.7488 21 1 1 1 0 4.0721 22 1 1 0 0 2.5412 23 1 1 -1 0 4.8252 24 1 1 1 -1 7.0385 25 1 1 0 -1 3.3337 26 1 1 -1 -1 5.2080 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3252 atoms have been selected out of 3326 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 741 247 247 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1464 488 488 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1677 550 548 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1563 521 521 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 126 42 42 1.03 Total of12377 atoms and 4110 groups and 4103 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3326 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1097 Number of atoms = 3326 Number of groups = 1102 Number of bonds = 3319 Number of angles = 1201 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2176 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1097 Number of atoms = 3326 Number of groups = 1102 Number of bonds = 3319 Number of angles = 1201 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2176 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.068" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1097" Evaluating: 1097-7 Parameter: NUMWAT <- "1090" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1090" Comparing "1081" and "1090". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.068" Parameter: BOX -> "32.068" Parameter: BOX -> "32.068" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.06800 B = 32.06800 C = 32.06800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2177 2 1 -1 0 -1 3.3575 3 1 -1 1 -1 4.7460 4 1 0 -1 -1 3.6800 5 1 0 0 -1 0.5128 6 1 0 1 -1 4.9051 7 1 -1 -1 0 4.0696 8 1 -1 0 0 2.5398 9 1 -1 1 0 4.8224 10 1 0 -1 0 1.1945 11 1 0 1 0 1.1945 12 1 -1 -1 1 7.0353 13 1 -1 0 1 3.3310 14 1 -1 1 1 5.2052 15 1 0 -1 1 4.9051 16 1 0 0 1 0.5128 17 1 0 1 1 3.6800 18 1 1 1 1 7.2177 19 1 1 0 1 3.3575 20 1 1 -1 1 4.7460 21 1 1 1 0 4.0696 22 1 1 0 0 2.5398 23 1 1 -1 0 4.8224 24 1 1 1 -1 7.0353 25 1 1 0 -1 3.3310 26 1 1 -1 -1 5.2052 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3252 atoms have been selected out of 3326 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 741 247 247 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1464 488 488 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1677 550 548 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1563 521 521 0.00 12 C012 has 111 37 37 0.00 13 C013 has 489 163 163 0.00 14 C014 has 126 42 42 1.03 Total of12383 atoms and 4112 groups and 4105 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3326 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1097 Number of atoms = 3326 Number of groups = 1102 Number of bonds = 3319 Number of angles = 1201 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2176 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1097 Number of atoms = 3326 Number of groups = 1102 Number of bonds = 3319 Number of angles = 1201 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2176 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.066" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1097" Evaluating: 1097-7 Parameter: NUMWAT <- "1090" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1090" Comparing "1081" and "1090". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.066" Parameter: BOX -> "32.066" Parameter: BOX -> "32.066" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.06600 B = 32.06600 C = 32.06600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2201 2 1 -1 0 -1 3.3547 3 1 -1 1 -1 4.7433 4 1 0 -1 -1 3.6773 5 1 0 0 -1 0.5125 6 1 0 1 -1 4.9039 7 1 -1 -1 0 4.0670 8 1 -1 0 0 2.5384 9 1 -1 1 0 4.8196 10 1 0 -1 0 1.1946 11 1 0 1 0 1.1946 12 1 -1 -1 1 7.0321 13 1 -1 0 1 3.3282 14 1 -1 1 1 5.2025 15 1 0 -1 1 4.9039 16 1 0 0 1 0.5125 17 1 0 1 1 3.6773 18 1 1 1 1 7.2201 19 1 1 0 1 3.3547 20 1 1 -1 1 4.7433 21 1 1 1 0 4.0670 22 1 1 0 0 2.5384 23 1 1 -1 0 4.8196 24 1 1 1 -1 7.0321 25 1 1 0 -1 3.3282 26 1 1 -1 -1 5.2025 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3252 atoms have been selected out of 3326 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 178 OPERATED ON BY TRANSFORMATION C008 RESIDUE 709 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 492 164 164 0.00 2 C002 has 738 246 246 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1461 487 487 0.00 6 C006 has 441 147 147 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1674 549 547 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1566 522 522 0.00 12 C012 has 111 37 37 0.00 13 C013 has 492 164 164 0.00 14 C014 has 126 42 42 1.02 Total of12377 atoms and 4110 groups and 4103 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 6 atoms have been selected out of 3326 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 2 residues deleted. DELTIC: 6 bonds deleted DELTIC: 2 angles deleted DELTIC: 4 donors deleted DELTIC: 2 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1095 Number of atoms = 3320 Number of groups = 1100 Number of bonds = 3313 Number of angles = 1199 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1097 Number of HB donors = 2172 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1095 Number of atoms = 3320 Number of groups = 1100 Number of bonds = 3313 Number of angles = 1199 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1097 Number of HB donors = 2172 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.064" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1095" Evaluating: 1095-7 Parameter: NUMWAT <- "1088" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1088" Comparing "1081" and "1088". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.064" Parameter: BOX -> "32.064" Parameter: BOX -> "32.064" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.06400 B = 32.06400 C = 32.06400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2224 2 1 -1 0 -1 3.3519 3 1 -1 1 -1 4.7406 4 1 0 -1 -1 3.6746 5 1 0 0 -1 0.5122 6 1 0 1 -1 4.9027 7 1 -1 -1 0 4.0644 8 1 -1 0 0 2.5370 9 1 -1 1 0 4.8168 10 1 0 -1 0 1.1946 11 1 0 1 0 1.1946 12 1 -1 -1 1 7.0289 13 1 -1 0 1 3.3255 14 1 -1 1 1 5.1998 15 1 0 -1 1 4.9027 16 1 0 0 1 0.5122 17 1 0 1 1 3.6746 18 1 1 1 1 7.2224 19 1 1 0 1 3.3519 20 1 1 -1 1 4.7406 21 1 1 1 0 4.0644 22 1 1 0 0 2.5370 23 1 1 -1 0 4.8168 24 1 1 1 -1 7.0289 25 1 1 0 -1 3.3255 26 1 1 -1 -1 5.1998 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3246 atoms have been selected out of 3320 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 492 164 164 0.00 2 C002 has 738 246 246 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1461 487 487 0.00 6 C006 has 444 148 148 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1671 548 546 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1563 521 521 0.00 12 C012 has 111 37 37 0.00 13 C013 has 489 163 163 0.00 14 C014 has 129 43 43 1.02 Total of12368 atoms and 4107 groups and 4100 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3320 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1095 Number of atoms = 3320 Number of groups = 1100 Number of bonds = 3313 Number of angles = 1199 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1097 Number of HB donors = 2172 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1095 Number of atoms = 3320 Number of groups = 1100 Number of bonds = 3313 Number of angles = 1199 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1097 Number of HB donors = 2172 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.062" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1095" Evaluating: 1095-7 Parameter: NUMWAT <- "1088" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1088" Comparing "1081" and "1088". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.062" Parameter: BOX -> "32.062" Parameter: BOX -> "32.062" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.06200 B = 32.06200 C = 32.06200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2248 2 1 -1 0 -1 3.3491 3 1 -1 1 -1 4.7378 4 1 0 -1 -1 3.6719 5 1 0 0 -1 0.5118 6 1 0 1 -1 4.9015 7 1 -1 -1 0 4.0619 8 1 -1 0 0 2.5356 9 1 -1 1 0 4.8139 10 1 0 -1 0 1.1947 11 1 0 1 0 1.1947 12 1 -1 -1 1 7.0257 13 1 -1 0 1 3.3228 14 1 -1 1 1 5.1971 15 1 0 -1 1 4.9015 16 1 0 0 1 0.5118 17 1 0 1 1 3.6719 18 1 1 1 1 7.2248 19 1 1 0 1 3.3491 20 1 1 -1 1 4.7378 21 1 1 1 0 4.0619 22 1 1 0 0 2.5356 23 1 1 -1 0 4.8139 24 1 1 1 -1 7.0257 25 1 1 0 -1 3.3228 26 1 1 -1 -1 5.1971 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3246 atoms have been selected out of 3320 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 492 164 164 0.00 2 C002 has 738 246 246 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1461 487 487 0.00 6 C006 has 444 148 148 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1671 548 546 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1563 521 521 0.00 12 C012 has 111 37 37 0.00 13 C013 has 489 163 163 0.00 14 C014 has 129 43 43 1.02 Total of12368 atoms and 4107 groups and 4100 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3320 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1095 Number of atoms = 3320 Number of groups = 1100 Number of bonds = 3313 Number of angles = 1199 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1097 Number of HB donors = 2172 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1095 Number of atoms = 3320 Number of groups = 1100 Number of bonds = 3313 Number of angles = 1199 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1097 Number of HB donors = 2172 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.06" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1095" Evaluating: 1095-7 Parameter: NUMWAT <- "1088" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1088" Comparing "1081" and "1088". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.06" Parameter: BOX -> "32.06" Parameter: BOX -> "32.06" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.06000 B = 32.06000 C = 32.06000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2272 2 1 -1 0 -1 3.3463 3 1 -1 1 -1 4.7351 4 1 0 -1 -1 3.6692 5 1 0 0 -1 0.5115 6 1 0 1 -1 4.9003 7 1 -1 -1 0 4.0593 8 1 -1 0 0 2.5342 9 1 -1 1 0 4.8111 10 1 0 -1 0 1.1947 11 1 0 1 0 1.1947 12 1 -1 -1 1 7.0225 13 1 -1 0 1 3.3200 14 1 -1 1 1 5.1943 15 1 0 -1 1 4.9003 16 1 0 0 1 0.5115 17 1 0 1 1 3.6692 18 1 1 1 1 7.2272 19 1 1 0 1 3.3463 20 1 1 -1 1 4.7351 21 1 1 1 0 4.0593 22 1 1 0 0 2.5342 23 1 1 -1 0 4.8111 24 1 1 1 -1 7.0225 25 1 1 0 -1 3.3200 26 1 1 -1 -1 5.1943 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3246 atoms have been selected out of 3320 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 492 164 164 0.00 2 C002 has 738 246 246 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1461 487 487 0.00 6 C006 has 444 148 148 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1671 548 546 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1563 521 521 0.00 12 C012 has 111 37 37 0.00 13 C013 has 489 163 163 0.00 14 C014 has 129 43 43 1.02 Total of12368 atoms and 4107 groups and 4100 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3320 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1095 Number of atoms = 3320 Number of groups = 1100 Number of bonds = 3313 Number of angles = 1199 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1097 Number of HB donors = 2172 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1095 Number of atoms = 3320 Number of groups = 1100 Number of bonds = 3313 Number of angles = 1199 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1097 Number of HB donors = 2172 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.058" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1095" Evaluating: 1095-7 Parameter: NUMWAT <- "1088" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1088" Comparing "1081" and "1088". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.058" Parameter: BOX -> "32.058" Parameter: BOX -> "32.058" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.05800 B = 32.05800 C = 32.05800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2295 2 1 -1 0 -1 3.3435 3 1 -1 1 -1 4.7323 4 1 0 -1 -1 3.6666 5 1 0 0 -1 0.5112 6 1 0 1 -1 4.8991 7 1 -1 -1 0 4.0567 8 1 -1 0 0 2.5328 9 1 -1 1 0 4.8083 10 1 0 -1 0 1.1948 11 1 0 1 0 1.1948 12 1 -1 -1 1 7.0193 13 1 -1 0 1 3.3173 14 1 -1 1 1 5.1916 15 1 0 -1 1 4.8991 16 1 0 0 1 0.5112 17 1 0 1 1 3.6666 18 1 1 1 1 7.2295 19 1 1 0 1 3.3435 20 1 1 -1 1 4.7323 21 1 1 1 0 4.0567 22 1 1 0 0 2.5328 23 1 1 -1 0 4.8083 24 1 1 1 -1 7.0193 25 1 1 0 -1 3.3173 26 1 1 -1 -1 5.1916 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3246 atoms have been selected out of 3320 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 492 164 164 0.00 2 C002 has 741 247 247 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1461 487 487 0.00 6 C006 has 444 148 148 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1671 548 546 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1563 521 521 0.00 12 C012 has 111 37 37 0.00 13 C013 has 489 163 163 0.00 14 C014 has 129 43 43 1.02 Total of12371 atoms and 4108 groups and 4101 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3320 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1095 Number of atoms = 3320 Number of groups = 1100 Number of bonds = 3313 Number of angles = 1199 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1097 Number of HB donors = 2172 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1095 Number of atoms = 3320 Number of groups = 1100 Number of bonds = 3313 Number of angles = 1199 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1097 Number of HB donors = 2172 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.056" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1095" Evaluating: 1095-7 Parameter: NUMWAT <- "1088" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1088" Comparing "1081" and "1088". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.056" Parameter: BOX -> "32.056" Parameter: BOX -> "32.056" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.05600 B = 32.05600 C = 32.05600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2319 2 1 -1 0 -1 3.3407 3 1 -1 1 -1 4.7296 4 1 0 -1 -1 3.6639 5 1 0 0 -1 0.5109 6 1 0 1 -1 4.8979 7 1 -1 -1 0 4.0542 8 1 -1 0 0 2.5314 9 1 -1 1 0 4.8055 10 1 0 -1 0 1.1949 11 1 0 1 0 1.1949 12 1 -1 -1 1 7.0161 13 1 -1 0 1 3.3146 14 1 -1 1 1 5.1889 15 1 0 -1 1 4.8979 16 1 0 0 1 0.5109 17 1 0 1 1 3.6639 18 1 1 1 1 7.2319 19 1 1 0 1 3.3407 20 1 1 -1 1 4.7296 21 1 1 1 0 4.0542 22 1 1 0 0 2.5314 23 1 1 -1 0 4.8055 24 1 1 1 -1 7.0161 25 1 1 0 -1 3.3146 26 1 1 -1 -1 5.1889 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3246 atoms have been selected out of 3320 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 492 164 164 0.00 2 C002 has 741 247 247 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1461 487 487 0.00 6 C006 has 444 148 148 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1671 548 546 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1563 521 521 0.00 12 C012 has 111 37 37 0.00 13 C013 has 489 163 163 0.00 14 C014 has 129 43 43 1.01 Total of12371 atoms and 4108 groups and 4101 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3320 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1095 Number of atoms = 3320 Number of groups = 1100 Number of bonds = 3313 Number of angles = 1199 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1097 Number of HB donors = 2172 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1095 Number of atoms = 3320 Number of groups = 1100 Number of bonds = 3313 Number of angles = 1199 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1097 Number of HB donors = 2172 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.054" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1095" Evaluating: 1095-7 Parameter: NUMWAT <- "1088" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1088" Comparing "1081" and "1088". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.054" Parameter: BOX -> "32.054" Parameter: BOX -> "32.054" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.05400 B = 32.05400 C = 32.05400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2343 2 1 -1 0 -1 3.3379 3 1 -1 1 -1 4.7269 4 1 0 -1 -1 3.6612 5 1 0 0 -1 0.5106 6 1 0 1 -1 4.8967 7 1 -1 -1 0 4.0516 8 1 -1 0 0 2.5300 9 1 -1 1 0 4.8026 10 1 0 -1 0 1.1949 11 1 0 1 0 1.1949 12 1 -1 -1 1 7.0129 13 1 -1 0 1 3.3118 14 1 -1 1 1 5.1862 15 1 0 -1 1 4.8967 16 1 0 0 1 0.5106 17 1 0 1 1 3.6612 18 1 1 1 1 7.2343 19 1 1 0 1 3.3379 20 1 1 -1 1 4.7269 21 1 1 1 0 4.0516 22 1 1 0 0 2.5300 23 1 1 -1 0 4.8026 24 1 1 1 -1 7.0129 25 1 1 0 -1 3.3118 26 1 1 -1 -1 5.1862 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3246 atoms have been selected out of 3320 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 492 164 164 0.00 2 C002 has 741 247 247 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1461 487 487 0.00 6 C006 has 444 148 148 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1671 548 546 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1563 521 521 0.00 12 C012 has 114 38 38 0.00 13 C013 has 489 163 163 0.00 14 C014 has 129 43 43 1.01 Total of12374 atoms and 4109 groups and 4102 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3320 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1095 Number of atoms = 3320 Number of groups = 1100 Number of bonds = 3313 Number of angles = 1199 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1097 Number of HB donors = 2172 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1095 Number of atoms = 3320 Number of groups = 1100 Number of bonds = 3313 Number of angles = 1199 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1097 Number of HB donors = 2172 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.052" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1095" Evaluating: 1095-7 Parameter: NUMWAT <- "1088" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1088" Comparing "1081" and "1088". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.052" Parameter: BOX -> "32.052" Parameter: BOX -> "32.052" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.05200 B = 32.05200 C = 32.05200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2366 2 1 -1 0 -1 3.3351 3 1 -1 1 -1 4.7241 4 1 0 -1 -1 3.6585 5 1 0 0 -1 0.5103 6 1 0 1 -1 4.8955 7 1 -1 -1 0 4.0490 8 1 -1 0 0 2.5286 9 1 -1 1 0 4.7998 10 1 0 -1 0 1.1950 11 1 0 1 0 1.1950 12 1 -1 -1 1 7.0097 13 1 -1 0 1 3.3091 14 1 -1 1 1 5.1835 15 1 0 -1 1 4.8955 16 1 0 0 1 0.5103 17 1 0 1 1 3.6585 18 1 1 1 1 7.2366 19 1 1 0 1 3.3351 20 1 1 -1 1 4.7241 21 1 1 1 0 4.0490 22 1 1 0 0 2.5286 23 1 1 -1 0 4.7998 24 1 1 1 -1 7.0097 25 1 1 0 -1 3.3091 26 1 1 -1 -1 5.1835 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3246 atoms have been selected out of 3320 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 492 164 164 0.00 2 C002 has 741 247 247 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1461 487 487 0.00 6 C006 has 444 148 148 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1671 548 546 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1563 521 521 0.00 12 C012 has 114 38 38 0.00 13 C013 has 489 163 163 0.00 14 C014 has 129 43 43 1.01 Total of12374 atoms and 4109 groups and 4102 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3320 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1095 Number of atoms = 3320 Number of groups = 1100 Number of bonds = 3313 Number of angles = 1199 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1097 Number of HB donors = 2172 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1095 Number of atoms = 3320 Number of groups = 1100 Number of bonds = 3313 Number of angles = 1199 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1097 Number of HB donors = 2172 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.05" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1095" Evaluating: 1095-7 Parameter: NUMWAT <- "1088" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1088" Comparing "1081" and "1088". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.05" Parameter: BOX -> "32.05" Parameter: BOX -> "32.05" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.05000 B = 32.05000 C = 32.05000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2390 2 1 -1 0 -1 3.3323 3 1 -1 1 -1 4.7214 4 1 0 -1 -1 3.6558 5 1 0 0 -1 0.5101 6 1 0 1 -1 4.8943 7 1 -1 -1 0 4.0465 8 1 -1 0 0 2.5272 9 1 -1 1 0 4.7970 10 1 0 -1 0 1.1951 11 1 0 1 0 1.1951 12 1 -1 -1 1 7.0065 13 1 -1 0 1 3.3064 14 1 -1 1 1 5.1807 15 1 0 -1 1 4.8943 16 1 0 0 1 0.5101 17 1 0 1 1 3.6558 18 1 1 1 1 7.2390 19 1 1 0 1 3.3323 20 1 1 -1 1 4.7214 21 1 1 1 0 4.0465 22 1 1 0 0 2.5272 23 1 1 -1 0 4.7970 24 1 1 1 -1 7.0065 25 1 1 0 -1 3.3064 26 1 1 -1 -1 5.1807 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3246 atoms have been selected out of 3320 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 939 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 744 248 248 0.00 3 C003 has 114 38 38 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1461 487 487 0.00 6 C006 has 447 149 149 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1671 548 546 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1560 520 520 0.00 12 C012 has 114 38 38 0.00 13 C013 has 489 163 163 0.00 14 C014 has 129 43 43 1.01 Total of12371 atoms and 4108 groups and 4101 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3320 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1094 Number of atoms = 3317 Number of groups = 1099 Number of bonds = 3310 Number of angles = 1198 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1096 Number of HB donors = 2170 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1094 Number of atoms = 3317 Number of groups = 1099 Number of bonds = 3310 Number of angles = 1198 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1096 Number of HB donors = 2170 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.048" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1094" Evaluating: 1094-7 Parameter: NUMWAT <- "1087" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1087" Comparing "1081" and "1087". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.048" Parameter: BOX -> "32.048" Parameter: BOX -> "32.048" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.04800 B = 32.04800 C = 32.04800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2413 2 1 -1 0 -1 3.3295 3 1 -1 1 -1 4.7187 4 1 0 -1 -1 3.6531 5 1 0 0 -1 0.5098 6 1 0 1 -1 4.8931 7 1 -1 -1 0 4.0439 8 1 -1 0 0 2.5258 9 1 -1 1 0 4.7942 10 1 0 -1 0 1.1952 11 1 0 1 0 1.1952 12 1 -1 -1 1 7.0033 13 1 -1 0 1 3.3037 14 1 -1 1 1 5.1780 15 1 0 -1 1 4.8931 16 1 0 0 1 0.5098 17 1 0 1 1 3.6531 18 1 1 1 1 7.2413 19 1 1 0 1 3.3295 20 1 1 -1 1 4.7187 21 1 1 1 0 4.0439 22 1 1 0 0 2.5258 23 1 1 -1 0 4.7942 24 1 1 1 -1 7.0033 25 1 1 0 -1 3.3037 26 1 1 -1 -1 5.1780 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3243 atoms have been selected out of 3317 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 744 248 248 0.00 3 C003 has 114 38 38 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1458 486 486 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1671 548 546 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1560 520 520 0.00 12 C012 has 114 38 38 0.00 13 C013 has 489 163 163 0.00 14 C014 has 129 43 43 1.01 Total of12365 atoms and 4106 groups and 4099 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3317 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1094 Number of atoms = 3317 Number of groups = 1099 Number of bonds = 3310 Number of angles = 1198 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1096 Number of HB donors = 2170 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1094 Number of atoms = 3317 Number of groups = 1099 Number of bonds = 3310 Number of angles = 1198 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1096 Number of HB donors = 2170 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.046" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1094" Evaluating: 1094-7 Parameter: NUMWAT <- "1087" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1087" Comparing "1081" and "1087". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.046" Parameter: BOX -> "32.046" Parameter: BOX -> "32.046" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.04600 B = 32.04600 C = 32.04600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2437 2 1 -1 0 -1 3.3268 3 1 -1 1 -1 4.7159 4 1 0 -1 -1 3.6505 5 1 0 0 -1 0.5095 6 1 0 1 -1 4.8919 7 1 -1 -1 0 4.0413 8 1 -1 0 0 2.5244 9 1 -1 1 0 4.7914 10 1 0 -1 0 1.1953 11 1 0 1 0 1.1953 12 1 -1 -1 1 7.0001 13 1 -1 0 1 3.3009 14 1 -1 1 1 5.1753 15 1 0 -1 1 4.8919 16 1 0 0 1 0.5095 17 1 0 1 1 3.6505 18 1 1 1 1 7.2437 19 1 1 0 1 3.3268 20 1 1 -1 1 4.7159 21 1 1 1 0 4.0413 22 1 1 0 0 2.5244 23 1 1 -1 0 4.7914 24 1 1 1 -1 7.0001 25 1 1 0 -1 3.3009 26 1 1 -1 -1 5.1753 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3243 atoms have been selected out of 3317 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 744 248 248 0.00 3 C003 has 114 38 38 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1458 486 486 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1671 548 546 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1560 520 520 0.00 12 C012 has 114 38 38 0.00 13 C013 has 489 163 163 0.00 14 C014 has 129 43 43 1.00 Total of12365 atoms and 4106 groups and 4099 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3317 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1094 Number of atoms = 3317 Number of groups = 1099 Number of bonds = 3310 Number of angles = 1198 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1096 Number of HB donors = 2170 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1094 Number of atoms = 3317 Number of groups = 1099 Number of bonds = 3310 Number of angles = 1198 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1096 Number of HB donors = 2170 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.044" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1094" Evaluating: 1094-7 Parameter: NUMWAT <- "1087" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1087" Comparing "1081" and "1087". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.044" Parameter: BOX -> "32.044" Parameter: BOX -> "32.044" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.04400 B = 32.04400 C = 32.04400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2461 2 1 -1 0 -1 3.3240 3 1 -1 1 -1 4.7132 4 1 0 -1 -1 3.6478 5 1 0 0 -1 0.5093 6 1 0 1 -1 4.8907 7 1 -1 -1 0 4.0388 8 1 -1 0 0 2.5230 9 1 -1 1 0 4.7885 10 1 0 -1 0 1.1953 11 1 0 1 0 1.1953 12 1 -1 -1 1 6.9969 13 1 -1 0 1 3.2982 14 1 -1 1 1 5.1726 15 1 0 -1 1 4.8907 16 1 0 0 1 0.5093 17 1 0 1 1 3.6478 18 1 1 1 1 7.2461 19 1 1 0 1 3.3240 20 1 1 -1 1 4.7132 21 1 1 1 0 4.0388 22 1 1 0 0 2.5230 23 1 1 -1 0 4.7885 24 1 1 1 -1 6.9969 25 1 1 0 -1 3.2982 26 1 1 -1 -1 5.1726 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3243 atoms have been selected out of 3317 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 744 248 248 0.00 3 C003 has 114 38 38 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1458 486 486 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1671 548 546 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1560 520 520 0.00 12 C012 has 114 38 38 0.00 13 C013 has 489 163 163 0.00 14 C014 has 129 43 43 1.00 Total of12365 atoms and 4106 groups and 4099 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3317 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1094 Number of atoms = 3317 Number of groups = 1099 Number of bonds = 3310 Number of angles = 1198 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1096 Number of HB donors = 2170 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1094 Number of atoms = 3317 Number of groups = 1099 Number of bonds = 3310 Number of angles = 1198 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1096 Number of HB donors = 2170 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.042" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1094" Evaluating: 1094-7 Parameter: NUMWAT <- "1087" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1087" Comparing "1081" and "1087". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.042" Parameter: BOX -> "32.042" Parameter: BOX -> "32.042" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.04200 B = 32.04200 C = 32.04200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2484 2 1 -1 0 -1 3.3212 3 1 -1 1 -1 4.7105 4 1 0 -1 -1 3.6451 5 1 0 0 -1 0.5090 6 1 0 1 -1 4.8895 7 1 -1 -1 0 4.0362 8 1 -1 0 0 2.5216 9 1 -1 1 0 4.7857 10 1 0 -1 0 1.1954 11 1 0 1 0 1.1954 12 1 -1 -1 1 6.9937 13 1 -1 0 1 3.2955 14 1 -1 1 1 5.1699 15 1 0 -1 1 4.8895 16 1 0 0 1 0.5090 17 1 0 1 1 3.6451 18 1 1 1 1 7.2484 19 1 1 0 1 3.3212 20 1 1 -1 1 4.7105 21 1 1 1 0 4.0362 22 1 1 0 0 2.5216 23 1 1 -1 0 4.7857 24 1 1 1 -1 6.9937 25 1 1 0 -1 3.2955 26 1 1 -1 -1 5.1699 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3243 atoms have been selected out of 3317 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 744 248 248 0.00 3 C003 has 114 38 38 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1458 486 486 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1671 548 546 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1560 520 520 0.00 12 C012 has 114 38 38 0.00 13 C013 has 489 163 163 0.00 14 C014 has 129 43 43 1.00 Total of12365 atoms and 4106 groups and 4099 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3317 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1094 Number of atoms = 3317 Number of groups = 1099 Number of bonds = 3310 Number of angles = 1198 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1096 Number of HB donors = 2170 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1094 Number of atoms = 3317 Number of groups = 1099 Number of bonds = 3310 Number of angles = 1198 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1096 Number of HB donors = 2170 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.04" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1094" Evaluating: 1094-7 Parameter: NUMWAT <- "1087" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1087" Comparing "1081" and "1087". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.04" Parameter: BOX -> "32.04" Parameter: BOX -> "32.04" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.04000 B = 32.04000 C = 32.04000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2508 2 1 -1 0 -1 3.3184 3 1 -1 1 -1 4.7077 4 1 0 -1 -1 3.6424 5 1 0 0 -1 0.5088 6 1 0 1 -1 4.8884 7 1 -1 -1 0 4.0336 8 1 -1 0 0 2.5202 9 1 -1 1 0 4.7829 10 1 0 -1 0 1.1955 11 1 0 1 0 1.1955 12 1 -1 -1 1 6.9906 13 1 -1 0 1 3.2927 14 1 -1 1 1 5.1672 15 1 0 -1 1 4.8884 16 1 0 0 1 0.5088 17 1 0 1 1 3.6424 18 1 1 1 1 7.2508 19 1 1 0 1 3.3184 20 1 1 -1 1 4.7077 21 1 1 1 0 4.0336 22 1 1 0 0 2.5202 23 1 1 -1 0 4.7829 24 1 1 1 -1 6.9906 25 1 1 0 -1 3.2927 26 1 1 -1 -1 5.1672 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3243 atoms have been selected out of 3317 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 744 248 248 0.00 3 C003 has 114 38 38 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1458 486 486 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1671 548 546 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1560 520 520 0.00 12 C012 has 114 38 38 0.00 13 C013 has 489 163 163 0.00 14 C014 has 129 43 43 1.00 Total of12365 atoms and 4106 groups and 4099 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3317 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1094 Number of atoms = 3317 Number of groups = 1099 Number of bonds = 3310 Number of angles = 1198 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1096 Number of HB donors = 2170 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1094 Number of atoms = 3317 Number of groups = 1099 Number of bonds = 3310 Number of angles = 1198 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1096 Number of HB donors = 2170 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.038" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1094" Evaluating: 1094-7 Parameter: NUMWAT <- "1087" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1087" Comparing "1081" and "1087". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.038" Parameter: BOX -> "32.038" Parameter: BOX -> "32.038" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.03800 B = 32.03800 C = 32.03800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2532 2 1 -1 0 -1 3.3156 3 1 -1 1 -1 4.7050 4 1 0 -1 -1 3.6397 5 1 0 0 -1 0.5086 6 1 0 1 -1 4.8872 7 1 -1 -1 0 4.0311 8 1 -1 0 0 2.5188 9 1 -1 1 0 4.7801 10 1 0 -1 0 1.1956 11 1 0 1 0 1.1956 12 1 -1 -1 1 6.9874 13 1 -1 0 1 3.2900 14 1 -1 1 1 5.1645 15 1 0 -1 1 4.8872 16 1 0 0 1 0.5086 17 1 0 1 1 3.6397 18 1 1 1 1 7.2532 19 1 1 0 1 3.3156 20 1 1 -1 1 4.7050 21 1 1 1 0 4.0311 22 1 1 0 0 2.5188 23 1 1 -1 0 4.7801 24 1 1 1 -1 6.9874 25 1 1 0 -1 3.2900 26 1 1 -1 -1 5.1645 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3243 atoms have been selected out of 3317 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 45 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 744 248 248 0.00 3 C003 has 114 38 38 0.00 4 C004 has 627 209 209 0.00 5 C005 has 1461 487 487 0.00 6 C006 has 447 149 149 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1671 548 546 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1557 519 519 0.00 12 C012 has 114 38 38 0.00 13 C013 has 489 163 163 0.00 14 C014 has 129 43 43 1.00 Total of12371 atoms and 4108 groups and 4101 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3317 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1093 Number of atoms = 3314 Number of groups = 1098 Number of bonds = 3307 Number of angles = 1197 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1095 Number of HB donors = 2168 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1093 Number of atoms = 3314 Number of groups = 1098 Number of bonds = 3307 Number of angles = 1197 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1095 Number of HB donors = 2168 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.036" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1093" Evaluating: 1093-7 Parameter: NUMWAT <- "1086" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1086" Comparing "1081" and "1086". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.036" Parameter: BOX -> "32.036" Parameter: BOX -> "32.036" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.03600 B = 32.03600 C = 32.03600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2556 2 1 -1 0 -1 3.3128 3 1 -1 1 -1 4.7023 4 1 0 -1 -1 3.6370 5 1 0 0 -1 0.5083 6 1 0 1 -1 4.8860 7 1 -1 -1 0 4.0285 8 1 -1 0 0 2.5174 9 1 -1 1 0 4.7773 10 1 0 -1 0 1.1957 11 1 0 1 0 1.1957 12 1 -1 -1 1 6.9842 13 1 -1 0 1 3.2873 14 1 -1 1 1 5.1617 15 1 0 -1 1 4.8860 16 1 0 0 1 0.5083 17 1 0 1 1 3.6370 18 1 1 1 1 7.2556 19 1 1 0 1 3.3128 20 1 1 -1 1 4.7023 21 1 1 1 0 4.0285 22 1 1 0 0 2.5174 23 1 1 -1 0 4.7773 24 1 1 1 -1 6.9842 25 1 1 0 -1 3.2873 26 1 1 -1 -1 5.1617 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3240 atoms have been selected out of 3314 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 744 248 248 0.00 3 C003 has 114 38 38 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1458 486 486 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1671 548 546 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1557 519 519 0.00 12 C012 has 114 38 38 0.00 13 C013 has 489 163 163 0.00 14 C014 has 129 43 43 0.99 Total of12359 atoms and 4104 groups and 4097 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3314 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1093 Number of atoms = 3314 Number of groups = 1098 Number of bonds = 3307 Number of angles = 1197 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1095 Number of HB donors = 2168 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1093 Number of atoms = 3314 Number of groups = 1098 Number of bonds = 3307 Number of angles = 1197 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1095 Number of HB donors = 2168 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.034" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1093" Evaluating: 1093-7 Parameter: NUMWAT <- "1086" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1086" Comparing "1081" and "1086". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.034" Parameter: BOX -> "32.034" Parameter: BOX -> "32.034" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.03400 B = 32.03400 C = 32.03400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2579 2 1 -1 0 -1 3.3100 3 1 -1 1 -1 4.6996 4 1 0 -1 -1 3.6344 5 1 0 0 -1 0.5081 6 1 0 1 -1 4.8848 7 1 -1 -1 0 4.0259 8 1 -1 0 0 2.5160 9 1 -1 1 0 4.7744 10 1 0 -1 0 1.1958 11 1 0 1 0 1.1958 12 1 -1 -1 1 6.9810 13 1 -1 0 1 3.2845 14 1 -1 1 1 5.1590 15 1 0 -1 1 4.8848 16 1 0 0 1 0.5081 17 1 0 1 1 3.6344 18 1 1 1 1 7.2579 19 1 1 0 1 3.3100 20 1 1 -1 1 4.6996 21 1 1 1 0 4.0259 22 1 1 0 0 2.5160 23 1 1 -1 0 4.7744 24 1 1 1 -1 6.9810 25 1 1 0 -1 3.2845 26 1 1 -1 -1 5.1590 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3240 atoms have been selected out of 3314 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 747 249 249 0.00 3 C003 has 114 38 38 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1458 486 486 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1671 548 546 0.00 9 C009 has 423 141 141 0.00 10 C010 has 1557 519 519 0.00 12 C012 has 114 38 38 0.00 13 C013 has 489 163 163 0.00 14 C014 has 129 43 43 0.99 Total of12362 atoms and 4105 groups and 4098 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3314 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1093 Number of atoms = 3314 Number of groups = 1098 Number of bonds = 3307 Number of angles = 1197 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1095 Number of HB donors = 2168 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1093 Number of atoms = 3314 Number of groups = 1098 Number of bonds = 3307 Number of angles = 1197 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1095 Number of HB donors = 2168 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.032" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1093" Evaluating: 1093-7 Parameter: NUMWAT <- "1086" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1086" Comparing "1081" and "1086". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.032" Parameter: BOX -> "32.032" Parameter: BOX -> "32.032" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.03200 B = 32.03200 C = 32.03200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2603 2 1 -1 0 -1 3.3072 3 1 -1 1 -1 4.6968 4 1 0 -1 -1 3.6317 5 1 0 0 -1 0.5079 6 1 0 1 -1 4.8836 7 1 -1 -1 0 4.0234 8 1 -1 0 0 2.5147 9 1 -1 1 0 4.7716 10 1 0 -1 0 1.1959 11 1 0 1 0 1.1959 12 1 -1 -1 1 6.9778 13 1 -1 0 1 3.2818 14 1 -1 1 1 5.1563 15 1 0 -1 1 4.8836 16 1 0 0 1 0.5079 17 1 0 1 1 3.6317 18 1 1 1 1 7.2603 19 1 1 0 1 3.3072 20 1 1 -1 1 4.6968 21 1 1 1 0 4.0234 22 1 1 0 0 2.5147 23 1 1 -1 0 4.7716 24 1 1 1 -1 6.9778 25 1 1 0 -1 3.2818 26 1 1 -1 -1 5.1563 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3240 atoms have been selected out of 3314 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 750 250 250 0.00 3 C003 has 114 38 38 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1461 487 487 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1671 548 546 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1557 519 519 0.00 12 C012 has 114 38 38 0.00 13 C013 has 489 163 163 0.00 14 C014 has 129 43 43 0.99 Total of12371 atoms and 4108 groups and 4101 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3314 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1093 Number of atoms = 3314 Number of groups = 1098 Number of bonds = 3307 Number of angles = 1197 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1095 Number of HB donors = 2168 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1093 Number of atoms = 3314 Number of groups = 1098 Number of bonds = 3307 Number of angles = 1197 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1095 Number of HB donors = 2168 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.03" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1093" Evaluating: 1093-7 Parameter: NUMWAT <- "1086" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1086" Comparing "1081" and "1086". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.03" Parameter: BOX -> "32.03" Parameter: BOX -> "32.03" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.03000 B = 32.03000 C = 32.03000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2627 2 1 -1 0 -1 3.3044 3 1 -1 1 -1 4.6941 4 1 0 -1 -1 3.6290 5 1 0 0 -1 0.5077 6 1 0 1 -1 4.8824 7 1 -1 -1 0 4.0208 8 1 -1 0 0 2.5133 9 1 -1 1 0 4.7688 10 1 0 -1 0 1.1960 11 1 0 1 0 1.1960 12 1 -1 -1 1 6.9746 13 1 -1 0 1 3.2791 14 1 -1 1 1 5.1536 15 1 0 -1 1 4.8824 16 1 0 0 1 0.5077 17 1 0 1 1 3.6290 18 1 1 1 1 7.2627 19 1 1 0 1 3.3044 20 1 1 -1 1 4.6941 21 1 1 1 0 4.0208 22 1 1 0 0 2.5133 23 1 1 -1 0 4.7688 24 1 1 1 -1 6.9746 25 1 1 0 -1 3.2791 26 1 1 -1 -1 5.1536 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3240 atoms have been selected out of 3314 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 750 250 250 0.00 3 C003 has 114 38 38 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1461 487 487 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1671 548 546 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1557 519 519 0.00 12 C012 has 114 38 38 0.00 13 C013 has 489 163 163 0.00 14 C014 has 129 43 43 0.99 Total of12371 atoms and 4108 groups and 4101 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3314 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1093 Number of atoms = 3314 Number of groups = 1098 Number of bonds = 3307 Number of angles = 1197 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1095 Number of HB donors = 2168 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1093 Number of atoms = 3314 Number of groups = 1098 Number of bonds = 3307 Number of angles = 1197 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1095 Number of HB donors = 2168 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.028" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1093" Evaluating: 1093-7 Parameter: NUMWAT <- "1086" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1086" Comparing "1081" and "1086". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.028" Parameter: BOX -> "32.028" Parameter: BOX -> "32.028" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.02800 B = 32.02800 C = 32.02800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2651 2 1 -1 0 -1 3.3016 3 1 -1 1 -1 4.6914 4 1 0 -1 -1 3.6263 5 1 0 0 -1 0.5075 6 1 0 1 -1 4.8813 7 1 -1 -1 0 4.0183 8 1 -1 0 0 2.5119 9 1 -1 1 0 4.7660 10 1 0 -1 0 1.1962 11 1 0 1 0 1.1962 12 1 -1 -1 1 6.9714 13 1 -1 0 1 3.2763 14 1 -1 1 1 5.1509 15 1 0 -1 1 4.8813 16 1 0 0 1 0.5075 17 1 0 1 1 3.6263 18 1 1 1 1 7.2651 19 1 1 0 1 3.3016 20 1 1 -1 1 4.6914 21 1 1 1 0 4.0183 22 1 1 0 0 2.5119 23 1 1 -1 0 4.7660 24 1 1 1 -1 6.9714 25 1 1 0 -1 3.2763 26 1 1 -1 -1 5.1509 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3240 atoms have been selected out of 3314 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 753 251 251 0.00 3 C003 has 114 38 38 0.00 4 C004 has 624 208 208 0.00 5 C005 has 1461 487 487 0.00 6 C006 has 444 148 148 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1671 548 546 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1557 519 519 0.00 12 C012 has 114 38 38 0.00 13 C013 has 489 163 163 0.00 14 C014 has 129 43 43 0.99 Total of12374 atoms and 4109 groups and 4102 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3314 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1093 Number of atoms = 3314 Number of groups = 1098 Number of bonds = 3307 Number of angles = 1197 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1095 Number of HB donors = 2168 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1093 Number of atoms = 3314 Number of groups = 1098 Number of bonds = 3307 Number of angles = 1197 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1095 Number of HB donors = 2168 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.026" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1093" Evaluating: 1093-7 Parameter: NUMWAT <- "1086" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1086" Comparing "1081" and "1086". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.026" Parameter: BOX -> "32.026" Parameter: BOX -> "32.026" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.02600 B = 32.02600 C = 32.02600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2674 2 1 -1 0 -1 3.2988 3 1 -1 1 -1 4.6887 4 1 0 -1 -1 3.6236 5 1 0 0 -1 0.5073 6 1 0 1 -1 4.8801 7 1 -1 -1 0 4.0157 8 1 -1 0 0 2.5105 9 1 -1 1 0 4.7632 10 1 0 -1 0 1.1963 11 1 0 1 0 1.1963 12 1 -1 -1 1 6.9682 13 1 -1 0 1 3.2736 14 1 -1 1 1 5.1482 15 1 0 -1 1 4.8801 16 1 0 0 1 0.5073 17 1 0 1 1 3.6236 18 1 1 1 1 7.2674 19 1 1 0 1 3.2988 20 1 1 -1 1 4.6887 21 1 1 1 0 4.0157 22 1 1 0 0 2.5105 23 1 1 -1 0 4.7632 24 1 1 1 -1 6.9682 25 1 1 0 -1 3.2736 26 1 1 -1 -1 5.1482 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3240 atoms have been selected out of 3314 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 542 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 753 251 251 0.00 3 C003 has 114 38 38 0.16 4 C004 has 627 209 209 0.00 5 C005 has 1461 487 487 0.00 6 C006 has 438 146 146 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1671 548 546 0.00 9 C009 has 429 143 143 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 111 37 37 0.00 13 C013 has 489 163 163 0.00 14 C014 has 132 44 44 1.32 Total of12368 atoms and 4107 groups and 4100 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3314 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1092 Number of atoms = 3311 Number of groups = 1097 Number of bonds = 3304 Number of angles = 1196 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1094 Number of HB donors = 2166 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1092 Number of atoms = 3311 Number of groups = 1097 Number of bonds = 3304 Number of angles = 1196 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1094 Number of HB donors = 2166 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.024" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1092" Evaluating: 1092-7 Parameter: NUMWAT <- "1085" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1085" Comparing "1081" and "1085". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.024" Parameter: BOX -> "32.024" Parameter: BOX -> "32.024" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.02400 B = 32.02400 C = 32.02400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2698 2 1 -1 0 -1 3.2961 3 1 -1 1 -1 4.6860 4 1 0 -1 -1 3.6210 5 1 0 0 -1 0.5072 6 1 0 1 -1 4.8789 7 1 -1 -1 0 4.0131 8 1 -1 0 0 2.5091 9 1 -1 1 0 4.7603 10 1 0 -1 0 1.1964 11 1 0 1 0 1.1964 12 1 -1 -1 1 6.9650 13 1 -1 0 1 3.2709 14 1 -1 1 1 5.1455 15 1 0 -1 1 4.8789 16 1 0 0 1 0.5072 17 1 0 1 1 3.6210 18 1 1 1 1 7.2698 19 1 1 0 1 3.2961 20 1 1 -1 1 4.6860 21 1 1 1 0 4.0131 22 1 1 0 0 2.5091 23 1 1 -1 0 4.7603 24 1 1 1 -1 6.9650 25 1 1 0 -1 3.2709 26 1 1 -1 -1 5.1455 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3237 atoms have been selected out of 3311 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 753 251 251 0.00 3 C003 has 114 38 38 0.15 4 C004 has 624 208 208 0.00 5 C005 has 1461 487 487 0.00 6 C006 has 438 146 146 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1668 547 545 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 114 38 38 0.00 13 C013 has 486 162 162 0.00 14 C014 has 129 43 43 1.32 Total of12353 atoms and 4102 groups and 4095 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3311 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1092 Number of atoms = 3311 Number of groups = 1097 Number of bonds = 3304 Number of angles = 1196 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1094 Number of HB donors = 2166 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1092 Number of atoms = 3311 Number of groups = 1097 Number of bonds = 3304 Number of angles = 1196 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1094 Number of HB donors = 2166 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.022" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1092" Evaluating: 1092-7 Parameter: NUMWAT <- "1085" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1085" Comparing "1081" and "1085". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.022" Parameter: BOX -> "32.022" Parameter: BOX -> "32.022" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.02200 B = 32.02200 C = 32.02200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2722 2 1 -1 0 -1 3.2933 3 1 -1 1 -1 4.6832 4 1 0 -1 -1 3.6183 5 1 0 0 -1 0.5070 6 1 0 1 -1 4.8777 7 1 -1 -1 0 4.0106 8 1 -1 0 0 2.5077 9 1 -1 1 0 4.7575 10 1 0 -1 0 1.1965 11 1 0 1 0 1.1965 12 1 -1 -1 1 6.9618 13 1 -1 0 1 3.2682 14 1 -1 1 1 5.1428 15 1 0 -1 1 4.8777 16 1 0 0 1 0.5070 17 1 0 1 1 3.6183 18 1 1 1 1 7.2722 19 1 1 0 1 3.2933 20 1 1 -1 1 4.6832 21 1 1 1 0 4.0106 22 1 1 0 0 2.5077 23 1 1 -1 0 4.7575 24 1 1 1 -1 6.9618 25 1 1 0 -1 3.2682 26 1 1 -1 -1 5.1428 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3237 atoms have been selected out of 3311 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 753 251 251 0.00 3 C003 has 117 39 39 0.15 4 C004 has 624 208 208 0.00 5 C005 has 1461 487 487 0.00 6 C006 has 438 146 146 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1668 547 545 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 114 38 38 0.00 13 C013 has 486 162 162 0.00 14 C014 has 129 43 43 1.32 Total of12356 atoms and 4103 groups and 4096 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3311 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1092 Number of atoms = 3311 Number of groups = 1097 Number of bonds = 3304 Number of angles = 1196 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1094 Number of HB donors = 2166 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1092 Number of atoms = 3311 Number of groups = 1097 Number of bonds = 3304 Number of angles = 1196 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1094 Number of HB donors = 2166 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.02" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1092" Evaluating: 1092-7 Parameter: NUMWAT <- "1085" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1085" Comparing "1081" and "1085". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.02" Parameter: BOX -> "32.02" Parameter: BOX -> "32.02" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.02000 B = 32.02000 C = 32.02000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2746 2 1 -1 0 -1 3.2905 3 1 -1 1 -1 4.6805 4 1 0 -1 -1 3.6156 5 1 0 0 -1 0.5068 6 1 0 1 -1 4.8765 7 1 -1 -1 0 4.0080 8 1 -1 0 0 2.5063 9 1 -1 1 0 4.7547 10 1 0 -1 0 1.1966 11 1 0 1 0 1.1966 12 1 -1 -1 1 6.9586 13 1 -1 0 1 3.2654 14 1 -1 1 1 5.1401 15 1 0 -1 1 4.8765 16 1 0 0 1 0.5068 17 1 0 1 1 3.6156 18 1 1 1 1 7.2746 19 1 1 0 1 3.2905 20 1 1 -1 1 4.6805 21 1 1 1 0 4.0080 22 1 1 0 0 2.5063 23 1 1 -1 0 4.7547 24 1 1 1 -1 6.9586 25 1 1 0 -1 3.2654 26 1 1 -1 -1 5.1401 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3237 atoms have been selected out of 3311 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 492 164 164 0.00 2 C002 has 753 251 251 0.00 3 C003 has 117 39 39 0.15 4 C004 has 624 208 208 0.00 5 C005 has 1461 487 487 0.00 6 C006 has 438 146 146 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1668 547 545 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 114 38 38 0.00 13 C013 has 486 162 162 0.00 14 C014 has 129 43 43 1.31 Total of12359 atoms and 4104 groups and 4097 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3311 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1092 Number of atoms = 3311 Number of groups = 1097 Number of bonds = 3304 Number of angles = 1196 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1094 Number of HB donors = 2166 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1092 Number of atoms = 3311 Number of groups = 1097 Number of bonds = 3304 Number of angles = 1196 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1094 Number of HB donors = 2166 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.018" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1092" Evaluating: 1092-7 Parameter: NUMWAT <- "1085" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1085" Comparing "1081" and "1085". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.018" Parameter: BOX -> "32.018" Parameter: BOX -> "32.018" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.01800 B = 32.01800 C = 32.01800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2769 2 1 -1 0 -1 3.2877 3 1 -1 1 -1 4.6778 4 1 0 -1 -1 3.6129 5 1 0 0 -1 0.5067 6 1 0 1 -1 4.8754 7 1 -1 -1 0 4.0055 8 1 -1 0 0 2.5049 9 1 -1 1 0 4.7519 10 1 0 -1 0 1.1968 11 1 0 1 0 1.1968 12 1 -1 -1 1 6.9555 13 1 -1 0 1 3.2627 14 1 -1 1 1 5.1374 15 1 0 -1 1 4.8754 16 1 0 0 1 0.5067 17 1 0 1 1 3.6129 18 1 1 1 1 7.2769 19 1 1 0 1 3.2877 20 1 1 -1 1 4.6778 21 1 1 1 0 4.0055 22 1 1 0 0 2.5049 23 1 1 -1 0 4.7519 24 1 1 1 -1 6.9555 25 1 1 0 -1 3.2627 26 1 1 -1 -1 5.1374 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3237 atoms have been selected out of 3311 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 492 164 164 0.00 2 C002 has 753 251 251 0.00 3 C003 has 117 39 39 0.15 4 C004 has 624 208 208 0.00 5 C005 has 1461 487 487 0.00 6 C006 has 438 146 146 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1668 547 545 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 114 38 38 0.00 13 C013 has 486 162 162 0.00 14 C014 has 129 43 43 1.31 Total of12359 atoms and 4104 groups and 4097 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3311 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1092 Number of atoms = 3311 Number of groups = 1097 Number of bonds = 3304 Number of angles = 1196 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1094 Number of HB donors = 2166 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1092 Number of atoms = 3311 Number of groups = 1097 Number of bonds = 3304 Number of angles = 1196 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1094 Number of HB donors = 2166 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.016" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1092" Evaluating: 1092-7 Parameter: NUMWAT <- "1085" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1085" Comparing "1081" and "1085". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.016" Parameter: BOX -> "32.016" Parameter: BOX -> "32.016" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.01600 B = 32.01600 C = 32.01600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2793 2 1 -1 0 -1 3.2849 3 1 -1 1 -1 4.6751 4 1 0 -1 -1 3.6102 5 1 0 0 -1 0.5065 6 1 0 1 -1 4.8742 7 1 -1 -1 0 4.0029 8 1 -1 0 0 2.5035 9 1 -1 1 0 4.7490 10 1 0 -1 0 1.1969 11 1 0 1 0 1.1969 12 1 -1 -1 1 6.9523 13 1 -1 0 1 3.2600 14 1 -1 1 1 5.1347 15 1 0 -1 1 4.8742 16 1 0 0 1 0.5065 17 1 0 1 1 3.6102 18 1 1 1 1 7.2793 19 1 1 0 1 3.2849 20 1 1 -1 1 4.6751 21 1 1 1 0 4.0029 22 1 1 0 0 2.5035 23 1 1 -1 0 4.7490 24 1 1 1 -1 6.9523 25 1 1 0 -1 3.2600 26 1 1 -1 -1 5.1347 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3237 atoms have been selected out of 3311 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 492 164 164 0.00 2 C002 has 753 251 251 0.00 3 C003 has 117 39 39 0.15 4 C004 has 624 208 208 0.00 5 C005 has 1461 487 487 0.00 6 C006 has 438 146 146 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1668 547 545 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 114 38 38 0.00 13 C013 has 486 162 162 0.00 14 C014 has 129 43 43 1.31 Total of12359 atoms and 4104 groups and 4097 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3311 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1092 Number of atoms = 3311 Number of groups = 1097 Number of bonds = 3304 Number of angles = 1196 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1094 Number of HB donors = 2166 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1092 Number of atoms = 3311 Number of groups = 1097 Number of bonds = 3304 Number of angles = 1196 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1094 Number of HB donors = 2166 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.014" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1092" Evaluating: 1092-7 Parameter: NUMWAT <- "1085" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1085" Comparing "1081" and "1085". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.014" Parameter: BOX -> "32.014" Parameter: BOX -> "32.014" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.01400 B = 32.01400 C = 32.01400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2817 2 1 -1 0 -1 3.2821 3 1 -1 1 -1 4.6724 4 1 0 -1 -1 3.6076 5 1 0 0 -1 0.5064 6 1 0 1 -1 4.8730 7 1 -1 -1 0 4.0003 8 1 -1 0 0 2.5022 9 1 -1 1 0 4.7462 10 1 0 -1 0 1.1970 11 1 0 1 0 1.1970 12 1 -1 -1 1 6.9491 13 1 -1 0 1 3.2572 14 1 -1 1 1 5.1320 15 1 0 -1 1 4.8730 16 1 0 0 1 0.5064 17 1 0 1 1 3.6076 18 1 1 1 1 7.2817 19 1 1 0 1 3.2821 20 1 1 -1 1 4.6724 21 1 1 1 0 4.0003 22 1 1 0 0 2.5022 23 1 1 -1 0 4.7462 24 1 1 1 -1 6.9491 25 1 1 0 -1 3.2572 26 1 1 -1 -1 5.1320 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3237 atoms have been selected out of 3311 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 492 164 164 0.00 2 C002 has 753 251 251 0.00 3 C003 has 117 39 39 0.14 4 C004 has 624 208 208 0.00 5 C005 has 1461 487 487 0.00 6 C006 has 438 146 146 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1668 547 545 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 114 38 38 0.00 13 C013 has 486 162 162 0.00 14 C014 has 132 44 44 1.31 Total of12362 atoms and 4105 groups and 4098 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3311 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1092 Number of atoms = 3311 Number of groups = 1097 Number of bonds = 3304 Number of angles = 1196 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1094 Number of HB donors = 2166 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1092 Number of atoms = 3311 Number of groups = 1097 Number of bonds = 3304 Number of angles = 1196 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1094 Number of HB donors = 2166 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.012" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1092" Evaluating: 1092-7 Parameter: NUMWAT <- "1085" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1085" Comparing "1081" and "1085". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.012" Parameter: BOX -> "32.012" Parameter: BOX -> "32.012" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.01200 B = 32.01200 C = 32.01200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2841 2 1 -1 0 -1 3.2793 3 1 -1 1 -1 4.6696 4 1 0 -1 -1 3.6049 5 1 0 0 -1 0.5063 6 1 0 1 -1 4.8719 7 1 -1 -1 0 3.9978 8 1 -1 0 0 2.5008 9 1 -1 1 0 4.7434 10 1 0 -1 0 1.1972 11 1 0 1 0 1.1972 12 1 -1 -1 1 6.9459 13 1 -1 0 1 3.2545 14 1 -1 1 1 5.1293 15 1 0 -1 1 4.8719 16 1 0 0 1 0.5063 17 1 0 1 1 3.6049 18 1 1 1 1 7.2841 19 1 1 0 1 3.2793 20 1 1 -1 1 4.6696 21 1 1 1 0 3.9978 22 1 1 0 0 2.5008 23 1 1 -1 0 4.7434 24 1 1 1 -1 6.9459 25 1 1 0 -1 3.2545 26 1 1 -1 -1 5.1293 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3237 atoms have been selected out of 3311 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 492 164 164 0.00 2 C002 has 753 251 251 0.00 3 C003 has 117 39 39 0.14 4 C004 has 624 208 208 0.00 5 C005 has 1461 487 487 0.00 6 C006 has 438 146 146 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1668 547 545 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 114 38 38 0.00 13 C013 has 486 162 162 0.00 14 C014 has 132 44 44 1.31 Total of12362 atoms and 4105 groups and 4098 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3311 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1092 Number of atoms = 3311 Number of groups = 1097 Number of bonds = 3304 Number of angles = 1196 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1094 Number of HB donors = 2166 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1092 Number of atoms = 3311 Number of groups = 1097 Number of bonds = 3304 Number of angles = 1196 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1094 Number of HB donors = 2166 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.01" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1092" Evaluating: 1092-7 Parameter: NUMWAT <- "1085" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1085" Comparing "1081" and "1085". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.01" Parameter: BOX -> "32.01" Parameter: BOX -> "32.01" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.01000 B = 32.01000 C = 32.01000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2865 2 1 -1 0 -1 3.2765 3 1 -1 1 -1 4.6669 4 1 0 -1 -1 3.6022 5 1 0 0 -1 0.5061 6 1 0 1 -1 4.8707 7 1 -1 -1 0 3.9952 8 1 -1 0 0 2.4994 9 1 -1 1 0 4.7406 10 1 0 -1 0 1.1973 11 1 0 1 0 1.1973 12 1 -1 -1 1 6.9427 13 1 -1 0 1 3.2518 14 1 -1 1 1 5.1266 15 1 0 -1 1 4.8707 16 1 0 0 1 0.5061 17 1 0 1 1 3.6022 18 1 1 1 1 7.2865 19 1 1 0 1 3.2765 20 1 1 -1 1 4.6669 21 1 1 1 0 3.9952 22 1 1 0 0 2.4994 23 1 1 -1 0 4.7406 24 1 1 1 -1 6.9427 25 1 1 0 -1 3.2518 26 1 1 -1 -1 5.1266 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3237 atoms have been selected out of 3311 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 492 164 164 0.00 2 C002 has 753 251 251 0.00 3 C003 has 117 39 39 0.14 4 C004 has 624 208 208 0.00 5 C005 has 1461 487 487 0.00 6 C006 has 438 146 146 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1668 547 545 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 114 38 38 0.00 13 C013 has 486 162 162 0.00 14 C014 has 132 44 44 1.30 Total of12362 atoms and 4105 groups and 4098 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3311 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1092 Number of atoms = 3311 Number of groups = 1097 Number of bonds = 3304 Number of angles = 1196 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1094 Number of HB donors = 2166 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1092 Number of atoms = 3311 Number of groups = 1097 Number of bonds = 3304 Number of angles = 1196 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1094 Number of HB donors = 2166 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.008" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1092" Evaluating: 1092-7 Parameter: NUMWAT <- "1085" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1085" Comparing "1081" and "1085". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.008" Parameter: BOX -> "32.008" Parameter: BOX -> "32.008" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.00800 B = 32.00800 C = 32.00800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2888 2 1 -1 0 -1 3.2737 3 1 -1 1 -1 4.6642 4 1 0 -1 -1 3.5995 5 1 0 0 -1 0.5060 6 1 0 1 -1 4.8695 7 1 -1 -1 0 3.9927 8 1 -1 0 0 2.4980 9 1 -1 1 0 4.7378 10 1 0 -1 0 1.1975 11 1 0 1 0 1.1975 12 1 -1 -1 1 6.9395 13 1 -1 0 1 3.2491 14 1 -1 1 1 5.1239 15 1 0 -1 1 4.8695 16 1 0 0 1 0.5060 17 1 0 1 1 3.5995 18 1 1 1 1 7.2888 19 1 1 0 1 3.2737 20 1 1 -1 1 4.6642 21 1 1 1 0 3.9927 22 1 1 0 0 2.4980 23 1 1 -1 0 4.7378 24 1 1 1 -1 6.9395 25 1 1 0 -1 3.2491 26 1 1 -1 -1 5.1239 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3237 atoms have been selected out of 3311 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 820 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 492 164 164 0.00 2 C002 has 750 250 250 0.00 3 C003 has 117 39 39 0.14 4 C004 has 624 208 208 0.00 5 C005 has 1461 487 487 0.00 6 C006 has 435 145 145 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1671 548 546 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 114 38 38 0.00 13 C013 has 486 162 162 0.00 14 C014 has 132 44 44 1.30 Total of12359 atoms and 4104 groups and 4097 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3311 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1091 Number of atoms = 3308 Number of groups = 1096 Number of bonds = 3301 Number of angles = 1195 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1093 Number of HB donors = 2164 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1091 Number of atoms = 3308 Number of groups = 1096 Number of bonds = 3301 Number of angles = 1195 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1093 Number of HB donors = 2164 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.006" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1091" Evaluating: 1091-7 Parameter: NUMWAT <- "1084" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1084" Comparing "1081" and "1084". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.006" Parameter: BOX -> "32.006" Parameter: BOX -> "32.006" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.00600 B = 32.00600 C = 32.00600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2912 2 1 -1 0 -1 3.2709 3 1 -1 1 -1 4.6615 4 1 0 -1 -1 3.5968 5 1 0 0 -1 0.5059 6 1 0 1 -1 4.8684 7 1 -1 -1 0 3.9901 8 1 -1 0 0 2.4966 9 1 -1 1 0 4.7349 10 1 0 -1 0 1.1976 11 1 0 1 0 1.1976 12 1 -1 -1 1 6.9363 13 1 -1 0 1 3.2463 14 1 -1 1 1 5.1212 15 1 0 -1 1 4.8684 16 1 0 0 1 0.5059 17 1 0 1 1 3.5968 18 1 1 1 1 7.2912 19 1 1 0 1 3.2709 20 1 1 -1 1 4.6615 21 1 1 1 0 3.9901 22 1 1 0 0 2.4966 23 1 1 -1 0 4.7349 24 1 1 1 -1 6.9363 25 1 1 0 -1 3.2463 26 1 1 -1 -1 5.1212 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3234 atoms have been selected out of 3308 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 492 164 164 0.00 2 C002 has 750 250 250 0.00 3 C003 has 120 40 40 0.14 4 C004 has 624 208 208 0.00 5 C005 has 1458 486 486 0.00 6 C006 has 435 145 145 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1668 547 545 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 114 38 38 0.00 13 C013 has 486 162 162 0.00 14 C014 has 132 44 44 1.30 Total of12356 atoms and 4103 groups and 4096 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3308 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1091 Number of atoms = 3308 Number of groups = 1096 Number of bonds = 3301 Number of angles = 1195 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1093 Number of HB donors = 2164 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1091 Number of atoms = 3308 Number of groups = 1096 Number of bonds = 3301 Number of angles = 1195 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1093 Number of HB donors = 2164 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.004" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1091" Evaluating: 1091-7 Parameter: NUMWAT <- "1084" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1084" Comparing "1081" and "1084". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.004" Parameter: BOX -> "32.004" Parameter: BOX -> "32.004" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.00400 B = 32.00400 C = 32.00400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2936 2 1 -1 0 -1 3.2682 3 1 -1 1 -1 4.6588 4 1 0 -1 -1 3.5942 5 1 0 0 -1 0.5058 6 1 0 1 -1 4.8672 7 1 -1 -1 0 3.9875 8 1 -1 0 0 2.4953 9 1 -1 1 0 4.7321 10 1 0 -1 0 1.1978 11 1 0 1 0 1.1978 12 1 -1 -1 1 6.9331 13 1 -1 0 1 3.2436 14 1 -1 1 1 5.1185 15 1 0 -1 1 4.8672 16 1 0 0 1 0.5058 17 1 0 1 1 3.5942 18 1 1 1 1 7.2936 19 1 1 0 1 3.2682 20 1 1 -1 1 4.6588 21 1 1 1 0 3.9875 22 1 1 0 0 2.4953 23 1 1 -1 0 4.7321 24 1 1 1 -1 6.9331 25 1 1 0 -1 3.2436 26 1 1 -1 -1 5.1185 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3234 atoms have been selected out of 3308 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 492 164 164 0.00 2 C002 has 750 250 250 0.00 3 C003 has 120 40 40 0.13 4 C004 has 624 208 208 0.00 5 C005 has 1458 486 486 0.00 6 C006 has 435 145 145 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1668 547 545 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 114 38 38 0.00 13 C013 has 486 162 162 0.00 14 C014 has 132 44 44 1.30 Total of12356 atoms and 4103 groups and 4096 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3308 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1091 Number of atoms = 3308 Number of groups = 1096 Number of bonds = 3301 Number of angles = 1195 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1093 Number of HB donors = 2164 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1091 Number of atoms = 3308 Number of groups = 1096 Number of bonds = 3301 Number of angles = 1195 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1093 Number of HB donors = 2164 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32.002" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1091" Evaluating: 1091-7 Parameter: NUMWAT <- "1084" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1084" Comparing "1081" and "1084". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32.002" Parameter: BOX -> "32.002" Parameter: BOX -> "32.002" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.00200 B = 32.00200 C = 32.00200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2960 2 1 -1 0 -1 3.2654 3 1 -1 1 -1 4.6561 4 1 0 -1 -1 3.5915 5 1 0 0 -1 0.5057 6 1 0 1 -1 4.8660 7 1 -1 -1 0 3.9850 8 1 -1 0 0 2.4939 9 1 -1 1 0 4.7293 10 1 0 -1 0 1.1979 11 1 0 1 0 1.1979 12 1 -1 -1 1 6.9300 13 1 -1 0 1 3.2409 14 1 -1 1 1 5.1158 15 1 0 -1 1 4.8660 16 1 0 0 1 0.5057 17 1 0 1 1 3.5915 18 1 1 1 1 7.2960 19 1 1 0 1 3.2654 20 1 1 -1 1 4.6561 21 1 1 1 0 3.9850 22 1 1 0 0 2.4939 23 1 1 -1 0 4.7293 24 1 1 1 -1 6.9300 25 1 1 0 -1 3.2409 26 1 1 -1 -1 5.1158 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3234 atoms have been selected out of 3308 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 492 164 164 0.00 2 C002 has 750 250 250 0.00 3 C003 has 120 40 40 0.13 4 C004 has 624 208 208 0.00 5 C005 has 1458 486 486 0.00 6 C006 has 435 145 145 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1668 547 545 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 114 38 38 0.00 13 C013 has 486 162 162 0.00 14 C014 has 132 44 44 1.30 Total of12356 atoms and 4103 groups and 4096 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3308 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1091 Number of atoms = 3308 Number of groups = 1096 Number of bonds = 3301 Number of angles = 1195 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1093 Number of HB donors = 2164 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1091 Number of atoms = 3308 Number of groups = 1096 Number of bonds = 3301 Number of angles = 1195 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1093 Number of HB donors = 2164 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "32" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1091" Evaluating: 1091-7 Parameter: NUMWAT <- "1084" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1084" Comparing "1081" and "1084". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "32" Parameter: BOX -> "32" Parameter: BOX -> "32" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 32.00000 B = 32.00000 C = 32.00000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.2984 2 1 -1 0 -1 3.2626 3 1 -1 1 -1 4.6534 4 1 0 -1 -1 3.5888 5 1 0 0 -1 0.5056 6 1 0 1 -1 4.8649 7 1 -1 -1 0 3.9824 8 1 -1 0 0 2.4925 9 1 -1 1 0 4.7265 10 1 0 -1 0 1.1981 11 1 0 1 0 1.1981 12 1 -1 -1 1 6.9268 13 1 -1 0 1 3.2381 14 1 -1 1 1 5.1131 15 1 0 -1 1 4.8649 16 1 0 0 1 0.5056 17 1 0 1 1 3.5888 18 1 1 1 1 7.2984 19 1 1 0 1 3.2626 20 1 1 -1 1 4.6534 21 1 1 1 0 3.9824 22 1 1 0 0 2.4925 23 1 1 -1 0 4.7265 24 1 1 1 -1 6.9268 25 1 1 0 -1 3.2381 26 1 1 -1 -1 5.1131 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3234 atoms have been selected out of 3308 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 492 164 164 0.00 2 C002 has 750 250 250 0.00 3 C003 has 120 40 40 0.13 4 C004 has 624 208 208 0.00 5 C005 has 1458 486 486 0.00 6 C006 has 435 145 145 0.00 7 C007 has 789 263 263 0.00 8 C008 has 1668 547 545 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 114 38 38 0.00 13 C013 has 486 162 162 0.00 14 C014 has 132 44 44 1.29 Total of12356 atoms and 4103 groups and 4096 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3308 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1091 Number of atoms = 3308 Number of groups = 1096 Number of bonds = 3301 Number of angles = 1195 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1093 Number of HB donors = 2164 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1091 Number of atoms = 3308 Number of groups = 1096 Number of bonds = 3301 Number of angles = 1195 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1093 Number of HB donors = 2164 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "31.998" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1091" Evaluating: 1091-7 Parameter: NUMWAT <- "1084" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1084" Comparing "1081" and "1084". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "31.998" Parameter: BOX -> "31.998" Parameter: BOX -> "31.998" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 31.99800 B = 31.99800 C = 31.99800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.3008 2 1 -1 0 -1 3.2598 3 1 -1 1 -1 4.6507 4 1 0 -1 -1 3.5861 5 1 0 0 -1 0.5056 6 1 0 1 -1 4.8637 7 1 -1 -1 0 3.9799 8 1 -1 0 0 2.4911 9 1 -1 1 0 4.7237 10 1 0 -1 0 1.1983 11 1 0 1 0 1.1983 12 1 -1 -1 1 6.9236 13 1 -1 0 1 3.2354 14 1 -1 1 1 5.1104 15 1 0 -1 1 4.8637 16 1 0 0 1 0.5056 17 1 0 1 1 3.5861 18 1 1 1 1 7.3008 19 1 1 0 1 3.2598 20 1 1 -1 1 4.6507 21 1 1 1 0 3.9799 22 1 1 0 0 2.4911 23 1 1 -1 0 4.7237 24 1 1 1 -1 6.9236 25 1 1 0 -1 3.2354 26 1 1 -1 -1 5.1104 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3234 atoms have been selected out of 3308 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 1079 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 750 250 250 0.00 3 C003 has 123 41 41 0.00 4 C004 has 621 207 207 0.00 5 C005 has 1458 486 486 0.00 6 C006 has 438 146 146 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1668 547 545 0.00 9 C009 has 429 143 143 0.00 10 C010 has 1551 517 517 0.00 12 C012 has 114 38 38 0.00 13 C013 has 486 162 162 0.00 14 C014 has 132 44 44 1.33 Total of12353 atoms and 4102 groups and 4095 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3308 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1090 Number of atoms = 3305 Number of groups = 1095 Number of bonds = 3298 Number of angles = 1194 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1092 Number of HB donors = 2162 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1090 Number of atoms = 3305 Number of groups = 1095 Number of bonds = 3298 Number of angles = 1194 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1092 Number of HB donors = 2162 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "31.996" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1090" Evaluating: 1090-7 Parameter: NUMWAT <- "1083" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1083" Comparing "1081" and "1083". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "31.996" Parameter: BOX -> "31.996" Parameter: BOX -> "31.996" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 31.99600 B = 31.99600 C = 31.99600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.3032 2 1 -1 0 -1 3.2570 3 1 -1 1 -1 4.6480 4 1 0 -1 -1 3.5834 5 1 0 0 -1 0.5055 6 1 0 1 -1 4.8626 7 1 -1 -1 0 3.9773 8 1 -1 0 0 2.4897 9 1 -1 1 0 4.7208 10 1 0 -1 0 1.1984 11 1 0 1 0 1.1984 12 1 -1 -1 1 6.9204 13 1 -1 0 1 3.2327 14 1 -1 1 1 5.1077 15 1 0 -1 1 4.8626 16 1 0 0 1 0.5055 17 1 0 1 1 3.5834 18 1 1 1 1 7.3032 19 1 1 0 1 3.2570 20 1 1 -1 1 4.6480 21 1 1 1 0 3.9773 22 1 1 0 0 2.4897 23 1 1 -1 0 4.7208 24 1 1 1 -1 6.9204 25 1 1 0 -1 3.2327 26 1 1 -1 -1 5.1077 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3231 atoms have been selected out of 3305 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 747 249 249 0.00 3 C003 has 120 40 40 0.16 4 C004 has 621 207 207 0.00 5 C005 has 1455 485 485 0.00 6 C006 has 435 145 145 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1665 546 544 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1551 517 517 0.00 12 C012 has 114 38 38 0.00 13 C013 has 486 162 162 0.00 14 C014 has 132 44 44 1.33 Total of12332 atoms and 4095 groups and 4088 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3305 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1090 Number of atoms = 3305 Number of groups = 1095 Number of bonds = 3298 Number of angles = 1194 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1092 Number of HB donors = 2162 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1090 Number of atoms = 3305 Number of groups = 1095 Number of bonds = 3298 Number of angles = 1194 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1092 Number of HB donors = 2162 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "31.994" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1090" Evaluating: 1090-7 Parameter: NUMWAT <- "1083" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1083" Comparing "1081" and "1083". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "31.994" Parameter: BOX -> "31.994" Parameter: BOX -> "31.994" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 31.99400 B = 31.99400 C = 31.99400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.3055 2 1 -1 0 -1 3.2542 3 1 -1 1 -1 4.6453 4 1 0 -1 -1 3.5808 5 1 0 0 -1 0.5054 6 1 0 1 -1 4.8614 7 1 -1 -1 0 3.9748 8 1 -1 0 0 2.4884 9 1 -1 1 0 4.7180 10 1 0 -1 0 1.1986 11 1 0 1 0 1.1986 12 1 -1 -1 1 6.9172 13 1 -1 0 1 3.2300 14 1 -1 1 1 5.1050 15 1 0 -1 1 4.8614 16 1 0 0 1 0.5054 17 1 0 1 1 3.5808 18 1 1 1 1 7.3055 19 1 1 0 1 3.2542 20 1 1 -1 1 4.6453 21 1 1 1 0 3.9748 22 1 1 0 0 2.4884 23 1 1 -1 0 4.7180 24 1 1 1 -1 6.9172 25 1 1 0 -1 3.2300 26 1 1 -1 -1 5.1050 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3231 atoms have been selected out of 3305 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 747 249 249 0.00 3 C003 has 120 40 40 0.16 4 C004 has 624 208 208 0.00 5 C005 has 1455 485 485 0.00 6 C006 has 438 146 146 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1665 546 544 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1551 517 517 0.00 12 C012 has 114 38 38 0.00 13 C013 has 486 162 162 0.00 14 C014 has 132 44 44 1.33 Total of12338 atoms and 4097 groups and 4090 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3305 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1090 Number of atoms = 3305 Number of groups = 1095 Number of bonds = 3298 Number of angles = 1194 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1092 Number of HB donors = 2162 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1090 Number of atoms = 3305 Number of groups = 1095 Number of bonds = 3298 Number of angles = 1194 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1092 Number of HB donors = 2162 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "31.992" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1090" Evaluating: 1090-7 Parameter: NUMWAT <- "1083" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1083" Comparing "1081" and "1083". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "31.992" Parameter: BOX -> "31.992" Parameter: BOX -> "31.992" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 31.99200 B = 31.99200 C = 31.99200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.3079 2 1 -1 0 -1 3.2514 3 1 -1 1 -1 4.6426 4 1 0 -1 -1 3.5781 5 1 0 0 -1 0.5054 6 1 0 1 -1 4.8602 7 1 -1 -1 0 3.9722 8 1 -1 0 0 2.4870 9 1 -1 1 0 4.7152 10 1 0 -1 0 1.1988 11 1 0 1 0 1.1988 12 1 -1 -1 1 6.9140 13 1 -1 0 1 3.2272 14 1 -1 1 1 5.1023 15 1 0 -1 1 4.8602 16 1 0 0 1 0.5054 17 1 0 1 1 3.5781 18 1 1 1 1 7.3079 19 1 1 0 1 3.2514 20 1 1 -1 1 4.6426 21 1 1 1 0 3.9722 22 1 1 0 0 2.4870 23 1 1 -1 0 4.7152 24 1 1 1 -1 6.9140 25 1 1 0 -1 3.2272 26 1 1 -1 -1 5.1023 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3231 atoms have been selected out of 3305 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 747 249 249 0.00 3 C003 has 120 40 40 0.16 4 C004 has 627 209 209 0.00 5 C005 has 1455 485 485 0.00 6 C006 has 438 146 146 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1668 547 545 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 114 38 38 0.00 13 C013 has 486 162 162 0.00 14 C014 has 132 44 44 1.32 Total of12347 atoms and 4100 groups and 4093 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3305 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1090 Number of atoms = 3305 Number of groups = 1095 Number of bonds = 3298 Number of angles = 1194 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1092 Number of HB donors = 2162 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1090 Number of atoms = 3305 Number of groups = 1095 Number of bonds = 3298 Number of angles = 1194 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1092 Number of HB donors = 2162 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "31.99" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1090" Evaluating: 1090-7 Parameter: NUMWAT <- "1083" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1083" Comparing "1081" and "1083". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "31.99" Parameter: BOX -> "31.99" Parameter: BOX -> "31.99" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 31.99000 B = 31.99000 C = 31.99000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.3103 2 1 -1 0 -1 3.2486 3 1 -1 1 -1 4.6398 4 1 0 -1 -1 3.5754 5 1 0 0 -1 0.5054 6 1 0 1 -1 4.8591 7 1 -1 -1 0 3.9696 8 1 -1 0 0 2.4856 9 1 -1 1 0 4.7124 10 1 0 -1 0 1.1990 11 1 0 1 0 1.1990 12 1 -1 -1 1 6.9108 13 1 -1 0 1 3.2245 14 1 -1 1 1 5.0996 15 1 0 -1 1 4.8591 16 1 0 0 1 0.5054 17 1 0 1 1 3.5754 18 1 1 1 1 7.3103 19 1 1 0 1 3.2486 20 1 1 -1 1 4.6398 21 1 1 1 0 3.9696 22 1 1 0 0 2.4856 23 1 1 -1 0 4.7124 24 1 1 1 -1 6.9108 25 1 1 0 -1 3.2245 26 1 1 -1 -1 5.0996 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3231 atoms have been selected out of 3305 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 747 249 249 0.00 3 C003 has 120 40 40 0.16 4 C004 has 627 209 209 0.00 5 C005 has 1455 485 485 0.00 6 C006 has 438 146 146 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1668 547 545 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 114 38 38 0.00 13 C013 has 486 162 162 0.00 14 C014 has 132 44 44 1.32 Total of12347 atoms and 4100 groups and 4093 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3305 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1090 Number of atoms = 3305 Number of groups = 1095 Number of bonds = 3298 Number of angles = 1194 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1092 Number of HB donors = 2162 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1090 Number of atoms = 3305 Number of groups = 1095 Number of bonds = 3298 Number of angles = 1194 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1092 Number of HB donors = 2162 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "31.988" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1090" Evaluating: 1090-7 Parameter: NUMWAT <- "1083" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1083" Comparing "1081" and "1083". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "31.988" Parameter: BOX -> "31.988" Parameter: BOX -> "31.988" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 31.98800 B = 31.98800 C = 31.98800 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.3127 2 1 -1 0 -1 3.2458 3 1 -1 1 -1 4.6371 4 1 0 -1 -1 3.5727 5 1 0 0 -1 0.5053 6 1 0 1 -1 4.8579 7 1 -1 -1 0 3.9671 8 1 -1 0 0 2.4842 9 1 -1 1 0 4.7096 10 1 0 -1 0 1.1991 11 1 0 1 0 1.1991 12 1 -1 -1 1 6.9077 13 1 -1 0 1 3.2218 14 1 -1 1 1 5.0969 15 1 0 -1 1 4.8579 16 1 0 0 1 0.5053 17 1 0 1 1 3.5727 18 1 1 1 1 7.3127 19 1 1 0 1 3.2458 20 1 1 -1 1 4.6371 21 1 1 1 0 3.9671 22 1 1 0 0 2.4842 23 1 1 -1 0 4.7096 24 1 1 1 -1 6.9077 25 1 1 0 -1 3.2218 26 1 1 -1 -1 5.0969 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3231 atoms have been selected out of 3305 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 747 249 249 0.00 3 C003 has 123 41 41 0.16 4 C004 has 627 209 209 0.00 5 C005 has 1455 485 485 0.00 6 C006 has 438 146 146 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1668 547 545 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1557 519 519 0.00 12 C012 has 114 38 38 0.00 13 C013 has 486 162 162 0.00 14 C014 has 132 44 44 1.32 Total of12353 atoms and 4102 groups and 4095 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3305 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1090 Number of atoms = 3305 Number of groups = 1095 Number of bonds = 3298 Number of angles = 1194 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1092 Number of HB donors = 2162 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1090 Number of atoms = 3305 Number of groups = 1095 Number of bonds = 3298 Number of angles = 1194 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1092 Number of HB donors = 2162 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "31.986" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1090" Evaluating: 1090-7 Parameter: NUMWAT <- "1083" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1083" Comparing "1081" and "1083". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "31.986" Parameter: BOX -> "31.986" Parameter: BOX -> "31.986" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 31.98600 B = 31.98600 C = 31.98600 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.3151 2 1 -1 0 -1 3.2430 3 1 -1 1 -1 4.6344 4 1 0 -1 -1 3.5701 5 1 0 0 -1 0.5053 6 1 0 1 -1 4.8568 7 1 -1 -1 0 3.9645 8 1 -1 0 0 2.4829 9 1 -1 1 0 4.7067 10 1 0 -1 0 1.1993 11 1 0 1 0 1.1993 12 1 -1 -1 1 6.9045 13 1 -1 0 1 3.2191 14 1 -1 1 1 5.0942 15 1 0 -1 1 4.8568 16 1 0 0 1 0.5053 17 1 0 1 1 3.5701 18 1 1 1 1 7.3151 19 1 1 0 1 3.2430 20 1 1 -1 1 4.6344 21 1 1 1 0 3.9645 22 1 1 0 0 2.4829 23 1 1 -1 0 4.7067 24 1 1 1 -1 6.9045 25 1 1 0 -1 3.2191 26 1 1 -1 -1 5.0942 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3231 atoms have been selected out of 3305 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 747 249 249 0.00 3 C003 has 123 41 41 0.15 4 C004 has 627 209 209 0.00 5 C005 has 1455 485 485 0.00 6 C006 has 438 146 146 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1668 547 545 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1557 519 519 0.00 12 C012 has 114 38 38 0.00 13 C013 has 486 162 162 0.00 14 C014 has 132 44 44 1.32 Total of12353 atoms and 4102 groups and 4095 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3305 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1090 Number of atoms = 3305 Number of groups = 1095 Number of bonds = 3298 Number of angles = 1194 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1092 Number of HB donors = 2162 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1090 Number of atoms = 3305 Number of groups = 1095 Number of bonds = 3298 Number of angles = 1194 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1092 Number of HB donors = 2162 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "31.984" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1090" Evaluating: 1090-7 Parameter: NUMWAT <- "1083" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1083" Comparing "1081" and "1083". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "31.984" Parameter: BOX -> "31.984" Parameter: BOX -> "31.984" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 31.98400 B = 31.98400 C = 31.98400 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.3175 2 1 -1 0 -1 3.2403 3 1 -1 1 -1 4.6317 4 1 0 -1 -1 3.5674 5 1 0 0 -1 0.5053 6 1 0 1 -1 4.8556 7 1 -1 -1 0 3.9620 8 1 -1 0 0 2.4815 9 1 -1 1 0 4.7039 10 1 0 -1 0 1.1995 11 1 0 1 0 1.1995 12 1 -1 -1 1 6.9013 13 1 -1 0 1 3.2163 14 1 -1 1 1 5.0915 15 1 0 -1 1 4.8556 16 1 0 0 1 0.5053 17 1 0 1 1 3.5674 18 1 1 1 1 7.3175 19 1 1 0 1 3.2403 20 1 1 -1 1 4.6317 21 1 1 1 0 3.9620 22 1 1 0 0 2.4815 23 1 1 -1 0 4.7039 24 1 1 1 -1 6.9013 25 1 1 0 -1 3.2163 26 1 1 -1 -1 5.0915 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3231 atoms have been selected out of 3305 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 466 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 759 253 253 0.00 3 C003 has 123 41 41 0.15 4 C004 has 627 209 209 0.00 5 C005 has 1455 485 485 0.00 6 C006 has 438 146 146 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1665 546 544 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1557 519 519 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 132 44 44 1.32 Total of12353 atoms and 4102 groups and 4095 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3305 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1089 Number of atoms = 3302 Number of groups = 1094 Number of bonds = 3295 Number of angles = 1193 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1091 Number of HB donors = 2160 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1089 Number of atoms = 3302 Number of groups = 1094 Number of bonds = 3295 Number of angles = 1193 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1091 Number of HB donors = 2160 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "31.982" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1089" Evaluating: 1089-7 Parameter: NUMWAT <- "1082" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1082" Comparing "1081" and "1082". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "31.982" Parameter: BOX -> "31.982" Parameter: BOX -> "31.982" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 31.98200 B = 31.98200 C = 31.98200 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.3199 2 1 -1 0 -1 3.2375 3 1 -1 1 -1 4.6290 4 1 0 -1 -1 3.5647 5 1 0 0 -1 0.5053 6 1 0 1 -1 4.8545 7 1 -1 -1 0 3.9594 8 1 -1 0 0 2.4801 9 1 -1 1 0 4.7011 10 1 0 -1 0 1.1997 11 1 0 1 0 1.1997 12 1 -1 -1 1 6.8981 13 1 -1 0 1 3.2136 14 1 -1 1 1 5.0889 15 1 0 -1 1 4.8545 16 1 0 0 1 0.5053 17 1 0 1 1 3.5647 18 1 1 1 1 7.3199 19 1 1 0 1 3.2375 20 1 1 -1 1 4.6290 21 1 1 1 0 3.9594 22 1 1 0 0 2.4801 23 1 1 -1 0 4.7011 24 1 1 1 -1 6.8981 25 1 1 0 -1 3.2136 26 1 1 -1 -1 5.0889 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3228 atoms have been selected out of 3302 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 489 163 163 0.00 2 C002 has 747 249 249 0.00 3 C003 has 123 41 41 0.15 4 C004 has 627 209 209 0.00 5 C005 has 1455 485 485 0.00 6 C006 has 438 146 146 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1665 546 544 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 111 37 37 0.00 13 C013 has 483 161 161 0.00 14 C014 has 132 44 44 1.31 Total of12335 atoms and 4096 groups and 4089 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3302 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1089 Number of atoms = 3302 Number of groups = 1094 Number of bonds = 3295 Number of angles = 1193 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1091 Number of HB donors = 2160 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1089 Number of atoms = 3302 Number of groups = 1094 Number of bonds = 3295 Number of angles = 1193 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1091 Number of HB donors = 2160 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "31.98" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1089" Evaluating: 1089-7 Parameter: NUMWAT <- "1082" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1082" Comparing "1081" and "1082". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 90.0 Parameter: ANGLE <- "90.0" CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "31.98" Parameter: BOX -> "31.98" Parameter: BOX -> "31.98" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 31.98000 B = 31.98000 C = 31.98000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 26 Number Symop A B C Distance 1 1 -1 -1 -1 7.3223 2 1 -1 0 -1 3.2347 3 1 -1 1 -1 4.6263 4 1 0 -1 -1 3.5620 5 1 0 0 -1 0.5053 6 1 0 1 -1 4.8533 7 1 -1 -1 0 3.9569 8 1 -1 0 0 2.4788 9 1 -1 1 0 4.6983 10 1 0 -1 0 1.1999 11 1 0 1 0 1.1999 12 1 -1 -1 1 6.8949 13 1 -1 0 1 3.2109 14 1 -1 1 1 5.0862 15 1 0 -1 1 4.8533 16 1 0 0 1 0.5053 17 1 0 1 1 3.5620 18 1 1 1 1 7.3223 19 1 1 0 1 3.2347 20 1 1 -1 1 4.6263 21 1 1 1 0 3.9569 22 1 1 0 0 2.4788 23 1 1 -1 0 4.6983 24 1 1 1 -1 6.8949 25 1 1 0 -1 3.2109 26 1 1 -1 -1 5.0862 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3228 atoms have been selected out of 3302 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 184 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 492 164 164 0.00 2 C002 has 750 250 250 0.00 3 C003 has 123 41 41 0.15 4 C004 has 627 209 209 0.00 5 C005 has 1458 486 486 0.00 6 C006 has 438 146 146 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1665 546 544 0.00 9 C009 has 426 142 142 0.00 10 C010 has 1554 518 518 0.00 12 C012 has 111 37 37 0.00 13 C013 has 480 160 160 0.00 14 C014 has 132 44 44 1.31 Total of12338 atoms and 4097 groups and 4090 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 3 atoms have been selected out of 3302 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1 residues deleted. DELTIC: 3 bonds deleted DELTIC: 1 angles deleted DELTIC: 2 donors deleted DELTIC: 1 acceptors deleted ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1088 Number of atoms = 3299 Number of groups = 1093 Number of bonds = 3292 Number of angles = 1192 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1090 Number of HB donors = 2158 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1088 Number of atoms = 3299 Number of groups = 1093 Number of bonds = 3292 Number of angles = 1192 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1090 Number of HB donors = 2158 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "31.978" CHARMM> CHARMM> calc numwat ?NRES - 7 RDCMND substituted energy or value "?NRES" to "1088" Evaluating: 1088-7 Parameter: NUMWAT <- "1081" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1081" Parameter: NUMWAT -> "1081" Comparing "1081" and "1081". IF test evaluated as false. Skipping command CHARMM> incr box by @boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "31.98" CHARMM> CHARMM> CHARMM> CHARMM> crystal define cubic @box @box @box @angle @angle @angle Parameter: BOX -> "31.98" Parameter: BOX -> "31.98" Parameter: BOX -> "31.98" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Parameter: ANGLE -> "90.0" Crystal Parameters : Crystal Type = CUBI A = 31.98000 B = 31.98000 C = 31.98000 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> crystal build cutoff @cutimg Parameter: CUTIMG -> "1" XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 1.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -2 TO 2 Lattice Vector B -2 TO 2 Lattice Vector C -2 TO 2 The number of transformations generated = 14 Number Symop A B C Distance 1 1 -1 -1 -1 7.3223 2 1 -1 0 -1 3.2347 3 1 0 -1 -1 3.5620 4 1 0 0 -1 0.5053 5 1 -1 -1 0 3.9569 6 1 -1 0 0 2.4788 7 1 0 -1 0 1.1999 8 1 0 1 0 1.1999 9 1 0 0 1 0.5053 10 1 0 1 1 3.5620 11 1 1 1 1 7.3223 12 1 1 0 1 3.2347 13 1 1 1 0 3.9569 14 1 1 0 0 2.4788 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 14 Transformations have been processed. CHARMM> CHARMM> image byresidue select .not. SOLUTE end SELRPN> 3225 atoms have been selected out of 3299 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> coor copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> update cutim 1.0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 6 2 2 0.00 2 C002 has 3 1 1 0.00 3 C003 has 18 6 6 0.00 4 C004 has 96 32 32 0.00 5 C005 has 6 2 2 0.00 6 C006 has 78 26 26 0.00 7 C007 has 84 28 28 0.00 Total of 3590 atoms and 1190 groups and 1185 residues were included CHARMM> coor diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coor dist comp weig CHARMM> delete atom sele .byres. prop wcomp .gt. 0.0 end SELRPN> 0 atoms have been selected out of 3299 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1088 Number of atoms = 3299 Number of groups = 1093 Number of bonds = 3292 Number of angles = 1192 Number of dihedrals = 176 Number of impropers = 5 Number of cross-terms = 0 Number of HB acceptors = 1090 Number of HB donors = 2158 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> CHARMM> CHARMM> CHARMM> open unit 1 write card name @sim_@ffname.psf Parameter: SIM -> "AC" Parameter: FFNAME -> "C36" VOPEN> Attempting to open::ac_c36.psf:: OPNLGU> Unit 1 opened for WRITE access to /uufs/chpc.utah.edu/common/home/u0723235/tmp/charmm-example/ac/run2/ac_c36.psf CHARMM> write psf unit 1 card RDTITL> * AC "Initial ApC model" RDTITL> * 31.98 31.98 31.98 90 90 90 RDTITL> * 3 NA+ IONS + 1081 WATERS RDTITL> * CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> open unit 1 write card name @sim_@ffname.cor Parameter: SIM -> "AC" Parameter: FFNAME -> "C36" VOPEN> Attempting to open::ac_c36.cor:: OPNLGU> Unit 1 opened for WRITE access to /uufs/chpc.utah.edu/common/home/u0723235/tmp/charmm-example/ac/run2/ac_c36.cor CHARMM> coor write unit 1 card select all end RDTITL> * AC "Initial ApC model" RDTITL> * 31.98 31.98 31.98 90 90 90 RDTITL> * 3 NA+ IONS + 1081 WATERS RDTITL> * SELRPN> 3299 atoms have been selected out of 3299 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> close unit 1 CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. CHARMM> CHARMM> open unit 1 write card name @sim_@ffname.pdb Parameter: SIM -> "AC" Parameter: FFNAME -> "C36" VOPEN> Attempting to open::ac_c36.pdb:: OPNLGU> Unit 1 opened for WRITE access to /uufs/chpc.utah.edu/common/home/u0723235/tmp/charmm-example/ac/run2/ac_c36.pdb CHARMM> coor write unit 1 pdb select all end RDTITL> * AC "Initial ApC model" RDTITL> * 31.98 31.98 31.98 90 90 90 RDTITL> * 3 NA+ IONS + 1081 WATERS RDTITL> * Write CHARMM-pdb format SELRPN> 3299 atoms have been selected out of 3299 CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" $$$$$$ New timer profile $$$$$ Total time 35.56 Other: 0.00 NORMAL TERMINATION BY END OF FILE MOST SEVERE WARNING WAS AT LEVEL 0 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 35.56 SECONDS CPU TIME: 35.41 SECONDS