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)@kin Created on 11/10/15 at 17:06:52 by user: u0181375 Maximum number of ATOMS: 240480, and RESidues: 80160 PID of the current process is: 29312 RDTITL> * -----------------------------* CHARMM SETUP SCRIPT RDTITL> * -----------------------------* RDTITL> CHARMM> CHARMM> CHARMM> set sim aa Parameter: SIM <- "AA" CHARMM> set ff all36_na Parameter: FF <- "ALL36_NA" CHARMM> set ffname c36 Parameter: FFNAME <- "C36" CHARMM> set input "aa_charmm.pdb" Parameter: INPUT <- ""aa_charmm.pdb"" CHARMM> set inputions "aa_ions.pdb" Parameter: INPUTIONS <- ""aa_ions.pdb"" CHARMM> set outvac "aa-c36-vac.pdb" Parameter: OUTVAC <- ""aa-c36-vac.pdb"" CHARMM> set outcio "aa-c36-cio.pdb" Parameter: OUTCIO <- ""aa-c36-cio.pdb"" CHARMM> CHARMM> set comment "Initial ApA model" Parameter: COMMENT <- ""Initial ApA model"" CHARMM> CHARMM> ! CHARMM> ! number of waters and guess on initial box size CHARMM> ! CHARMM> set waters = 1075 Parameter: WATERS <- "1075" CHARMM> set box = 36.00 Parameter: BOX <- "36.00" 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/u0181375/aa-charmm/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/u0181375/aa-charmm/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 ADE RESIDUE SEQUENCE -- 2 RESIDUES ADE ADE 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 ADE . 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 = 65 Number of groups = 7 Number of bonds = 70 Number of angles = 122 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 16 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 -> ""aa_charmm.pdb"" VOPEN> Attempting to open::aa_charmm.pdb:: OPNLGU> Unit 1 opened for READONLY access to /uufs/chpc.utah.edu/common/home/u0181375/aa-charmm/aa_charmm.pdb CHARMM> read coordinates pdb unit 1 select segid rna end read CHARMM-pdb format SELRPN> 65 atoms have been selected out of 65 SPATIAL COORDINATES BEING READ FROM UNIT 1 TITLE> * 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 = 65 Number of groups = 7 Number of bonds = 70 Number of angles = 122 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 16 Number of HB donors = 8 Number of NB exclusions = 0 Total charge = -1.00000 CHARMM> CHARMM> coor orient mass select all end SELRPN> 65 atoms have been selected out of 65 ORIENT THE COORDINATES TO ALIGN WITH AXIS MOMENTS 1433.24617131 -1726.26741471 -160.25179511 12948.18017643 -685.84465528 1701.87477138 Transpose of the rotation matrix 0.056739 -0.987993 0.143701 -0.916390 0.005588 0.400248 -0.396245 -0.154396 -0.905070 CENTER OF ATOMS BEFORE TRANSLATION 2.83276 3.99752 3.37958 AXIS OF ROTATION IS 0.713491 -0.694584 -0.092110 ANGLE IS 157.13 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> coor stat sele all end SELRPN> 65 atoms have been selected out of 65 STATISTICS FOR 65 SELECTED ATOMS: XMIN = -7.881333 XMAX = 10.184098 XAVE = -0.008419 YMIN = -4.898298 YMAX = 4.829791 YAVE = -0.045077 ZMIN = -3.173021 ZMAX = 3.827438 ZAVE = 0.230675 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 -> "AA" Parameter: FFNAME -> "C36" VOPEN> Attempting to open::aa_c36_vac.psf:: OPNLGU> Unit 1 opened for WRITE access to /uufs/chpc.utah.edu/common/home/u0181375/aa-charmm/aa_c36_vac.psf CHARMM> write psf unit 1 card RDTITL> * AA "Initial ApA 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 -> "AA" Parameter: FFNAME -> "C36" VOPEN> Attempting to open::aa_c36_vac.pdb:: OPNLGU> Unit 1 opened for WRITE access to /uufs/chpc.utah.edu/common/home/u0181375/aa-charmm/aa_c36_vac.pdb CHARMM> coor write unit 1 pdb select all end RDTITL> * AA "Initial ApA model" RDTITL> * Write CHARMM-pdb format SELRPN> 65 atoms have been selected out of 65 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 -> "AA" Parameter: FFNAME -> "C36" VOPEN> Attempting to open::aa_c36_vac.cor:: OPNLGU> Unit 1 opened for WRITE access to /uufs/chpc.utah.edu/common/home/u0181375/aa-charmm/aa_c36_vac.cor CHARMM> coor write unit 1 card select all end RDTITL> * AA "Initial ApA model" RDTITL> * SELRPN> 65 atoms have been selected out of 65 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 = 76 Number of groups = 18 Number of bonds = 70 Number of angles = 122 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 16 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 -> ""aa_ions.pdb"" VOPEN> Attempting to open::aa_ions.pdb:: OPNLGU> Unit 1 opened for READONLY access to /uufs/chpc.utah.edu/common/home/u0181375/aa-charmm/aa_ions.pdb CHARMM> read coordinates pdb unit 1 select segid ions end read CHARMM-pdb format SELRPN> 11 atoms have been selected out of 76 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> 76 atoms have been selected out of 76 ORIENT THE COORDINATES TO ALIGN WITH AXIS MOMENTS 10828.27243179 -11938.56499574 93.40252663 27872.31049719 -1659.45897854 21423.80978773 Transpose of the rotation matrix 0.118148 -0.884106 0.452103 0.992170 0.086535 -0.090060 0.040500 0.459203 0.887408 CENTER OF ATOMS BEFORE TRANSLATION -0.56058 3.55261 -1.04405 AXIS OF ROTATION IS -0.274923 -0.206020 -0.939134 ANGLE IS 87.36 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> coordinate statistics select all end SELRPN> 76 atoms have been selected out of 76 STATISTICS FOR 76 SELECTED ATOMS: XMIN = -12.700061 XMAX = 7.592326 XAVE = 2.285616 YMIN = -7.762173 YMAX = 10.221574 YAVE = 0.095402 ZMIN = -3.566863 ZMAX = 8.494044 ZAVE = -0.214979 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 -> "AA" Parameter: FFNAME -> "C36" VOPEN> Attempting to open::aa_c36_cio.psf:: OPNLGU> Unit 1 opened for WRITE access to /uufs/chpc.utah.edu/common/home/u0181375/aa-charmm/aa_c36_cio.psf CHARMM> write psf unit 1 card RDTITL> * AA "Initial ApA 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 -> "AA" Parameter: FFNAME -> "C36" VOPEN> Attempting to open::aa_c36_cio.pdb:: OPNLGU> Unit 1 opened for WRITE access to /uufs/chpc.utah.edu/common/home/u0181375/aa-charmm/aa_c36_cio.pdb CHARMM> coor write unit 1 pdb select all end RDTITL> * AA "Initial ApA model" RDTITL> * 1 NA+ + 5 NACL IONS RDTITL> * Write CHARMM-pdb format SELRPN> 76 atoms have been selected out of 76 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 -> "AA" Parameter: FFNAME -> "C36" VOPEN> Attempting to open::aa_c36_cio.cor:: OPNLGU> Unit 1 opened for WRITE access to /uufs/chpc.utah.edu/common/home/u0181375/aa-charmm/aa_c36_cio.cor CHARMM> coor write unit 1 card select all end RDTITL> * AA "Initial ApA model" RDTITL> * 3 NA+ IONS RDTITL> * SELRPN> 76 atoms have been selected out of 76 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> 76 atoms have been selected out of 76 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 = 3076 Number of groups = 1018 Number of bonds = 3070 Number of angles = 1122 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1016 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/u0181375/aa-charmm/wat1000.cor.tip3p CHARMM> read coordinates card unit 1 append select segid wat end SELRPN> 3000 atoms have been selected out of 3076 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 = 6076 Number of groups = 2018 Number of bonds = 6070 Number of angles = 2122 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 2016 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 6076 SELRPN> 3000 atoms have been selected out of 6076 CHARMM> coor translate xdir @boxlen select segid watx end Parameter: BOXLEN -> "31.1661028" SELRPN> 3000 atoms have been selected out of 6076 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 = 6076 Number of groups = 2018 Number of bonds = 6070 Number of angles = 2122 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 2016 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 = 12076 Number of groups = 4018 Number of bonds = 12070 Number of angles = 4122 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 4016 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 12076 SELRPN> 6000 atoms have been selected out of 12076 CHARMM> coor translate ydir @boxlen select segid waty end Parameter: BOXLEN -> "31.1661028" SELRPN> 6000 atoms have been selected out of 12076 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 = 12076 Number of groups = 4018 Number of bonds = 12070 Number of angles = 4122 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 4016 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 = 24076 Number of groups = 8018 Number of bonds = 24070 Number of angles = 8122 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 8016 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 24076 SELRPN> 12000 atoms have been selected out of 24076 CHARMM> coor translate zdir @boxlen select segid watz end Parameter: BOXLEN -> "31.1661028" SELRPN> 12000 atoms have been selected out of 24076 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 = 24076 Number of groups = 8018 Number of bonds = 24070 Number of angles = 8122 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 8016 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 24076 CHARMM> CHARMM> coordinate orient mass norotate select segid wat end SELRPN> 24000 atoms have been selected out of 24076 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> 24076 atoms have been selected out of 24076 STATISTICS FOR 24076 SELECTED ATOMS: XMIN = -32.097027 XMAX = 31.829076 XAVE = -0.048078 YMIN = -31.944267 YMAX = 31.846836 YAVE = -0.050958 ZMIN = -31.704296 ZMAX = 31.894806 ZAVE = -0.056184 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 -> "36.00" Evaluating: 36.00/2.0+2.0 Parameter: HALFBOX <- "20" CHARMM> CHARMM> !if box .gt. @maxbox stop CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property x .lt. -@halfbox )) end Parameter: HALFBOX -> "20" SELRPN> 4356 atoms have been selected out of 24076 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1452 residues deleted. DELTIC: 4356 bonds deleted DELTIC: 1452 angles deleted DELTIC: 2904 donors deleted DELTIC: 1452 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 = 6561 Number of atoms = 19720 Number of groups = 6566 Number of bonds = 19714 Number of angles = 6670 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 6564 Number of HB donors = 13104 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 -> "20" SELRPN> 4380 atoms have been selected out of 19720 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 1460 residues deleted. DELTIC: 4380 bonds deleted DELTIC: 1460 angles deleted DELTIC: 2920 donors deleted DELTIC: 1460 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 = 5101 Number of atoms = 15340 Number of groups = 5106 Number of bonds = 15334 Number of angles = 5210 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 5104 Number of HB donors = 10184 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 -> "20" SELRPN> 2736 atoms have been selected out of 15340 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 912 residues deleted. DELTIC: 2736 bonds deleted DELTIC: 912 angles deleted DELTIC: 1824 donors deleted DELTIC: 912 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 = 4189 Number of atoms = 12604 Number of groups = 4194 Number of bonds = 12598 Number of angles = 4298 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 4192 Number of HB donors = 8360 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 -> "20" SELRPN> 2724 atoms have been selected out of 12604 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 908 residues deleted. DELTIC: 2724 bonds deleted DELTIC: 908 angles deleted DELTIC: 1816 donors deleted DELTIC: 908 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 = 3281 Number of atoms = 9880 Number of groups = 3286 Number of bonds = 9874 Number of angles = 3390 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 3284 Number of HB donors = 6544 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 -> "20" SELRPN> 1749 atoms have been selected out of 9880 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 583 residues deleted. DELTIC: 1749 bonds deleted DELTIC: 583 angles deleted DELTIC: 1166 donors deleted DELTIC: 583 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 = 2698 Number of atoms = 8131 Number of groups = 2703 Number of bonds = 8125 Number of angles = 2807 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 2701 Number of HB donors = 5378 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 -> "20" SELRPN> 1767 atoms have been selected out of 8131 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 589 residues deleted. DELTIC: 1767 bonds deleted DELTIC: 589 angles deleted DELTIC: 1178 donors deleted DELTIC: 589 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 = 2109 Number of atoms = 6364 Number of groups = 2114 Number of bonds = 6358 Number of angles = 2218 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 2112 Number of HB donors = 4200 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 2109 Number of atoms = 6364 Number of groups = 2114 Number of bonds = 6358 Number of angles = 2218 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 2112 Number of HB donors = 4200 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> label loop2 CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "36.00" Parameter: BOX -> "36.00" Parameter: BOX -> "36.00" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 36.00000 B = 36.00000 C = 36.00000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 36 Number Symop A B C Distance 1 1 -2 -2 -2 7.0192 2 1 -2 -1 -2 13.4653 3 1 -2 -2 -1 12.6303 4 1 -2 -1 -1 11.1701 5 1 -1 -2 -1 13.9997 6 1 -1 -1 -1 2.6552 7 1 -1 0 -1 9.9564 8 1 -1 1 -1 13.2765 9 1 0 -1 -1 11.5382 10 1 0 0 -1 8.1386 11 1 0 1 -1 5.1346 12 1 -1 -1 0 8.2379 13 1 -1 0 0 9.5070 14 1 -1 1 0 5.1268 15 1 0 -1 0 7.5756 16 1 0 1 0 7.5756 17 1 -1 -1 1 12.2528 18 1 -1 0 1 6.2781 19 1 -1 1 1 11.9925 20 1 0 -1 1 5.1346 21 1 0 0 1 8.1386 22 1 0 1 1 11.5382 23 1 2 2 2 7.0192 24 1 2 1 2 13.4653 25 1 2 2 1 12.6303 26 1 2 1 1 11.1701 27 1 1 2 1 13.9997 28 1 1 1 1 2.6552 29 1 1 0 1 9.9564 30 1 1 -1 1 13.2765 31 1 1 1 0 8.2379 32 1 1 0 0 9.5070 33 1 1 -1 0 5.1268 34 1 1 1 -1 12.2528 35 1 1 0 -1 6.2781 36 1 1 -1 -1 11.9925 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 36 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 6288 atoms have been selected out of 6364 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 15 OPERATED ON BY TRANSFORMATION C028 RESIDUE 18 OPERATED ON BY TRANSFORMATION C028 RESIDUE 19 OPERATED ON BY TRANSFORMATION C028 RESIDUE 20 OPERATED ON BY TRANSFORMATION C028 RESIDUE 21 OPERATED ON BY TRANSFORMATION C028 RESIDUE 24 OPERATED ON BY TRANSFORMATION C028 RESIDUE 25 OPERATED ON BY TRANSFORMATION C028 RESIDUE 26 OPERATED ON BY TRANSFORMATION C028 RESIDUE 27 OPERATED ON BY TRANSFORMATION C016 RESIDUE 30 OPERATED ON BY TRANSFORMATION C028 RESIDUE 34 OPERATED ON BY TRANSFORMATION C028 RESIDUE 36 OPERATED ON BY TRANSFORMATION C028 RESIDUE 39 OPERATED ON BY TRANSFORMATION C028 RESIDUE 40 OPERATED ON BY TRANSFORMATION C028 RESIDUE 41 OPERATED ON BY TRANSFORMATION C028 RESIDUE 47 OPERATED ON BY TRANSFORMATION C028 RESIDUE 48 OPERATED ON BY 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TRANSFORMATION C029 RESIDUE 753 OPERATED ON BY TRANSFORMATION C015 RESIDUE 759 OPERATED ON BY TRANSFORMATION C032 RESIDUE 763 OPERATED ON BY TRANSFORMATION C015 RESIDUE 764 OPERATED ON BY TRANSFORMATION C021 RESIDUE 765 OPERATED ON BY TRANSFORMATION C015 RESIDUE 768 OPERATED ON BY TRANSFORMATION C021 RESIDUE 769 OPERATED ON BY TRANSFORMATION C021 RESIDUE 770 OPERATED ON BY TRANSFORMATION C021 RESIDUE 772 OPERATED ON BY TRANSFORMATION C015 RESIDUE 775 OPERATED ON BY TRANSFORMATION C029 RESIDUE 776 OPERATED ON BY TRANSFORMATION C029 RESIDUE 779 OPERATED ON BY TRANSFORMATION C029 RESIDUE 780 OPERATED ON BY TRANSFORMATION C029 RESIDUE 782 OPERATED ON BY TRANSFORMATION C015 RESIDUE 783 OPERATED ON BY TRANSFORMATION C029 RESIDUE 784 OPERATED ON BY TRANSFORMATION C021 RESIDUE 785 OPERATED ON BY TRANSFORMATION C029 RESIDUE 787 OPERATED ON BY TRANSFORMATION C015 RESIDUE 793 OPERATED ON BY TRANSFORMATION C015 RESIDUE 794 OPERATED ON BY TRANSFORMATION C021 RESIDUE 795 OPERATED ON BY TRANSFORMATION C032 RESIDUE 797 OPERATED ON BY TRANSFORMATION C029 RESIDUE 799 OPERATED ON BY TRANSFORMATION C015 RESIDUE 804 OPERATED ON BY TRANSFORMATION C012 RESIDUE 805 OPERATED ON BY TRANSFORMATION C013 RESIDUE 806 OPERATED ON BY TRANSFORMATION C021 RESIDUE 807 OPERATED ON BY TRANSFORMATION C013 RESIDUE 808 OPERATED ON BY TRANSFORMATION C021 RESIDUE 810 OPERATED ON BY TRANSFORMATION C012 RESIDUE 811 OPERATED ON BY TRANSFORMATION C021 RESIDUE 812 OPERATED ON BY TRANSFORMATION C021 RESIDUE 814 OPERATED ON BY TRANSFORMATION C012 RESIDUE 815 OPERATED ON BY TRANSFORMATION C012 RESIDUE 816 OPERATED ON BY TRANSFORMATION C012 RESIDUE 824 OPERATED ON BY TRANSFORMATION C012 RESIDUE 828 OPERATED ON BY TRANSFORMATION C012 RESIDUE 829 OPERATED ON BY TRANSFORMATION C012 RESIDUE 831 OPERATED ON BY TRANSFORMATION C021 RESIDUE 832 OPERATED ON BY TRANSFORMATION C012 RESIDUE 833 OPERATED ON BY TRANSFORMATION C012 RESIDUE 835 OPERATED ON BY TRANSFORMATION C012 RESIDUE 837 OPERATED ON BY TRANSFORMATION C021 RESIDUE 843 OPERATED ON BY TRANSFORMATION C012 RESIDUE 844 OPERATED ON BY TRANSFORMATION C021 RESIDUE 847 OPERATED ON BY TRANSFORMATION C021 RESIDUE 850 OPERATED ON BY TRANSFORMATION C013 RESIDUE 851 OPERATED ON BY TRANSFORMATION C021 RESIDUE 852 OPERATED ON BY TRANSFORMATION C021 RESIDUE 853 OPERATED ON BY TRANSFORMATION C012 RESIDUE 854 OPERATED ON BY TRANSFORMATION C012 RESIDUE 861 OPERATED ON BY TRANSFORMATION C015 RESIDUE 866 OPERATED ON BY TRANSFORMATION C021 RESIDUE 867 OPERATED ON BY TRANSFORMATION C015 RESIDUE 868 OPERATED ON BY TRANSFORMATION C021 RESIDUE 869 OPERATED ON BY TRANSFORMATION C021 RESIDUE 871 OPERATED ON BY TRANSFORMATION C012 RESIDUE 872 OPERATED ON BY TRANSFORMATION C021 RESIDUE 874 OPERATED ON BY TRANSFORMATION C012 RESIDUE 875 OPERATED ON BY TRANSFORMATION C021 RESIDUE 876 OPERATED ON BY TRANSFORMATION C021 RESIDUE 879 OPERATED ON BY TRANSFORMATION C012 RESIDUE 881 OPERATED ON BY TRANSFORMATION C012 RESIDUE 883 OPERATED ON BY TRANSFORMATION C012 RESIDUE 885 OPERATED ON BY TRANSFORMATION C013 RESIDUE 887 OPERATED ON BY TRANSFORMATION C012 RESIDUE 889 OPERATED ON BY TRANSFORMATION C021 RESIDUE 890 OPERATED ON BY TRANSFORMATION C021 RESIDUE 892 OPERATED ON BY TRANSFORMATION C021 RESIDUE 893 OPERATED ON BY TRANSFORMATION C012 RESIDUE 894 OPERATED ON BY TRANSFORMATION C012 RESIDUE 897 OPERATED ON BY TRANSFORMATION C021 RESIDUE 899 OPERATED ON BY TRANSFORMATION C021 RESIDUE 902 OPERATED ON BY TRANSFORMATION C012 RESIDUE 905 OPERATED ON BY TRANSFORMATION C021 RESIDUE 906 OPERATED ON BY TRANSFORMATION C021 RESIDUE 912 OPERATED ON BY TRANSFORMATION C021 RESIDUE 916 OPERATED ON BY TRANSFORMATION C021 RESIDUE 917 OPERATED ON BY TRANSFORMATION C012 RESIDUE 922 OPERATED ON BY TRANSFORMATION C021 RESIDUE 923 OPERATED ON BY TRANSFORMATION C012 RESIDUE 925 OPERATED ON BY TRANSFORMATION C021 RESIDUE 926 OPERATED ON BY TRANSFORMATION C021 RESIDUE 927 OPERATED ON BY TRANSFORMATION C021 RESIDUE 929 OPERATED ON BY TRANSFORMATION C012 RESIDUE 930 OPERATED ON BY TRANSFORMATION C012 RESIDUE 938 OPERATED ON BY TRANSFORMATION C012 RESIDUE 947 OPERATED ON BY TRANSFORMATION C021 RESIDUE 951 OPERATED ON BY TRANSFORMATION C021 RESIDUE 955 OPERATED ON BY TRANSFORMATION C015 RESIDUE 956 OPERATED ON BY TRANSFORMATION C012 RESIDUE 958 OPERATED ON BY TRANSFORMATION C012 RESIDUE 959 OPERATED ON BY TRANSFORMATION C021 RESIDUE 960 OPERATED ON BY TRANSFORMATION C012 RESIDUE 966 OPERATED ON BY TRANSFORMATION C012 RESIDUE 968 OPERATED ON BY TRANSFORMATION C021 RESIDUE 972 OPERATED ON BY TRANSFORMATION C021 RESIDUE 973 OPERATED ON BY TRANSFORMATION C012 RESIDUE 975 OPERATED ON BY TRANSFORMATION C012 RESIDUE 976 OPERATED ON BY TRANSFORMATION C012 RESIDUE 977 OPERATED ON BY TRANSFORMATION C013 RESIDUE 979 OPERATED ON BY TRANSFORMATION C015 RESIDUE 980 OPERATED ON BY TRANSFORMATION C012 RESIDUE 982 OPERATED ON BY TRANSFORMATION C012 RESIDUE 989 OPERATED ON BY TRANSFORMATION C013 RESIDUE 990 OPERATED ON BY TRANSFORMATION C012 RESIDUE 993 OPERATED ON BY TRANSFORMATION C012 RESIDUE 994 OPERATED ON BY TRANSFORMATION C012 RESIDUE 995 OPERATED ON BY TRANSFORMATION C012 RESIDUE 997 OPERATED ON BY TRANSFORMATION C021 RESIDUE 999 OPERATED ON BY TRANSFORMATION C012 RESIDUE 1004 OPERATED ON BY TRANSFORMATION C013 RESIDUE 1006 OPERATED ON BY TRANSFORMATION C021 RESIDUE 1008 OPERATED ON BY TRANSFORMATION C012 RESIDUE 1012 OPERATED ON BY TRANSFORMATION C012 RESIDUE 1013 OPERATED ON BY TRANSFORMATION C012 RESIDUE 1014 OPERATED ON BY TRANSFORMATION C015 RESIDUE 1016 OPERATED ON BY TRANSFORMATION C021 RESIDUE 1018 OPERATED ON BY TRANSFORMATION C021 RESIDUE 1021 OPERATED ON BY TRANSFORMATION C021 RESIDUE 1022 OPERATED ON BY TRANSFORMATION C015 RESIDUE 1024 OPERATED ON BY TRANSFORMATION C012 RESIDUE 1026 OPERATED ON BY TRANSFORMATION C015 RESIDUE 1027 OPERATED ON BY TRANSFORMATION C021 RESIDUE 1030 OPERATED ON BY TRANSFORMATION C015 RESIDUE 1032 OPERATED ON BY TRANSFORMATION C012 RESIDUE 1036 OPERATED ON BY TRANSFORMATION C021 RESIDUE 1037 OPERATED ON BY TRANSFORMATION C021 RESIDUE 1038 OPERATED ON BY TRANSFORMATION C013 RESIDUE 1042 OPERATED ON BY TRANSFORMATION C021 RESIDUE 1045 OPERATED ON BY TRANSFORMATION C021 RESIDUE 1046 OPERATED ON BY TRANSFORMATION C021 RESIDUE 1047 OPERATED ON BY TRANSFORMATION C012 RESIDUE 1049 OPERATED ON BY TRANSFORMATION C012 RESIDUE 1050 OPERATED ON BY TRANSFORMATION C021 RESIDUE 1051 OPERATED ON BY TRANSFORMATION C021 RESIDUE 1053 OPERATED ON BY TRANSFORMATION C012 RESIDUE 1061 OPERATED ON BY TRANSFORMATION C012 RESIDUE 1062 OPERATED ON BY TRANSFORMATION C012 RESIDUE 1063 OPERATED ON BY TRANSFORMATION C021 RESIDUE 1070 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1071 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1072 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1073 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1075 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1076 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1079 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1083 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1085 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1086 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1087 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1088 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1090 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1091 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1092 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1095 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1101 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1102 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1104 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1105 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1106 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1109 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1110 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1112 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1113 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1114 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1116 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1118 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1119 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1121 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1122 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1125 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1126 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1128 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1129 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1132 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1133 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1134 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1135 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1137 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1141 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1142 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1144 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1145 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1147 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1149 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1150 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1151 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1154 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1155 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1156 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1157 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1159 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1163 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1165 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1166 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1170 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1174 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1175 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1176 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1178 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1179 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1181 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1185 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1187 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1189 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1191 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1192 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1197 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1198 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1202 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1211 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1216 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1217 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1221 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1224 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1228 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1235 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1241 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1242 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1247 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1248 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1250 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1251 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1252 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1253 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1258 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1261 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1263 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1264 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1267 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1270 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1271 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1273 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1274 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1276 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1280 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1281 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1285 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1287 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1288 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1289 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1290 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1292 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1295 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1296 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1298 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1302 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1306 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1310 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1314 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1315 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1320 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1323 OPERATED ON BY TRANSFORMATION C031 RESIDUE 1324 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1331 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1332 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1336 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1338 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1340 OPERATED ON BY TRANSFORMATION C013 RESIDUE 1343 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1344 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1346 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1349 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1350 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1351 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1356 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1357 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1360 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1361 OPERATED ON BY TRANSFORMATION C013 RESIDUE 1364 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1365 OPERATED ON BY TRANSFORMATION C013 RESIDUE 1372 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1374 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1380 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1384 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1388 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1391 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1392 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1393 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1394 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1395 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1396 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1397 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1399 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1402 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1403 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1406 OPERATED ON BY TRANSFORMATION C013 RESIDUE 1408 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1410 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1412 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1415 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1417 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1420 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1421 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1422 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1423 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1424 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1426 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1427 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1430 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1432 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1434 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1435 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1439 OPERATED ON BY TRANSFORMATION C013 RESIDUE 1440 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1444 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1445 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1449 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1451 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1455 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1456 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1460 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1467 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1468 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1473 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1475 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1480 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1482 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1491 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1493 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1496 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1498 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1502 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1503 OPERATED ON BY TRANSFORMATION C013 RESIDUE 1504 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1505 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1506 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1509 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1511 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1516 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1519 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1521 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1524 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1526 OPERATED ON BY TRANSFORMATION C013 RESIDUE 1532 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1533 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1535 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1537 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1538 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1539 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1541 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1543 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1544 OPERATED ON BY TRANSFORMATION C013 RESIDUE 1545 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1547 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1548 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1552 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1555 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1556 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1557 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1558 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1559 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1561 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1563 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1567 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1568 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1569 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1570 OPERATED ON BY TRANSFORMATION C013 RESIDUE 1571 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1575 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1580 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1581 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1583 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1584 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1586 OPERATED ON BY TRANSFORMATION C007 RESIDUE 1589 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1592 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1595 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1596 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1599 OPERATED ON BY TRANSFORMATION C015 RESIDUE 1600 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1602 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1603 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1604 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1605 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1606 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1608 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1611 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1614 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1615 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1622 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1623 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1624 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1634 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1636 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1639 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1640 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1641 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1644 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1646 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1649 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1654 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1655 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1656 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1657 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1658 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1662 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1663 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1667 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1670 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1676 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1677 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1683 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1686 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1693 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1695 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1696 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1697 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1698 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1700 OPERATED ON BY TRANSFORMATION C015 RESIDUE 1702 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1703 OPERATED ON BY TRANSFORMATION C015 RESIDUE 1704 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1707 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1710 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1711 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1713 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1714 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1716 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1717 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1718 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1719 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1720 OPERATED ON BY TRANSFORMATION C015 RESIDUE 1723 OPERATED ON BY TRANSFORMATION C015 RESIDUE 1725 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1728 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1731 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1732 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1733 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1737 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1739 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1740 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1744 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1747 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1748 OPERATED ON BY TRANSFORMATION C015 RESIDUE 1749 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1752 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1755 OPERATED ON BY TRANSFORMATION C015 RESIDUE 1757 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1758 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1761 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1762 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1767 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1771 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1773 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1777 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1778 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1779 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1780 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1782 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1784 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1787 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1790 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1792 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1793 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1797 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1798 OPERATED ON BY TRANSFORMATION C015 RESIDUE 1799 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1800 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1801 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1802 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1803 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1811 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1815 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1816 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1817 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1820 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1822 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1824 OPERATED ON BY TRANSFORMATION C015 RESIDUE 1825 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1826 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1829 OPERATED ON BY TRANSFORMATION C015 RESIDUE 1830 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1832 OPERATED ON BY TRANSFORMATION C032 RESIDUE 1833 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1837 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1838 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1842 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1849 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1850 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1852 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1853 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1854 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1856 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1857 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1861 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1863 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1866 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1867 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1872 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1875 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1878 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1879 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1880 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1886 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1889 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1891 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1894 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1895 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1900 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1902 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1903 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1904 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1907 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1911 OPERATED ON BY TRANSFORMATION C009 RESIDUE 1914 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1915 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1916 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1920 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1922 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1925 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1928 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1929 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1930 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1932 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1937 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1939 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1940 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1942 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1945 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1948 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1949 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1953 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1955 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1959 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1960 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1962 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1964 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1965 OPERATED ON BY TRANSFORMATION C012 RESIDUE 1966 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1971 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1974 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1975 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1977 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1978 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1979 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1983 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1984 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1987 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1988 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1990 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1991 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1992 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1994 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1996 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2000 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2001 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2006 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2010 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2011 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2012 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2015 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2020 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2021 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2024 OPERATED ON BY TRANSFORMATION C007 RESIDUE 2025 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2026 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2028 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2030 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2033 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2037 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2039 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2041 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2045 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2048 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2049 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2050 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2051 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2053 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2055 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2057 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2059 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2061 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2062 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2063 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2064 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2065 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2067 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2068 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2070 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2072 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2075 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2081 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2083 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2084 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2086 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2088 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2091 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2092 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2093 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2096 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2097 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2098 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2101 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2104 OPERATED ON BY TRANSFORMATION C006 RESIDUE 2106 OPERATED ON BY TRANSFORMATION C006 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 0 0 0 11.71 2 C002 has 0 0 0 11.73 3 C003 has 0 0 0 9.53 4 C004 has 366 122 122 6.63 5 C005 has 48 16 16 11.32 6 C006 has 4323 1441 1441 0.00 7 C007 has 1620 540 540 0.00 8 C008 has 0 0 0 11.97 9 C009 has 1569 523 523 0.00 10 C010 has 2286 762 762 0.00 11 C011 has 0 0 0 7.21 12 C012 has 1542 514 514 0.00 13 C013 has 2301 767 767 0.00 14 C014 has 0 0 0 4.38 15 C015 has 2247 749 749 0.00 17 C017 has 0 0 0 12.00 18 C018 has 0 0 0 3.74 19 C019 has 0 0 0 6.57 Total of22666 atoms and 7548 groups and 7543 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 2724 atoms have been selected out of 6364 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 908 residues deleted. DELTIC: 2724 bonds deleted DELTIC: 908 angles deleted DELTIC: 1816 donors deleted DELTIC: 908 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 = 3640 Number of groups = 1206 Number of bonds = 3634 Number of angles = 1310 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1204 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 = 3640 Number of groups = 1206 Number of bonds = 3634 Number of angles = 1310 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1204 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 <- "35.998" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1201" Evaluating: 1201-13 Parameter: NUMWAT <- "1188" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1188" Comparing "1075" and "1188". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.998" Parameter: BOX -> "35.998" Parameter: BOX -> "35.998" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.99800 B = 35.99800 C = 35.99800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.9372 2 1 -1 -2 -1 13.1586 3 1 -1 -1 -1 4.5519 4 1 -1 0 -1 3.0614 5 1 0 -1 -1 4.4529 6 1 0 0 -1 4.6212 7 1 -1 -1 0 1.1463 8 1 -1 0 0 2.6318 9 1 0 -1 0 4.5533 10 1 0 1 0 4.5533 11 1 0 0 1 4.6212 12 1 0 1 1 4.4529 13 1 2 1 1 8.9372 14 1 1 2 1 13.1586 15 1 1 1 1 4.5519 16 1 1 0 1 3.0614 17 1 1 1 0 1.1463 18 1 1 0 0 2.6318 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3640 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 7.02 2 C002 has 21 7 7 11.32 3 C003 has 2652 884 884 0.00 4 C004 has 867 289 289 0.00 5 C005 has 822 274 274 0.00 6 C006 has 1242 414 414 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1281 427 427 0.00 9 C009 has 1272 424 424 0.00 Total of12775 atoms and 4251 groups and 4246 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3640 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3640 Number of groups = 1206 Number of bonds = 3634 Number of angles = 1310 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1204 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 = 3640 Number of groups = 1206 Number of bonds = 3634 Number of angles = 1310 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1204 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 <- "35.996" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1201" Evaluating: 1201-13 Parameter: NUMWAT <- "1188" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1188" Comparing "1075" and "1188". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.996" Parameter: BOX -> "35.996" Parameter: BOX -> "35.996" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.99600 B = 35.99600 C = 35.99600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.9342 2 1 -1 -2 -1 13.1564 3 1 -1 -1 -1 4.5502 4 1 -1 0 -1 3.0612 5 1 0 -1 -1 4.4533 6 1 0 0 -1 4.6217 7 1 -1 -1 0 1.1461 8 1 -1 0 0 2.6308 9 1 0 -1 0 4.5533 10 1 0 1 0 4.5533 11 1 0 0 1 4.6217 12 1 0 1 1 4.4533 13 1 2 1 1 8.9342 14 1 1 2 1 13.1564 15 1 1 1 1 4.5502 16 1 1 0 1 3.0612 17 1 1 1 0 1.1461 18 1 1 0 0 2.6308 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3640 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 7.02 2 C002 has 21 7 7 11.32 3 C003 has 2652 884 884 0.00 4 C004 has 867 289 289 0.00 5 C005 has 822 274 274 0.00 6 C006 has 1245 415 415 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1281 427 427 0.00 9 C009 has 1272 424 424 0.00 Total of12778 atoms and 4252 groups and 4247 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3640 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3640 Number of groups = 1206 Number of bonds = 3634 Number of angles = 1310 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1204 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 = 3640 Number of groups = 1206 Number of bonds = 3634 Number of angles = 1310 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1204 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 <- "35.994" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1201" Evaluating: 1201-13 Parameter: NUMWAT <- "1188" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1188" Comparing "1075" and "1188". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.994" Parameter: BOX -> "35.994" Parameter: BOX -> "35.994" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.99400 B = 35.99400 C = 35.99400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.9311 2 1 -1 -2 -1 13.1542 3 1 -1 -1 -1 4.5485 4 1 -1 0 -1 3.0611 5 1 0 -1 -1 4.4536 6 1 0 0 -1 4.6221 7 1 -1 -1 0 1.1460 8 1 -1 0 0 2.6298 9 1 0 -1 0 4.5533 10 1 0 1 0 4.5533 11 1 0 0 1 4.6221 12 1 0 1 1 4.4536 13 1 2 1 1 8.9311 14 1 1 2 1 13.1542 15 1 1 1 1 4.5485 16 1 1 0 1 3.0611 17 1 1 1 0 1.1460 18 1 1 0 0 2.6298 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3640 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 7.01 2 C002 has 21 7 7 11.31 3 C003 has 2652 884 884 0.00 4 C004 has 867 289 289 0.00 5 C005 has 822 274 274 0.00 6 C006 has 1245 415 415 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1281 427 427 0.00 9 C009 has 1272 424 424 0.00 Total of12778 atoms and 4252 groups and 4247 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3640 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3640 Number of groups = 1206 Number of bonds = 3634 Number of angles = 1310 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1204 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 = 3640 Number of groups = 1206 Number of bonds = 3634 Number of angles = 1310 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1204 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 <- "35.992" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1201" Evaluating: 1201-13 Parameter: NUMWAT <- "1188" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1188" Comparing "1075" and "1188". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.992" Parameter: BOX -> "35.992" Parameter: BOX -> "35.992" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.99200 B = 35.99200 C = 35.99200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.9281 2 1 -1 -2 -1 13.1520 3 1 -1 -1 -1 4.5468 4 1 -1 0 -1 3.0610 5 1 0 -1 -1 4.4540 6 1 0 0 -1 4.6226 7 1 -1 -1 0 1.1458 8 1 -1 0 0 2.6288 9 1 0 -1 0 4.5533 10 1 0 1 0 4.5533 11 1 0 0 1 4.6226 12 1 0 1 1 4.4540 13 1 2 1 1 8.9281 14 1 1 2 1 13.1520 15 1 1 1 1 4.5468 16 1 1 0 1 3.0610 17 1 1 1 0 1.1458 18 1 1 0 0 2.6288 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3640 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 7.01 2 C002 has 21 7 7 11.31 3 C003 has 2652 884 884 0.00 4 C004 has 867 289 289 0.00 5 C005 has 825 275 275 0.00 6 C006 has 1245 415 415 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1281 427 427 0.00 9 C009 has 1272 424 424 0.00 Total of12781 atoms and 4253 groups and 4248 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3640 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3640 Number of groups = 1206 Number of bonds = 3634 Number of angles = 1310 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1204 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 = 3640 Number of groups = 1206 Number of bonds = 3634 Number of angles = 1310 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1204 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 <- "35.99" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1201" Evaluating: 1201-13 Parameter: NUMWAT <- "1188" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1188" Comparing "1075" and "1188". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.99" Parameter: BOX -> "35.99" Parameter: BOX -> "35.99" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.99000 B = 35.99000 C = 35.99000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.9251 2 1 -1 -2 -1 13.1498 3 1 -1 -1 -1 4.5451 4 1 -1 0 -1 3.0609 5 1 0 -1 -1 4.4543 6 1 0 0 -1 4.6231 7 1 -1 -1 0 1.1456 8 1 -1 0 0 2.6278 9 1 0 -1 0 4.5533 10 1 0 1 0 4.5533 11 1 0 0 1 4.6231 12 1 0 1 1 4.4543 13 1 2 1 1 8.9251 14 1 1 2 1 13.1498 15 1 1 1 1 4.5451 16 1 1 0 1 3.0609 17 1 1 1 0 1.1456 18 1 1 0 0 2.6278 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3640 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 7.01 2 C002 has 21 7 7 11.31 3 C003 has 2652 884 884 0.00 4 C004 has 867 289 289 0.00 5 C005 has 825 275 275 0.00 6 C006 has 1245 415 415 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1281 427 427 0.00 9 C009 has 1272 424 424 0.00 Total of12781 atoms and 4253 groups and 4248 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3640 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3640 Number of groups = 1206 Number of bonds = 3634 Number of angles = 1310 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1204 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 = 3640 Number of groups = 1206 Number of bonds = 3634 Number of angles = 1310 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1204 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 <- "35.988" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1201" Evaluating: 1201-13 Parameter: NUMWAT <- "1188" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1188" Comparing "1075" and "1188". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.988" Parameter: BOX -> "35.988" Parameter: BOX -> "35.988" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.98800 B = 35.98800 C = 35.98800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.9220 2 1 -1 -2 -1 13.1475 3 1 -1 -1 -1 4.5433 4 1 -1 0 -1 3.0608 5 1 0 -1 -1 4.4547 6 1 0 0 -1 4.6235 7 1 -1 -1 0 1.1455 8 1 -1 0 0 2.6268 9 1 0 -1 0 4.5533 10 1 0 1 0 4.5533 11 1 0 0 1 4.6235 12 1 0 1 1 4.4547 13 1 2 1 1 8.9220 14 1 1 2 1 13.1475 15 1 1 1 1 4.5433 16 1 1 0 1 3.0608 17 1 1 1 0 1.1455 18 1 1 0 0 2.6268 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3640 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 7.00 2 C002 has 21 7 7 11.30 3 C003 has 2652 884 884 0.00 4 C004 has 867 289 289 0.00 5 C005 has 825 275 275 0.00 6 C006 has 1245 415 415 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1281 427 427 0.00 9 C009 has 1272 424 424 0.00 Total of12781 atoms and 4253 groups and 4248 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3640 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3640 Number of groups = 1206 Number of bonds = 3634 Number of angles = 1310 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1204 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 = 3640 Number of groups = 1206 Number of bonds = 3634 Number of angles = 1310 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1204 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 <- "35.986" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1201" Evaluating: 1201-13 Parameter: NUMWAT <- "1188" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1188" Comparing "1075" and "1188". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.986" Parameter: BOX -> "35.986" Parameter: BOX -> "35.986" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.98600 B = 35.98600 C = 35.98600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.9190 2 1 -1 -2 -1 13.1453 3 1 -1 -1 -1 4.5416 4 1 -1 0 -1 3.0607 5 1 0 -1 -1 4.4551 6 1 0 0 -1 4.6240 7 1 -1 -1 0 1.1453 8 1 -1 0 0 2.6258 9 1 0 -1 0 4.5533 10 1 0 1 0 4.5533 11 1 0 0 1 4.6240 12 1 0 1 1 4.4551 13 1 2 1 1 8.9190 14 1 1 2 1 13.1453 15 1 1 1 1 4.5416 16 1 1 0 1 3.0607 17 1 1 1 0 1.1453 18 1 1 0 0 2.6258 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3640 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 7.00 2 C002 has 21 7 7 11.30 3 C003 has 2652 884 884 0.00 4 C004 has 867 289 289 0.00 5 C005 has 825 275 275 0.00 6 C006 has 1245 415 415 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1281 427 427 0.00 9 C009 has 1272 424 424 0.00 Total of12781 atoms and 4253 groups and 4248 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3640 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3640 Number of groups = 1206 Number of bonds = 3634 Number of angles = 1310 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1204 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 = 3640 Number of groups = 1206 Number of bonds = 3634 Number of angles = 1310 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1204 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 <- "35.984" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1201" Evaluating: 1201-13 Parameter: NUMWAT <- "1188" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1188" Comparing "1075" and "1188". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.984" Parameter: BOX -> "35.984" Parameter: BOX -> "35.984" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.98400 B = 35.98400 C = 35.98400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.9159 2 1 -1 -2 -1 13.1431 3 1 -1 -1 -1 4.5399 4 1 -1 0 -1 3.0606 5 1 0 -1 -1 4.4554 6 1 0 0 -1 4.6245 7 1 -1 -1 0 1.1452 8 1 -1 0 0 2.6248 9 1 0 -1 0 4.5533 10 1 0 1 0 4.5533 11 1 0 0 1 4.6245 12 1 0 1 1 4.4554 13 1 2 1 1 8.9159 14 1 1 2 1 13.1431 15 1 1 1 1 4.5399 16 1 1 0 1 3.0606 17 1 1 1 0 1.1452 18 1 1 0 0 2.6248 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3640 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 7.00 2 C002 has 21 7 7 11.30 3 C003 has 2652 884 884 0.00 4 C004 has 867 289 289 0.00 5 C005 has 825 275 275 0.00 6 C006 has 1245 415 415 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1281 427 427 0.00 9 C009 has 1272 424 424 0.00 Total of12781 atoms and 4253 groups and 4248 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3640 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3640 Number of groups = 1206 Number of bonds = 3634 Number of angles = 1310 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1204 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 = 3640 Number of groups = 1206 Number of bonds = 3634 Number of angles = 1310 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1204 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 <- "35.982" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1201" Evaluating: 1201-13 Parameter: NUMWAT <- "1188" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1188" Comparing "1075" and "1188". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.982" Parameter: BOX -> "35.982" Parameter: BOX -> "35.982" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.98200 B = 35.98200 C = 35.98200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.9129 2 1 -1 -2 -1 13.1409 3 1 -1 -1 -1 4.5382 4 1 -1 0 -1 3.0605 5 1 0 -1 -1 4.4558 6 1 0 0 -1 4.6249 7 1 -1 -1 0 1.1450 8 1 -1 0 0 2.6239 9 1 0 -1 0 4.5533 10 1 0 1 0 4.5533 11 1 0 0 1 4.6249 12 1 0 1 1 4.4558 13 1 2 1 1 8.9129 14 1 1 2 1 13.1409 15 1 1 1 1 4.5382 16 1 1 0 1 3.0605 17 1 1 1 0 1.1450 18 1 1 0 0 2.6239 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3640 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.99 2 C002 has 21 7 7 11.30 3 C003 has 2652 884 884 0.00 4 C004 has 867 289 289 0.00 5 C005 has 828 276 276 0.00 6 C006 has 1245 415 415 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1281 427 427 0.00 9 C009 has 1272 424 424 0.00 Total of12784 atoms and 4254 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 3640 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3640 Number of groups = 1206 Number of bonds = 3634 Number of angles = 1310 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1204 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 = 3640 Number of groups = 1206 Number of bonds = 3634 Number of angles = 1310 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1204 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 <- "35.98" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1201" Evaluating: 1201-13 Parameter: NUMWAT <- "1188" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1188" Comparing "1075" and "1188". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.98" Parameter: BOX -> "35.98" Parameter: BOX -> "35.98" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.98000 B = 35.98000 C = 35.98000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.9099 2 1 -1 -2 -1 13.1387 3 1 -1 -1 -1 4.5365 4 1 -1 0 -1 3.0603 5 1 0 -1 -1 4.4562 6 1 0 0 -1 4.6254 7 1 -1 -1 0 1.1449 8 1 -1 0 0 2.6229 9 1 0 -1 0 4.5534 10 1 0 1 0 4.5534 11 1 0 0 1 4.6254 12 1 0 1 1 4.4562 13 1 2 1 1 8.9099 14 1 1 2 1 13.1387 15 1 1 1 1 4.5365 16 1 1 0 1 3.0603 17 1 1 1 0 1.1449 18 1 1 0 0 2.6229 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3640 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.99 2 C002 has 21 7 7 11.29 3 C003 has 2652 884 884 0.00 4 C004 has 867 289 289 0.00 5 C005 has 828 276 276 0.00 6 C006 has 1245 415 415 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1281 427 427 0.00 9 C009 has 1272 424 424 0.00 Total of12784 atoms and 4254 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 3640 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3640 Number of groups = 1206 Number of bonds = 3634 Number of angles = 1310 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1204 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 = 3640 Number of groups = 1206 Number of bonds = 3634 Number of angles = 1310 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1204 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 <- "35.978" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1201" Evaluating: 1201-13 Parameter: NUMWAT <- "1188" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1188" Comparing "1075" and "1188". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.978" Parameter: BOX -> "35.978" Parameter: BOX -> "35.978" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.97800 B = 35.97800 C = 35.97800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.9068 2 1 -1 -2 -1 13.1365 3 1 -1 -1 -1 4.5348 4 1 -1 0 -1 3.0602 5 1 0 -1 -1 4.4565 6 1 0 0 -1 4.6258 7 1 -1 -1 0 1.1448 8 1 -1 0 0 2.6219 9 1 0 -1 0 4.5534 10 1 0 1 0 4.5534 11 1 0 0 1 4.6258 12 1 0 1 1 4.4565 13 1 2 1 1 8.9068 14 1 1 2 1 13.1365 15 1 1 1 1 4.5348 16 1 1 0 1 3.0602 17 1 1 1 0 1.1448 18 1 1 0 0 2.6219 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3640 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.99 2 C002 has 21 7 7 11.29 3 C003 has 2652 884 884 0.00 4 C004 has 867 289 289 0.00 5 C005 has 828 276 276 0.00 6 C006 has 1245 415 415 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1281 427 427 0.00 9 C009 has 1272 424 424 0.00 Total of12784 atoms and 4254 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 3640 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3640 Number of groups = 1206 Number of bonds = 3634 Number of angles = 1310 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1204 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 = 3640 Number of groups = 1206 Number of bonds = 3634 Number of angles = 1310 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1204 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 <- "35.976" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1201" Evaluating: 1201-13 Parameter: NUMWAT <- "1188" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1188" Comparing "1075" and "1188". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.976" Parameter: BOX -> "35.976" Parameter: BOX -> "35.976" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.97600 B = 35.97600 C = 35.97600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.9038 2 1 -1 -2 -1 13.1343 3 1 -1 -1 -1 4.5331 4 1 -1 0 -1 3.0601 5 1 0 -1 -1 4.4569 6 1 0 0 -1 4.6263 7 1 -1 -1 0 1.1446 8 1 -1 0 0 2.6209 9 1 0 -1 0 4.5534 10 1 0 1 0 4.5534 11 1 0 0 1 4.6263 12 1 0 1 1 4.4569 13 1 2 1 1 8.9038 14 1 1 2 1 13.1343 15 1 1 1 1 4.5331 16 1 1 0 1 3.0601 17 1 1 1 0 1.1446 18 1 1 0 0 2.6209 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3640 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 604 OPERATED ON BY TRANSFORMATION C011 RESIDUE 688 OPERATED ON BY TRANSFORMATION C017 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.98 2 C002 has 21 7 7 11.29 3 C003 has 2658 886 886 0.00 4 C004 has 867 289 289 0.00 5 C005 has 828 276 276 0.00 6 C006 has 1239 413 413 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1281 427 427 0.00 9 C009 has 1275 425 425 0.00 Total of12787 atoms and 4255 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> 6 atoms have been selected out of 3640 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 = 1199 Number of atoms = 3634 Number of groups = 1204 Number of bonds = 3628 Number of angles = 1308 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1202 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 = 3634 Number of groups = 1204 Number of bonds = 3628 Number of angles = 1308 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1202 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 <- "35.974" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1199" Evaluating: 1199-13 Parameter: NUMWAT <- "1186" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1186" Comparing "1075" and "1186". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.974" Parameter: BOX -> "35.974" Parameter: BOX -> "35.974" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.97400 B = 35.97400 C = 35.97400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.9008 2 1 -1 -2 -1 13.1321 3 1 -1 -1 -1 4.5314 4 1 -1 0 -1 3.0600 5 1 0 -1 -1 4.4573 6 1 0 0 -1 4.6268 7 1 -1 -1 0 1.1445 8 1 -1 0 0 2.6199 9 1 0 -1 0 4.5534 10 1 0 1 0 4.5534 11 1 0 0 1 4.6268 12 1 0 1 1 4.4573 13 1 2 1 1 8.9008 14 1 1 2 1 13.1321 15 1 1 1 1 4.5314 16 1 1 0 1 3.0600 17 1 1 1 0 1.1445 18 1 1 0 0 2.6199 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3634 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.98 2 C002 has 21 7 7 11.28 3 C003 has 2652 884 884 0.00 4 C004 has 864 288 288 0.00 5 C005 has 828 276 276 0.00 6 C006 has 1236 412 412 0.00 7 C007 has 807 269 269 0.00 8 C008 has 1278 426 426 0.00 9 C009 has 1272 424 424 0.00 Total of12757 atoms and 4245 groups and 4240 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3634 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3634 Number of groups = 1204 Number of bonds = 3628 Number of angles = 1308 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1202 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 = 3634 Number of groups = 1204 Number of bonds = 3628 Number of angles = 1308 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1202 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 <- "35.972" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1199" Evaluating: 1199-13 Parameter: NUMWAT <- "1186" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1186" Comparing "1075" and "1186". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.972" Parameter: BOX -> "35.972" Parameter: BOX -> "35.972" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.97200 B = 35.97200 C = 35.97200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8977 2 1 -1 -2 -1 13.1299 3 1 -1 -1 -1 4.5297 4 1 -1 0 -1 3.0599 5 1 0 -1 -1 4.4576 6 1 0 0 -1 4.6272 7 1 -1 -1 0 1.1444 8 1 -1 0 0 2.6190 9 1 0 -1 0 4.5534 10 1 0 1 0 4.5534 11 1 0 0 1 4.6272 12 1 0 1 1 4.4576 13 1 2 1 1 8.8977 14 1 1 2 1 13.1299 15 1 1 1 1 4.5297 16 1 1 0 1 3.0599 17 1 1 1 0 1.1444 18 1 1 0 0 2.6190 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3634 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.98 2 C002 has 21 7 7 11.28 3 C003 has 2652 884 884 0.00 4 C004 has 864 288 288 0.00 5 C005 has 828 276 276 0.00 6 C006 has 1236 412 412 0.00 7 C007 has 807 269 269 0.00 8 C008 has 1278 426 426 0.00 9 C009 has 1275 425 425 0.00 Total of12760 atoms and 4246 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> 0 atoms have been selected out of 3634 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3634 Number of groups = 1204 Number of bonds = 3628 Number of angles = 1308 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1202 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 = 3634 Number of groups = 1204 Number of bonds = 3628 Number of angles = 1308 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1202 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 <- "35.97" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1199" Evaluating: 1199-13 Parameter: NUMWAT <- "1186" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1186" Comparing "1075" and "1186". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.97" Parameter: BOX -> "35.97" Parameter: BOX -> "35.97" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.97000 B = 35.97000 C = 35.97000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8947 2 1 -1 -2 -1 13.1277 3 1 -1 -1 -1 4.5280 4 1 -1 0 -1 3.0598 5 1 0 -1 -1 4.4580 6 1 0 0 -1 4.6277 7 1 -1 -1 0 1.1443 8 1 -1 0 0 2.6180 9 1 0 -1 0 4.5534 10 1 0 1 0 4.5534 11 1 0 0 1 4.6277 12 1 0 1 1 4.4580 13 1 2 1 1 8.8947 14 1 1 2 1 13.1277 15 1 1 1 1 4.5280 16 1 1 0 1 3.0598 17 1 1 1 0 1.1443 18 1 1 0 0 2.6180 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3634 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 843 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.98 2 C002 has 24 8 8 11.28 3 C003 has 2649 883 883 0.00 4 C004 has 861 287 287 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1242 414 414 0.00 7 C007 has 807 269 269 0.00 8 C008 has 1278 426 426 0.00 9 C009 has 1275 425 425 0.00 Total of12772 atoms and 4250 groups and 4245 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3634 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 = 3631 Number of groups = 1203 Number of bonds = 3625 Number of angles = 1307 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1201 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 = 3631 Number of groups = 1203 Number of bonds = 3625 Number of angles = 1307 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1201 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 <- "35.968" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1198" Evaluating: 1198-13 Parameter: NUMWAT <- "1185" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1185" Comparing "1075" and "1185". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.968" Parameter: BOX -> "35.968" Parameter: BOX -> "35.968" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.96800 B = 35.96800 C = 35.96800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8916 2 1 -1 -2 -1 13.1254 3 1 -1 -1 -1 4.5263 4 1 -1 0 -1 3.0597 5 1 0 -1 -1 4.4584 6 1 0 0 -1 4.6282 7 1 -1 -1 0 1.1442 8 1 -1 0 0 2.6170 9 1 0 -1 0 4.5534 10 1 0 1 0 4.5534 11 1 0 0 1 4.6282 12 1 0 1 1 4.4584 13 1 2 1 1 8.8916 14 1 1 2 1 13.1254 15 1 1 1 1 4.5263 16 1 1 0 1 3.0597 17 1 1 1 0 1.1442 18 1 1 0 0 2.6170 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3631 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.97 2 C002 has 24 8 8 11.27 3 C003 has 2649 883 883 0.00 4 C004 has 861 287 287 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1239 413 413 0.00 7 C007 has 807 269 269 0.00 8 C008 has 1275 425 425 0.00 9 C009 has 1275 425 425 0.00 Total of12760 atoms and 4246 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> 0 atoms have been selected out of 3631 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3631 Number of groups = 1203 Number of bonds = 3625 Number of angles = 1307 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1201 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 = 3631 Number of groups = 1203 Number of bonds = 3625 Number of angles = 1307 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1201 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 <- "35.966" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1198" Evaluating: 1198-13 Parameter: NUMWAT <- "1185" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1185" Comparing "1075" and "1185". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.966" Parameter: BOX -> "35.966" Parameter: BOX -> "35.966" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.96600 B = 35.96600 C = 35.96600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8886 2 1 -1 -2 -1 13.1232 3 1 -1 -1 -1 4.5246 4 1 -1 0 -1 3.0597 5 1 0 -1 -1 4.4587 6 1 0 0 -1 4.6287 7 1 -1 -1 0 1.1441 8 1 -1 0 0 2.6160 9 1 0 -1 0 4.5535 10 1 0 1 0 4.5535 11 1 0 0 1 4.6287 12 1 0 1 1 4.4587 13 1 2 1 1 8.8886 14 1 1 2 1 13.1232 15 1 1 1 1 4.5246 16 1 1 0 1 3.0597 17 1 1 1 0 1.1441 18 1 1 0 0 2.6160 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3631 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.97 2 C002 has 24 8 8 11.27 3 C003 has 2649 883 883 0.00 4 C004 has 861 287 287 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1239 413 413 0.00 7 C007 has 807 269 269 0.00 8 C008 has 1275 425 425 0.00 9 C009 has 1275 425 425 0.00 Total of12760 atoms and 4246 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> 0 atoms have been selected out of 3631 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3631 Number of groups = 1203 Number of bonds = 3625 Number of angles = 1307 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1201 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 = 3631 Number of groups = 1203 Number of bonds = 3625 Number of angles = 1307 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1201 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 <- "35.964" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1198" Evaluating: 1198-13 Parameter: NUMWAT <- "1185" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1185" Comparing "1075" and "1185". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.964" Parameter: BOX -> "35.964" Parameter: BOX -> "35.964" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.96400 B = 35.96400 C = 35.96400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8856 2 1 -1 -2 -1 13.9983 3 1 -1 -1 -1 4.5229 4 1 -1 0 -1 3.0596 5 1 0 -1 -1 4.4591 6 1 0 0 -1 4.6291 7 1 -1 -1 0 1.1440 8 1 -1 0 0 2.6151 9 1 0 -1 0 4.5535 10 1 0 1 0 4.5535 11 1 0 0 1 4.6291 12 1 0 1 1 4.4591 13 1 2 1 1 8.8856 14 1 1 2 1 13.9983 15 1 1 1 1 4.5229 16 1 1 0 1 3.0596 17 1 1 1 0 1.1440 18 1 1 0 0 2.6151 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3631 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.97 2 C002 has 24 8 8 11.27 3 C003 has 2649 883 883 0.00 4 C004 has 861 287 287 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1242 414 414 0.00 7 C007 has 807 269 269 0.00 8 C008 has 1275 425 425 0.00 9 C009 has 1275 425 425 0.00 Total of12763 atoms and 4247 groups and 4242 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3631 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3631 Number of groups = 1203 Number of bonds = 3625 Number of angles = 1307 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1201 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 = 3631 Number of groups = 1203 Number of bonds = 3625 Number of angles = 1307 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1201 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 <- "35.962" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1198" Evaluating: 1198-13 Parameter: NUMWAT <- "1185" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1185" Comparing "1075" and "1185". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.962" Parameter: BOX -> "35.962" Parameter: BOX -> "35.962" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.96200 B = 35.96200 C = 35.96200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8825 2 1 -1 -2 -1 13.9952 3 1 -1 -1 -1 4.5212 4 1 -1 0 -1 3.0595 5 1 0 -1 -1 4.4595 6 1 0 0 -1 4.6296 7 1 -1 -1 0 1.1439 8 1 -1 0 0 2.6141 9 1 0 -1 0 4.5535 10 1 0 1 0 4.5535 11 1 0 0 1 4.6296 12 1 0 1 1 4.4595 13 1 2 1 1 8.8825 14 1 1 2 1 13.9952 15 1 1 1 1 4.5212 16 1 1 0 1 3.0595 17 1 1 1 0 1.1439 18 1 1 0 0 2.6141 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3631 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 889 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.96 2 C002 has 27 9 9 11.26 3 C003 has 2649 883 883 0.00 4 C004 has 858 286 286 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1239 413 413 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1275 425 425 0.00 Total of12766 atoms and 4248 groups and 4243 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3631 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 = 3628 Number of groups = 1202 Number of bonds = 3622 Number of angles = 1306 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1200 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 = 3628 Number of groups = 1202 Number of bonds = 3622 Number of angles = 1306 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1200 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 <- "35.96" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1197" Evaluating: 1197-13 Parameter: NUMWAT <- "1184" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1184" Comparing "1075" and "1184". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.96" Parameter: BOX -> "35.96" Parameter: BOX -> "35.96" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.96000 B = 35.96000 C = 35.96000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8795 2 1 -1 -2 -1 13.9921 3 1 -1 -1 -1 4.5195 4 1 -1 0 -1 3.0594 5 1 0 -1 -1 4.4599 6 1 0 0 -1 4.6301 7 1 -1 -1 0 1.1438 8 1 -1 0 0 2.6131 9 1 0 -1 0 4.5535 10 1 0 1 0 4.5535 11 1 0 0 1 4.6301 12 1 0 1 1 4.4599 13 1 2 1 1 8.8795 14 1 1 2 1 13.9921 15 1 1 1 1 4.5195 16 1 1 0 1 3.0594 17 1 1 1 0 1.1438 18 1 1 0 0 2.6131 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3628 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.96 2 C002 has 24 8 8 11.26 3 C003 has 2646 882 882 0.00 4 C004 has 858 286 286 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1239 413 413 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1275 425 425 0.00 9 C009 has 1272 424 424 0.00 Total of12751 atoms and 4243 groups and 4238 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3628 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3628 Number of groups = 1202 Number of bonds = 3622 Number of angles = 1306 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1200 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 = 3628 Number of groups = 1202 Number of bonds = 3622 Number of angles = 1306 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1200 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 <- "35.958" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1197" Evaluating: 1197-13 Parameter: NUMWAT <- "1184" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1184" Comparing "1075" and "1184". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.958" Parameter: BOX -> "35.958" Parameter: BOX -> "35.958" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.95800 B = 35.95800 C = 35.95800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8765 2 1 -1 -2 -1 13.9891 3 1 -1 -1 -1 4.5179 4 1 -1 0 -1 3.0593 5 1 0 -1 -1 4.4603 6 1 0 0 -1 4.6305 7 1 -1 -1 0 1.1437 8 1 -1 0 0 2.6121 9 1 0 -1 0 4.5536 10 1 0 1 0 4.5536 11 1 0 0 1 4.6305 12 1 0 1 1 4.4603 13 1 2 1 1 8.8765 14 1 1 2 1 13.9891 15 1 1 1 1 4.5179 16 1 1 0 1 3.0593 17 1 1 1 0 1.1437 18 1 1 0 0 2.6121 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3628 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.96 2 C002 has 24 8 8 11.26 3 C003 has 2646 882 882 0.00 4 C004 has 858 286 286 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1239 413 413 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1275 425 425 0.00 9 C009 has 1272 424 424 0.00 Total of12754 atoms and 4244 groups and 4239 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3628 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3628 Number of groups = 1202 Number of bonds = 3622 Number of angles = 1306 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1200 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 = 3628 Number of groups = 1202 Number of bonds = 3622 Number of angles = 1306 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1200 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 <- "35.956" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1197" Evaluating: 1197-13 Parameter: NUMWAT <- "1184" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1184" Comparing "1075" and "1184". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.956" Parameter: BOX -> "35.956" Parameter: BOX -> "35.956" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.95600 B = 35.95600 C = 35.95600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8734 2 1 -1 -2 -1 13.9860 3 1 -1 -1 -1 4.5162 4 1 -1 0 -1 3.0592 5 1 0 -1 -1 4.4606 6 1 0 0 -1 4.6310 7 1 -1 -1 0 1.1436 8 1 -1 0 0 2.6112 9 1 0 -1 0 4.5536 10 1 0 1 0 4.5536 11 1 0 0 1 4.6310 12 1 0 1 1 4.4606 13 1 2 1 1 8.8734 14 1 1 2 1 13.9860 15 1 1 1 1 4.5162 16 1 1 0 1 3.0592 17 1 1 1 0 1.1436 18 1 1 0 0 2.6112 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3628 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 509 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 162 54 54 6.95 2 C002 has 24 8 8 11.26 3 C003 has 2646 882 882 0.00 4 C004 has 858 286 286 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1242 414 414 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1275 425 425 0.00 Total of12754 atoms and 4244 groups and 4239 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3628 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 = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.954" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.954" Parameter: BOX -> "35.954" Parameter: BOX -> "35.954" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.95400 B = 35.95400 C = 35.95400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8704 2 1 -1 -2 -1 13.9829 3 1 -1 -1 -1 4.5145 4 1 -1 0 -1 3.0591 5 1 0 -1 -1 4.4610 6 1 0 0 -1 4.6315 7 1 -1 -1 0 1.1436 8 1 -1 0 0 2.6102 9 1 0 -1 0 4.5536 10 1 0 1 0 4.5536 11 1 0 0 1 4.6315 12 1 0 1 1 4.4610 13 1 2 1 1 8.8704 14 1 1 2 1 13.9829 15 1 1 1 1 4.5145 16 1 1 0 1 3.0591 17 1 1 1 0 1.1436 18 1 1 0 0 2.6102 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 162 54 54 6.95 2 C002 has 24 8 8 11.25 3 C003 has 2643 881 881 0.00 4 C004 has 861 287 287 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1242 414 414 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1272 424 424 0.00 Total of12745 atoms and 4241 groups and 4236 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.952" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.952" Parameter: BOX -> "35.952" Parameter: BOX -> "35.952" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.95200 B = 35.95200 C = 35.95200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8674 2 1 -1 -2 -1 13.9798 3 1 -1 -1 -1 4.5128 4 1 -1 0 -1 3.0591 5 1 0 -1 -1 4.4614 6 1 0 0 -1 4.6320 7 1 -1 -1 0 1.1435 8 1 -1 0 0 2.6092 9 1 0 -1 0 4.5536 10 1 0 1 0 4.5536 11 1 0 0 1 4.6320 12 1 0 1 1 4.4614 13 1 2 1 1 8.8674 14 1 1 2 1 13.9798 15 1 1 1 1 4.5128 16 1 1 0 1 3.0591 17 1 1 1 0 1.1435 18 1 1 0 0 2.6092 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 162 54 54 6.95 2 C002 has 24 8 8 11.25 3 C003 has 2643 881 881 0.00 4 C004 has 861 287 287 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1242 414 414 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1272 424 424 0.00 Total of12745 atoms and 4241 groups and 4236 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.95" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.95" Parameter: BOX -> "35.95" Parameter: BOX -> "35.95" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.95000 B = 35.95000 C = 35.95000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8643 2 1 -1 -2 -1 13.9768 3 1 -1 -1 -1 4.5111 4 1 -1 0 -1 3.0590 5 1 0 -1 -1 4.4618 6 1 0 0 -1 4.6324 7 1 -1 -1 0 1.1434 8 1 -1 0 0 2.6083 9 1 0 -1 0 4.5537 10 1 0 1 0 4.5537 11 1 0 0 1 4.6324 12 1 0 1 1 4.4618 13 1 2 1 1 8.8643 14 1 1 2 1 13.9768 15 1 1 1 1 4.5111 16 1 1 0 1 3.0590 17 1 1 1 0 1.1434 18 1 1 0 0 2.6083 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 162 54 54 6.94 2 C002 has 27 9 9 11.25 3 C003 has 2643 881 881 0.00 4 C004 has 861 287 287 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1242 414 414 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1272 424 424 0.00 Total of12748 atoms and 4242 groups and 4237 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.948" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.948" Parameter: BOX -> "35.948" Parameter: BOX -> "35.948" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.94800 B = 35.94800 C = 35.94800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8613 2 1 -1 -2 -1 13.9737 3 1 -1 -1 -1 4.5094 4 1 -1 0 -1 3.0589 5 1 0 -1 -1 4.4622 6 1 0 0 -1 4.6329 7 1 -1 -1 0 1.1434 8 1 -1 0 0 2.6073 9 1 0 -1 0 4.5537 10 1 0 1 0 4.5537 11 1 0 0 1 4.6329 12 1 0 1 1 4.4622 13 1 2 1 1 8.8613 14 1 1 2 1 13.9737 15 1 1 1 1 4.5094 16 1 1 0 1 3.0589 17 1 1 1 0 1.1434 18 1 1 0 0 2.6073 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 162 54 54 6.94 2 C002 has 27 9 9 11.24 3 C003 has 2643 881 881 0.00 4 C004 has 861 287 287 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1242 414 414 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1272 424 424 0.00 Total of12748 atoms and 4242 groups and 4237 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.946" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.946" Parameter: BOX -> "35.946" Parameter: BOX -> "35.946" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.94600 B = 35.94600 C = 35.94600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8583 2 1 -1 -2 -1 13.9706 3 1 -1 -1 -1 4.5077 4 1 -1 0 -1 3.0588 5 1 0 -1 -1 4.4625 6 1 0 0 -1 4.6334 7 1 -1 -1 0 1.1433 8 1 -1 0 0 2.6064 9 1 0 -1 0 4.5537 10 1 0 1 0 4.5537 11 1 0 0 1 4.6334 12 1 0 1 1 4.4625 13 1 2 1 1 8.8583 14 1 1 2 1 13.9706 15 1 1 1 1 4.5077 16 1 1 0 1 3.0588 17 1 1 1 0 1.1433 18 1 1 0 0 2.6064 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 162 54 54 6.94 2 C002 has 27 9 9 11.24 3 C003 has 2643 881 881 0.00 4 C004 has 861 287 287 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1242 414 414 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1272 424 424 0.00 Total of12748 atoms and 4242 groups and 4237 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.944" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.944" Parameter: BOX -> "35.944" Parameter: BOX -> "35.944" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.94400 B = 35.94400 C = 35.94400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8552 2 1 -1 -2 -1 13.9676 3 1 -1 -1 -1 4.5060 4 1 -1 0 -1 3.0587 5 1 0 -1 -1 4.4629 6 1 0 0 -1 4.6339 7 1 -1 -1 0 1.1433 8 1 -1 0 0 2.6054 9 1 0 -1 0 4.5537 10 1 0 1 0 4.5537 11 1 0 0 1 4.6339 12 1 0 1 1 4.4629 13 1 2 1 1 8.8552 14 1 1 2 1 13.9676 15 1 1 1 1 4.5060 16 1 1 0 1 3.0587 17 1 1 1 0 1.1433 18 1 1 0 0 2.6054 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.94 2 C002 has 27 9 9 11.24 3 C003 has 2643 881 881 0.00 4 C004 has 861 287 287 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1242 414 414 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1272 424 424 0.00 Total of12751 atoms and 4243 groups and 4238 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.942" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.942" Parameter: BOX -> "35.942" Parameter: BOX -> "35.942" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.94200 B = 35.94200 C = 35.94200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8522 2 1 -1 -2 -1 13.9645 3 1 -1 -1 -1 4.5043 4 1 -1 0 -1 3.0587 5 1 0 -1 -1 4.4633 6 1 0 0 -1 4.6344 7 1 -1 -1 0 1.1432 8 1 -1 0 0 2.6044 9 1 0 -1 0 4.5538 10 1 0 1 0 4.5538 11 1 0 0 1 4.6344 12 1 0 1 1 4.4633 13 1 2 1 1 8.8522 14 1 1 2 1 13.9645 15 1 1 1 1 4.5043 16 1 1 0 1 3.0587 17 1 1 1 0 1.1432 18 1 1 0 0 2.6044 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.93 2 C002 has 27 9 9 11.23 3 C003 has 2643 881 881 0.00 4 C004 has 861 287 287 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1242 414 414 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1272 424 424 0.00 Total of12751 atoms and 4243 groups and 4238 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.94" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.94" Parameter: BOX -> "35.94" Parameter: BOX -> "35.94" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.94000 B = 35.94000 C = 35.94000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8492 2 1 -1 -2 -1 13.9614 3 1 -1 -1 -1 4.5026 4 1 -1 0 -1 3.0586 5 1 0 -1 -1 4.4637 6 1 0 0 -1 4.6348 7 1 -1 -1 0 1.1432 8 1 -1 0 0 2.6035 9 1 0 -1 0 4.5538 10 1 0 1 0 4.5538 11 1 0 0 1 4.6348 12 1 0 1 1 4.4637 13 1 2 1 1 8.8492 14 1 1 2 1 13.9614 15 1 1 1 1 4.5026 16 1 1 0 1 3.0586 17 1 1 1 0 1.1432 18 1 1 0 0 2.6035 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.93 2 C002 has 27 9 9 11.23 3 C003 has 2643 881 881 0.00 4 C004 has 864 288 288 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1245 415 415 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1272 424 424 0.00 Total of12757 atoms and 4245 groups and 4240 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.938" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.938" Parameter: BOX -> "35.938" Parameter: BOX -> "35.938" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.93800 B = 35.93800 C = 35.93800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8461 2 1 -1 -2 -1 13.9583 3 1 -1 -1 -1 4.5009 4 1 -1 0 -1 3.0585 5 1 0 -1 -1 4.4641 6 1 0 0 -1 4.6353 7 1 -1 -1 0 1.1431 8 1 -1 0 0 2.6025 9 1 0 -1 0 4.5538 10 1 0 1 0 4.5538 11 1 0 0 1 4.6353 12 1 0 1 1 4.4641 13 1 2 1 1 8.8461 14 1 1 2 1 13.9583 15 1 1 1 1 4.5009 16 1 1 0 1 3.0585 17 1 1 1 0 1.1431 18 1 1 0 0 2.6025 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.93 2 C002 has 27 9 9 11.23 3 C003 has 2643 881 881 0.00 4 C004 has 864 288 288 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1245 415 415 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1275 425 425 0.00 Total of12760 atoms and 4246 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> 0 atoms have been selected out of 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.936" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.936" Parameter: BOX -> "35.936" Parameter: BOX -> "35.936" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.93600 B = 35.93600 C = 35.93600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8431 2 1 -1 -2 -1 13.9553 3 1 -1 -1 -1 4.4992 4 1 -1 0 -1 3.0585 5 1 0 -1 -1 4.4645 6 1 0 0 -1 4.6358 7 1 -1 -1 0 1.1431 8 1 -1 0 0 2.6016 9 1 0 -1 0 4.5539 10 1 0 1 0 4.5539 11 1 0 0 1 4.6358 12 1 0 1 1 4.4645 13 1 2 1 1 8.8431 14 1 1 2 1 13.9553 15 1 1 1 1 4.4992 16 1 1 0 1 3.0585 17 1 1 1 0 1.1431 18 1 1 0 0 2.6016 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.92 2 C002 has 27 9 9 11.22 3 C003 has 2643 881 881 0.00 4 C004 has 864 288 288 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1245 415 415 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1275 425 425 0.00 Total of12760 atoms and 4246 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> 0 atoms have been selected out of 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.934" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.934" Parameter: BOX -> "35.934" Parameter: BOX -> "35.934" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.93400 B = 35.93400 C = 35.93400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8400 2 1 -1 -2 -1 13.9522 3 1 -1 -1 -1 4.4975 4 1 -1 0 -1 3.0584 5 1 0 -1 -1 4.4649 6 1 0 0 -1 4.6363 7 1 -1 -1 0 1.1431 8 1 -1 0 0 2.6006 9 1 0 -1 0 4.5539 10 1 0 1 0 4.5539 11 1 0 0 1 4.6363 12 1 0 1 1 4.4649 13 1 2 1 1 8.8400 14 1 1 2 1 13.9522 15 1 1 1 1 4.4975 16 1 1 0 1 3.0584 17 1 1 1 0 1.1431 18 1 1 0 0 2.6006 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.92 2 C002 has 27 9 9 11.22 3 C003 has 2643 881 881 0.00 4 C004 has 864 288 288 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1245 415 415 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1275 425 425 0.00 Total of12760 atoms and 4246 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> 0 atoms have been selected out of 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.932" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.932" Parameter: BOX -> "35.932" Parameter: BOX -> "35.932" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.93200 B = 35.93200 C = 35.93200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8370 2 1 -1 -2 -1 13.9491 3 1 -1 -1 -1 4.4958 4 1 -1 0 -1 3.0583 5 1 0 -1 -1 4.4653 6 1 0 0 -1 4.6368 7 1 -1 -1 0 1.1431 8 1 -1 0 0 2.5996 9 1 0 -1 0 4.5539 10 1 0 1 0 4.5539 11 1 0 0 1 4.6368 12 1 0 1 1 4.4653 13 1 2 1 1 8.8370 14 1 1 2 1 13.9491 15 1 1 1 1 4.4958 16 1 1 0 1 3.0583 17 1 1 1 0 1.1431 18 1 1 0 0 2.5996 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.92 2 C002 has 27 9 9 11.22 3 C003 has 2643 881 881 0.00 4 C004 has 867 289 289 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1245 415 415 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1275 425 425 0.00 Total of12763 atoms and 4247 groups and 4242 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.93" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.93" Parameter: BOX -> "35.93" Parameter: BOX -> "35.93" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.93000 B = 35.93000 C = 35.93000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8340 2 1 -1 -2 -1 13.9461 3 1 -1 -1 -1 4.4941 4 1 -1 0 -1 3.0583 5 1 0 -1 -1 4.4657 6 1 0 0 -1 4.6373 7 1 -1 -1 0 1.1430 8 1 -1 0 0 2.5987 9 1 0 -1 0 4.5540 10 1 0 1 0 4.5540 11 1 0 0 1 4.6373 12 1 0 1 1 4.4657 13 1 2 1 1 8.8340 14 1 1 2 1 13.9461 15 1 1 1 1 4.4941 16 1 1 0 1 3.0583 17 1 1 1 0 1.1430 18 1 1 0 0 2.5987 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.91 2 C002 has 27 9 9 11.22 3 C003 has 2643 881 881 0.00 4 C004 has 867 289 289 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1251 417 417 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1275 425 425 0.00 Total of12769 atoms and 4249 groups and 4244 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.928" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.928" Parameter: BOX -> "35.928" Parameter: BOX -> "35.928" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.92800 B = 35.92800 C = 35.92800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8309 2 1 -1 -2 -1 13.9430 3 1 -1 -1 -1 4.4924 4 1 -1 0 -1 3.0582 5 1 0 -1 -1 4.4661 6 1 0 0 -1 4.6377 7 1 -1 -1 0 1.1430 8 1 -1 0 0 2.5977 9 1 0 -1 0 4.5540 10 1 0 1 0 4.5540 11 1 0 0 1 4.6377 12 1 0 1 1 4.4661 13 1 2 1 1 8.8309 14 1 1 2 1 13.9430 15 1 1 1 1 4.4924 16 1 1 0 1 3.0582 17 1 1 1 0 1.1430 18 1 1 0 0 2.5977 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.91 2 C002 has 27 9 9 11.21 3 C003 has 2643 881 881 0.00 4 C004 has 867 289 289 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1251 417 417 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1278 426 426 0.00 Total of12772 atoms and 4250 groups and 4245 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.926" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.926" Parameter: BOX -> "35.926" Parameter: BOX -> "35.926" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.92600 B = 35.92600 C = 35.92600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8279 2 1 -1 -2 -1 13.9399 3 1 -1 -1 -1 4.4907 4 1 -1 0 -1 3.0582 5 1 0 -1 -1 4.4665 6 1 0 0 -1 4.6382 7 1 -1 -1 0 1.1430 8 1 -1 0 0 2.5968 9 1 0 -1 0 4.5540 10 1 0 1 0 4.5540 11 1 0 0 1 4.6382 12 1 0 1 1 4.4665 13 1 2 1 1 8.8279 14 1 1 2 1 13.9399 15 1 1 1 1 4.4907 16 1 1 0 1 3.0582 17 1 1 1 0 1.1430 18 1 1 0 0 2.5968 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.91 2 C002 has 27 9 9 11.21 3 C003 has 2643 881 881 0.00 4 C004 has 867 289 289 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1251 417 417 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1278 426 426 0.00 Total of12772 atoms and 4250 groups and 4245 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.924" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.924" Parameter: BOX -> "35.924" Parameter: BOX -> "35.924" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.92400 B = 35.92400 C = 35.92400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8249 2 1 -1 -2 -1 13.9369 3 1 -1 -1 -1 4.4890 4 1 -1 0 -1 3.0581 5 1 0 -1 -1 4.4669 6 1 0 0 -1 4.6387 7 1 -1 -1 0 1.1430 8 1 -1 0 0 2.5958 9 1 0 -1 0 4.5541 10 1 0 1 0 4.5541 11 1 0 0 1 4.6387 12 1 0 1 1 4.4669 13 1 2 1 1 8.8249 14 1 1 2 1 13.9369 15 1 1 1 1 4.4890 16 1 1 0 1 3.0581 17 1 1 1 0 1.1430 18 1 1 0 0 2.5958 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.90 2 C002 has 27 9 9 11.21 3 C003 has 2643 881 881 0.00 4 C004 has 867 289 289 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1251 417 417 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1278 426 426 0.00 Total of12772 atoms and 4250 groups and 4245 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.922" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.922" Parameter: BOX -> "35.922" Parameter: BOX -> "35.922" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.92200 B = 35.92200 C = 35.92200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8218 2 1 -1 -2 -1 13.9338 3 1 -1 -1 -1 4.4873 4 1 -1 0 -1 3.0580 5 1 0 -1 -1 4.4673 6 1 0 0 -1 4.6392 7 1 -1 -1 0 1.1430 8 1 -1 0 0 2.5949 9 1 0 -1 0 4.5541 10 1 0 1 0 4.5541 11 1 0 0 1 4.6392 12 1 0 1 1 4.4673 13 1 2 1 1 8.8218 14 1 1 2 1 13.9338 15 1 1 1 1 4.4873 16 1 1 0 1 3.0580 17 1 1 1 0 1.1430 18 1 1 0 0 2.5949 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.90 2 C002 has 27 9 9 11.20 3 C003 has 2643 881 881 0.00 4 C004 has 867 289 289 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1251 417 417 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1281 427 427 0.00 Total of12775 atoms and 4251 groups and 4246 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.92" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.92" Parameter: BOX -> "35.92" Parameter: BOX -> "35.92" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.92000 B = 35.92000 C = 35.92000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8188 2 1 -1 -2 -1 13.9307 3 1 -1 -1 -1 4.4856 4 1 -1 0 -1 3.0580 5 1 0 -1 -1 4.4677 6 1 0 0 -1 4.6397 7 1 -1 -1 0 1.1430 8 1 -1 0 0 2.5939 9 1 0 -1 0 4.5541 10 1 0 1 0 4.5541 11 1 0 0 1 4.6397 12 1 0 1 1 4.4677 13 1 2 1 1 8.8188 14 1 1 2 1 13.9307 15 1 1 1 1 4.4856 16 1 1 0 1 3.0580 17 1 1 1 0 1.1430 18 1 1 0 0 2.5939 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.90 2 C002 has 27 9 9 11.20 3 C003 has 2643 881 881 0.00 4 C004 has 870 290 290 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1251 417 417 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1281 427 427 0.00 Total of12781 atoms and 4253 groups and 4248 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.918" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.918" Parameter: BOX -> "35.918" Parameter: BOX -> "35.918" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.91800 B = 35.91800 C = 35.91800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8158 2 1 -1 -2 -1 13.9276 3 1 -1 -1 -1 4.4839 4 1 -1 0 -1 3.0579 5 1 0 -1 -1 4.4681 6 1 0 0 -1 4.6402 7 1 -1 -1 0 1.1430 8 1 -1 0 0 2.5930 9 1 0 -1 0 4.5542 10 1 0 1 0 4.5542 11 1 0 0 1 4.6402 12 1 0 1 1 4.4681 13 1 2 1 1 8.8158 14 1 1 2 1 13.9276 15 1 1 1 1 4.4839 16 1 1 0 1 3.0579 17 1 1 1 0 1.1430 18 1 1 0 0 2.5930 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.90 2 C002 has 27 9 9 11.20 3 C003 has 2646 882 882 0.00 4 C004 has 870 290 290 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1251 417 417 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1275 425 425 0.00 9 C009 has 1281 427 427 0.00 Total of12787 atoms and 4255 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 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.916" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.916" Parameter: BOX -> "35.916" Parameter: BOX -> "35.916" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.91600 B = 35.91600 C = 35.91600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8128 2 1 -1 -2 -1 13.9246 3 1 -1 -1 -1 4.4822 4 1 -1 0 -1 3.0579 5 1 0 -1 -1 4.4685 6 1 0 0 -1 4.6407 7 1 -1 -1 0 1.1430 8 1 -1 0 0 2.5921 9 1 0 -1 0 4.5542 10 1 0 1 0 4.5542 11 1 0 0 1 4.6407 12 1 0 1 1 4.4685 13 1 2 1 1 8.8128 14 1 1 2 1 13.9246 15 1 1 1 1 4.4822 16 1 1 0 1 3.0579 17 1 1 1 0 1.1430 18 1 1 0 0 2.5921 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.89 2 C002 has 27 9 9 11.19 3 C003 has 2646 882 882 0.00 4 C004 has 870 290 290 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1251 417 417 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1275 425 425 0.00 9 C009 has 1281 427 427 0.00 Total of12787 atoms and 4255 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 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.914" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.914" Parameter: BOX -> "35.914" Parameter: BOX -> "35.914" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.91400 B = 35.91400 C = 35.91400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8097 2 1 -1 -2 -1 13.9215 3 1 -1 -1 -1 4.4806 4 1 -1 0 -1 3.0578 5 1 0 -1 -1 4.4689 6 1 0 0 -1 4.6412 7 1 -1 -1 0 1.1430 8 1 -1 0 0 2.5911 9 1 0 -1 0 4.5543 10 1 0 1 0 4.5543 11 1 0 0 1 4.6412 12 1 0 1 1 4.4689 13 1 2 1 1 8.8097 14 1 1 2 1 13.9215 15 1 1 1 1 4.4806 16 1 1 0 1 3.0578 17 1 1 1 0 1.1430 18 1 1 0 0 2.5911 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.89 2 C002 has 27 9 9 11.19 3 C003 has 2646 882 882 0.00 4 C004 has 870 290 290 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1251 417 417 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1275 425 425 0.00 9 C009 has 1281 427 427 0.00 Total of12787 atoms and 4255 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 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.912" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.912" Parameter: BOX -> "35.912" Parameter: BOX -> "35.912" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.91200 B = 35.91200 C = 35.91200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8067 2 1 -1 -2 -1 13.9184 3 1 -1 -1 -1 4.4789 4 1 -1 0 -1 3.0578 5 1 0 -1 -1 4.4693 6 1 0 0 -1 4.6417 7 1 -1 -1 0 1.1431 8 1 -1 0 0 2.5902 9 1 0 -1 0 4.5543 10 1 0 1 0 4.5543 11 1 0 0 1 4.6417 12 1 0 1 1 4.4693 13 1 2 1 1 8.8067 14 1 1 2 1 13.9184 15 1 1 1 1 4.4789 16 1 1 0 1 3.0578 17 1 1 1 0 1.1431 18 1 1 0 0 2.5902 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.89 2 C002 has 27 9 9 11.19 3 C003 has 2646 882 882 0.00 4 C004 has 870 290 290 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1251 417 417 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1275 425 425 0.00 9 C009 has 1281 427 427 0.00 Total of12787 atoms and 4255 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 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.91" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.91" Parameter: BOX -> "35.91" Parameter: BOX -> "35.91" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.91000 B = 35.91000 C = 35.91000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8037 2 1 -1 -2 -1 13.9154 3 1 -1 -1 -1 4.4772 4 1 -1 0 -1 3.0578 5 1 0 -1 -1 4.4697 6 1 0 0 -1 4.6421 7 1 -1 -1 0 1.1431 8 1 -1 0 0 2.5892 9 1 0 -1 0 4.5544 10 1 0 1 0 4.5544 11 1 0 0 1 4.6421 12 1 0 1 1 4.4697 13 1 2 1 1 8.8037 14 1 1 2 1 13.9154 15 1 1 1 1 4.4772 16 1 1 0 1 3.0578 17 1 1 1 0 1.1431 18 1 1 0 0 2.5892 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.88 2 C002 has 27 9 9 11.18 3 C003 has 2646 882 882 0.00 4 C004 has 870 290 290 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1251 417 417 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1275 425 425 0.00 9 C009 has 1281 427 427 0.00 Total of12787 atoms and 4255 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 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.908" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.908" Parameter: BOX -> "35.908" Parameter: BOX -> "35.908" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.90800 B = 35.90800 C = 35.90800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8006 2 1 -1 -2 -1 13.9123 3 1 -1 -1 -1 4.4755 4 1 -1 0 -1 3.0577 5 1 0 -1 -1 4.4701 6 1 0 0 -1 4.6426 7 1 -1 -1 0 1.1431 8 1 -1 0 0 2.5883 9 1 0 -1 0 4.5544 10 1 0 1 0 4.5544 11 1 0 0 1 4.6426 12 1 0 1 1 4.4701 13 1 2 1 1 8.8006 14 1 1 2 1 13.9123 15 1 1 1 1 4.4755 16 1 1 0 1 3.0577 17 1 1 1 0 1.1431 18 1 1 0 0 2.5883 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.88 2 C002 has 27 9 9 11.18 3 C003 has 2646 882 882 0.00 4 C004 has 873 291 291 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1251 417 417 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1275 425 425 0.00 9 C009 has 1281 427 427 0.00 Total of12793 atoms and 4257 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 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.906" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.906" Parameter: BOX -> "35.906" Parameter: BOX -> "35.906" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.90600 B = 35.90600 C = 35.90600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7976 2 1 -1 -2 -1 13.9092 3 1 -1 -1 -1 4.4738 4 1 -1 0 -1 3.0577 5 1 0 -1 -1 4.4705 6 1 0 0 -1 4.6431 7 1 -1 -1 0 1.1432 8 1 -1 0 0 2.5874 9 1 0 -1 0 4.5544 10 1 0 1 0 4.5544 11 1 0 0 1 4.6431 12 1 0 1 1 4.4705 13 1 2 1 1 8.7976 14 1 1 2 1 13.9092 15 1 1 1 1 4.4738 16 1 1 0 1 3.0577 17 1 1 1 0 1.1432 18 1 1 0 0 2.5874 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.88 2 C002 has 27 9 9 11.18 3 C003 has 2646 882 882 0.00 4 C004 has 873 291 291 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1251 417 417 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1275 425 425 0.00 9 C009 has 1281 427 427 0.00 Total of12796 atoms and 4258 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 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.904" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.904" Parameter: BOX -> "35.904" Parameter: BOX -> "35.904" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.90400 B = 35.90400 C = 35.90400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7946 2 1 -1 -2 -1 13.9061 3 1 -1 -1 -1 4.4721 4 1 -1 0 -1 3.0576 5 1 0 -1 -1 4.4709 6 1 0 0 -1 4.6436 7 1 -1 -1 0 1.1432 8 1 -1 0 0 2.5864 9 1 0 -1 0 4.5545 10 1 0 1 0 4.5545 11 1 0 0 1 4.6436 12 1 0 1 1 4.4709 13 1 2 1 1 8.7946 14 1 1 2 1 13.9061 15 1 1 1 1 4.4721 16 1 1 0 1 3.0576 17 1 1 1 0 1.1432 18 1 1 0 0 2.5864 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.87 2 C002 has 27 9 9 11.18 3 C003 has 2646 882 882 0.00 4 C004 has 876 292 292 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1251 417 417 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1275 425 425 0.00 9 C009 has 1281 427 427 0.00 Total of12802 atoms and 4260 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 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.902" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.902" Parameter: BOX -> "35.902" Parameter: BOX -> "35.902" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.90200 B = 35.90200 C = 35.90200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7915 2 1 -1 -2 -1 13.9031 3 1 -1 -1 -1 4.4704 4 1 -1 0 -1 3.0576 5 1 0 -1 -1 4.4713 6 1 0 0 -1 4.6441 7 1 -1 -1 0 1.1433 8 1 -1 0 0 2.5855 9 1 0 -1 0 4.5545 10 1 0 1 0 4.5545 11 1 0 0 1 4.6441 12 1 0 1 1 4.4713 13 1 2 1 1 8.7915 14 1 1 2 1 13.9031 15 1 1 1 1 4.4704 16 1 1 0 1 3.0576 17 1 1 1 0 1.1433 18 1 1 0 0 2.5855 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.87 2 C002 has 27 9 9 11.17 3 C003 has 2646 882 882 0.00 4 C004 has 876 292 292 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1251 417 417 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1275 425 425 0.00 9 C009 has 1281 427 427 0.00 Total of12802 atoms and 4260 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 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.9" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.9" Parameter: BOX -> "35.9" Parameter: BOX -> "35.9" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.90000 B = 35.90000 C = 35.90000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7885 2 1 -1 -2 -1 13.9000 3 1 -1 -1 -1 4.4687 4 1 -1 0 -1 3.0576 5 1 0 -1 -1 4.4717 6 1 0 0 -1 4.6446 7 1 -1 -1 0 1.1433 8 1 -1 0 0 2.5845 9 1 0 -1 0 4.5546 10 1 0 1 0 4.5546 11 1 0 0 1 4.6446 12 1 0 1 1 4.4717 13 1 2 1 1 8.7885 14 1 1 2 1 13.9000 15 1 1 1 1 4.4687 16 1 1 0 1 3.0576 17 1 1 1 0 1.1433 18 1 1 0 0 2.5845 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.87 2 C002 has 27 9 9 11.17 3 C003 has 2646 882 882 0.00 4 C004 has 876 292 292 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1251 417 417 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1275 425 425 0.00 9 C009 has 1281 427 427 0.00 Total of12802 atoms and 4260 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 3625 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1196 Number of atoms = 3625 Number of groups = 1201 Number of bonds = 3619 Number of angles = 1305 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1199 Number of HB donors = 2374 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.898" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1196" Evaluating: 1196-13 Parameter: NUMWAT <- "1183" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1183" Comparing "1075" and "1183". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.898" Parameter: BOX -> "35.898" Parameter: BOX -> "35.898" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.89800 B = 35.89800 C = 35.89800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7855 2 1 -1 -2 -1 13.8969 3 1 -1 -1 -1 4.4670 4 1 -1 0 -1 3.0575 5 1 0 -1 -1 4.4721 6 1 0 0 -1 4.6451 7 1 -1 -1 0 1.1434 8 1 -1 0 0 2.5836 9 1 0 -1 0 4.5546 10 1 0 1 0 4.5546 11 1 0 0 1 4.6451 12 1 0 1 1 4.4721 13 1 2 1 1 8.7855 14 1 1 2 1 13.8969 15 1 1 1 1 4.4670 16 1 1 0 1 3.0575 17 1 1 1 0 1.1434 18 1 1 0 0 2.5836 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3549 atoms have been selected out of 3625 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 307 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 162 54 54 6.86 2 C002 has 27 9 9 11.17 3 C003 has 2646 882 882 0.00 4 C004 has 876 292 292 0.00 5 C005 has 840 280 280 0.00 6 C006 has 1254 418 418 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1278 426 426 0.00 9 C009 has 1281 427 427 0.00 Total of12808 atoms and 4262 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> 3 atoms have been selected out of 3625 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 = 1195 Number of atoms = 3622 Number of groups = 1200 Number of bonds = 3616 Number of angles = 1304 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1198 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 = 3622 Number of groups = 1200 Number of bonds = 3616 Number of angles = 1304 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1198 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 <- "35.896" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1195" Evaluating: 1195-13 Parameter: NUMWAT <- "1182" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1182" Comparing "1075" and "1182". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.896" Parameter: BOX -> "35.896" Parameter: BOX -> "35.896" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.89600 B = 35.89600 C = 35.89600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7824 2 1 -1 -2 -1 13.8939 3 1 -1 -1 -1 4.4653 4 1 -1 0 -1 3.0575 5 1 0 -1 -1 4.4726 6 1 0 0 -1 4.6456 7 1 -1 -1 0 1.1434 8 1 -1 0 0 2.5827 9 1 0 -1 0 4.5547 10 1 0 1 0 4.5547 11 1 0 0 1 4.6456 12 1 0 1 1 4.4726 13 1 2 1 1 8.7824 14 1 1 2 1 13.8939 15 1 1 1 1 4.4653 16 1 1 0 1 3.0575 17 1 1 1 0 1.1434 18 1 1 0 0 2.5827 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3622 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 162 54 54 6.86 2 C002 has 27 9 9 11.16 3 C003 has 2643 881 881 0.00 4 C004 has 876 292 292 0.00 5 C005 has 840 280 280 0.00 6 C006 has 1251 417 417 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1281 427 427 0.00 Total of12793 atoms and 4257 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 3622 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3622 Number of groups = 1200 Number of bonds = 3616 Number of angles = 1304 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1198 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 = 3622 Number of groups = 1200 Number of bonds = 3616 Number of angles = 1304 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1198 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 <- "35.894" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1195" Evaluating: 1195-13 Parameter: NUMWAT <- "1182" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1182" Comparing "1075" and "1182". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.894" Parameter: BOX -> "35.894" Parameter: BOX -> "35.894" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.89400 B = 35.89400 C = 35.89400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7794 2 1 -1 -2 -1 13.8908 3 1 -1 -1 -1 4.4636 4 1 -1 0 -1 3.0575 5 1 0 -1 -1 4.4730 6 1 0 0 -1 4.6461 7 1 -1 -1 0 1.1435 8 1 -1 0 0 2.5817 9 1 0 -1 0 4.5547 10 1 0 1 0 4.5547 11 1 0 0 1 4.6461 12 1 0 1 1 4.4730 13 1 2 1 1 8.7794 14 1 1 2 1 13.8908 15 1 1 1 1 4.4636 16 1 1 0 1 3.0575 17 1 1 1 0 1.1435 18 1 1 0 0 2.5817 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3622 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 133 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 162 54 54 6.86 2 C002 has 27 9 9 11.16 3 C003 has 2652 884 884 0.00 4 C004 has 876 292 292 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1251 417 417 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1281 427 427 0.00 Total of12805 atoms and 4261 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> 3 atoms have been selected out of 3622 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 = 3619 Number of groups = 1199 Number of bonds = 3613 Number of angles = 1303 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1197 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 = 3619 Number of groups = 1199 Number of bonds = 3613 Number of angles = 1303 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1197 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 <- "35.892" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1194" Evaluating: 1194-13 Parameter: NUMWAT <- "1181" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1181" Comparing "1075" and "1181". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.892" Parameter: BOX -> "35.892" Parameter: BOX -> "35.892" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.89200 B = 35.89200 C = 35.89200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7764 2 1 -1 -2 -1 13.8877 3 1 -1 -1 -1 4.1803 4 1 -1 0 -1 3.0574 5 1 0 -1 -1 4.4734 6 1 0 0 -1 4.6466 7 1 -1 -1 0 1.1436 8 1 -1 0 0 2.5808 9 1 0 -1 0 2.8999 10 1 0 1 0 2.8999 11 1 0 0 1 4.6466 12 1 0 1 1 4.4734 13 1 2 1 1 8.7764 14 1 1 2 1 13.8877 15 1 1 1 1 4.1803 16 1 1 0 1 3.0574 17 1 1 1 0 1.1436 18 1 1 0 0 2.5808 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3619 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 162 54 54 6.86 2 C002 has 27 9 9 11.16 3 C003 has 2649 883 883 0.00 4 C004 has 876 292 292 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1251 417 417 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1278 426 426 0.00 Total of12796 atoms and 4258 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 3619 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3619 Number of groups = 1199 Number of bonds = 3613 Number of angles = 1303 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1197 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 = 3619 Number of groups = 1199 Number of bonds = 3613 Number of angles = 1303 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1197 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 <- "35.89" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1194" Evaluating: 1194-13 Parameter: NUMWAT <- "1181" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1181" Comparing "1075" and "1181". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.89" Parameter: BOX -> "35.89" Parameter: BOX -> "35.89" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.89000 B = 35.89000 C = 35.89000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7733 2 1 -1 -2 -1 13.8847 3 1 -1 -1 -1 4.1800 4 1 -1 0 -1 3.0574 5 1 0 -1 -1 4.4738 6 1 0 0 -1 4.6471 7 1 -1 -1 0 1.1436 8 1 -1 0 0 2.5799 9 1 0 -1 0 2.8982 10 1 0 1 0 2.8982 11 1 0 0 1 4.6471 12 1 0 1 1 4.4738 13 1 2 1 1 8.7733 14 1 1 2 1 13.8847 15 1 1 1 1 4.1800 16 1 1 0 1 3.0574 17 1 1 1 0 1.1436 18 1 1 0 0 2.5799 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3619 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 C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 162 54 54 6.85 2 C002 has 27 9 9 11.15 3 C003 has 2652 884 884 0.00 4 C004 has 873 291 291 0.00 5 C005 has 846 282 282 0.00 6 C006 has 1248 416 416 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1272 424 424 0.00 Total of12790 atoms and 4256 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> 3 atoms have been selected out of 3619 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 = 1193 Number of atoms = 3616 Number of groups = 1198 Number of bonds = 3610 Number of angles = 1302 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1196 Number of HB donors = 2368 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1193 Number of atoms = 3616 Number of groups = 1198 Number of bonds = 3610 Number of angles = 1302 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1196 Number of HB donors = 2368 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.888" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1193" Evaluating: 1193-13 Parameter: NUMWAT <- "1180" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1180" Comparing "1075" and "1180". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.888" Parameter: BOX -> "35.888" Parameter: BOX -> "35.888" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.88800 B = 35.88800 C = 35.88800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7703 2 1 -1 -2 -1 13.8816 3 1 -1 -1 -1 4.1796 4 1 -1 0 -1 3.0574 5 1 0 -1 -1 4.4742 6 1 0 0 -1 4.6476 7 1 -1 -1 0 1.1437 8 1 -1 0 0 2.5790 9 1 0 -1 0 2.8966 10 1 0 1 0 2.8966 11 1 0 0 1 4.6476 12 1 0 1 1 4.4742 13 1 2 1 1 8.7703 14 1 1 2 1 13.8816 15 1 1 1 1 4.1796 16 1 1 0 1 3.0574 17 1 1 1 0 1.1437 18 1 1 0 0 2.5790 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3540 atoms have been selected out of 3616 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 279 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 162 54 54 6.85 2 C002 has 27 9 9 11.15 3 C003 has 2652 884 884 0.00 4 C004 has 876 292 292 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1233 411 411 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1269 423 423 0.00 9 C009 has 1269 423 423 0.00 Total of12766 atoms and 4248 groups and 4243 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3616 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 = 1192 Number of atoms = 3613 Number of groups = 1197 Number of bonds = 3607 Number of angles = 1301 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1195 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 = 3613 Number of groups = 1197 Number of bonds = 3607 Number of angles = 1301 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1195 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 <- "35.886" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1192" Evaluating: 1192-13 Parameter: NUMWAT <- "1179" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1179" Comparing "1075" and "1179". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.886" Parameter: BOX -> "35.886" Parameter: BOX -> "35.886" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.88600 B = 35.88600 C = 35.88600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7673 2 1 -1 -2 -1 13.8785 3 1 -1 -1 -1 4.1793 4 1 -1 0 -1 3.0574 5 1 0 -1 -1 4.4746 6 1 0 0 -1 4.6481 7 1 -1 -1 0 1.1438 8 1 -1 0 0 2.5780 9 1 0 -1 0 2.8949 10 1 0 1 0 2.8949 11 1 0 0 1 4.6481 12 1 0 1 1 4.4746 13 1 2 1 1 8.7673 14 1 1 2 1 13.8785 15 1 1 1 1 4.1793 16 1 1 0 1 3.0574 17 1 1 1 0 1.1438 18 1 1 0 0 2.5780 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3613 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 421 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 162 54 54 6.85 2 C002 has 27 9 9 11.15 3 C003 has 2655 885 885 0.00 4 C004 has 870 290 290 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1233 411 411 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1266 422 422 0.00 Total of12754 atoms and 4244 groups and 4239 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3613 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 = 1191 Number of atoms = 3610 Number of groups = 1196 Number of bonds = 3604 Number of angles = 1300 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1194 Number of HB donors = 2364 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1191 Number of atoms = 3610 Number of groups = 1196 Number of bonds = 3604 Number of angles = 1300 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1194 Number of HB donors = 2364 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.884" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1191" Evaluating: 1191-13 Parameter: NUMWAT <- "1178" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1178" Comparing "1075" and "1178". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.884" Parameter: BOX -> "35.884" Parameter: BOX -> "35.884" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.88400 B = 35.88400 C = 35.88400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7643 2 1 -1 -2 -1 13.8755 3 1 -1 -1 -1 4.1790 4 1 -1 0 -1 3.0573 5 1 0 -1 -1 4.4751 6 1 0 0 -1 4.6486 7 1 -1 -1 0 1.1439 8 1 -1 0 0 2.5771 9 1 0 -1 0 2.8933 10 1 0 1 0 2.8933 11 1 0 0 1 4.6486 12 1 0 1 1 4.4751 13 1 2 1 1 8.7643 14 1 1 2 1 13.8755 15 1 1 1 1 4.1790 16 1 1 0 1 3.0573 17 1 1 1 0 1.1439 18 1 1 0 0 2.5771 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3534 atoms have been selected out of 3610 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 162 54 54 6.84 2 C002 has 27 9 9 11.14 3 C003 has 2652 884 884 0.00 4 C004 has 867 289 289 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1230 410 410 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1269 423 423 0.00 9 C009 has 1266 422 422 0.00 Total of12739 atoms and 4239 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 3610 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1191 Number of atoms = 3610 Number of groups = 1196 Number of bonds = 3604 Number of angles = 1300 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1194 Number of HB donors = 2364 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1191 Number of atoms = 3610 Number of groups = 1196 Number of bonds = 3604 Number of angles = 1300 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1194 Number of HB donors = 2364 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.882" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1191" Evaluating: 1191-13 Parameter: NUMWAT <- "1178" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1178" Comparing "1075" and "1178". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.882" Parameter: BOX -> "35.882" Parameter: BOX -> "35.882" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.88200 B = 35.88200 C = 35.88200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7612 2 1 -1 -2 -1 13.8724 3 1 -1 -1 -1 4.1787 4 1 -1 0 -1 3.0573 5 1 0 -1 -1 4.4755 6 1 0 0 -1 4.6491 7 1 -1 -1 0 1.1440 8 1 -1 0 0 2.5762 9 1 0 -1 0 2.8916 10 1 0 1 0 2.8916 11 1 0 0 1 4.6491 12 1 0 1 1 4.4755 13 1 2 1 1 8.7612 14 1 1 2 1 13.8724 15 1 1 1 1 4.1787 16 1 1 0 1 3.0573 17 1 1 1 0 1.1440 18 1 1 0 0 2.5762 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3534 atoms have been selected out of 3610 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 162 54 54 6.84 2 C002 has 27 9 9 11.14 3 C003 has 2652 884 884 0.00 4 C004 has 867 289 289 0.00 5 C005 has 840 280 280 0.00 6 C006 has 1230 410 410 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1269 423 423 0.00 9 C009 has 1266 422 422 0.00 Total of12742 atoms and 4240 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 3610 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1191 Number of atoms = 3610 Number of groups = 1196 Number of bonds = 3604 Number of angles = 1300 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1194 Number of HB donors = 2364 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1191 Number of atoms = 3610 Number of groups = 1196 Number of bonds = 3604 Number of angles = 1300 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1194 Number of HB donors = 2364 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.88" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1191" Evaluating: 1191-13 Parameter: NUMWAT <- "1178" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1178" Comparing "1075" and "1178". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.88" Parameter: BOX -> "35.88" Parameter: BOX -> "35.88" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.88000 B = 35.88000 C = 35.88000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7582 2 1 -1 -2 -1 13.8693 3 1 -1 -1 -1 4.1783 4 1 -1 0 -1 3.0573 5 1 0 -1 -1 4.4759 6 1 0 0 -1 4.6496 7 1 -1 -1 0 1.1441 8 1 -1 0 0 2.5753 9 1 0 -1 0 2.8900 10 1 0 1 0 2.8900 11 1 0 0 1 4.6496 12 1 0 1 1 4.4759 13 1 2 1 1 8.7582 14 1 1 2 1 13.8693 15 1 1 1 1 4.1783 16 1 1 0 1 3.0573 17 1 1 1 0 1.1441 18 1 1 0 0 2.5753 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3534 atoms have been selected out of 3610 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 123 OPERATED ON BY TRANSFORMATION C015 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 162 54 54 6.84 2 C002 has 27 9 9 11.14 3 C003 has 2655 885 885 0.00 4 C004 has 867 289 289 0.00 5 C005 has 840 280 280 0.00 6 C006 has 1227 409 409 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1269 423 423 0.00 Total of12754 atoms and 4244 groups and 4239 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3610 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 = 1190 Number of atoms = 3607 Number of groups = 1195 Number of bonds = 3601 Number of angles = 1299 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1193 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 = 3607 Number of groups = 1195 Number of bonds = 3601 Number of angles = 1299 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1193 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 <- "35.878" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1190" Evaluating: 1190-13 Parameter: NUMWAT <- "1177" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1177" Comparing "1075" and "1177". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.878" Parameter: BOX -> "35.878" Parameter: BOX -> "35.878" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.87800 B = 35.87800 C = 35.87800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7552 2 1 -1 -2 -1 13.8662 3 1 -1 -1 -1 4.1780 4 1 -1 0 -1 3.0573 5 1 0 -1 -1 4.4763 6 1 0 0 -1 4.6501 7 1 -1 -1 0 1.1442 8 1 -1 0 0 2.5743 9 1 0 -1 0 2.8884 10 1 0 1 0 2.8884 11 1 0 0 1 4.6501 12 1 0 1 1 4.4763 13 1 2 1 1 8.7552 14 1 1 2 1 13.8662 15 1 1 1 1 4.1780 16 1 1 0 1 3.0573 17 1 1 1 0 1.1442 18 1 1 0 0 2.5743 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3607 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 707 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1146 OPERATED ON BY TRANSFORMATION C003 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.83 2 C002 has 27 9 9 11.14 3 C003 has 2646 882 882 0.00 4 C004 has 861 287 287 0.00 5 C005 has 840 280 280 0.00 6 C006 has 1230 410 410 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1263 421 421 0.00 Total of12727 atoms and 4235 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> 6 atoms have been selected out of 3607 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 = 3601 Number of groups = 1193 Number of bonds = 3595 Number of angles = 1297 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1191 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 = 3601 Number of groups = 1193 Number of bonds = 3595 Number of angles = 1297 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1191 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 <- "35.876" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1188" Evaluating: 1188-13 Parameter: NUMWAT <- "1175" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1175" Comparing "1075" and "1175". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.876" Parameter: BOX -> "35.876" Parameter: BOX -> "35.876" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.87600 B = 35.87600 C = 35.87600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7521 2 1 -1 -2 -1 13.8632 3 1 -1 -1 -1 4.1777 4 1 -1 0 -1 3.0573 5 1 0 -1 -1 4.4768 6 1 0 0 -1 4.6506 7 1 -1 -1 0 1.1443 8 1 -1 0 0 2.5734 9 1 0 -1 0 2.8867 10 1 0 1 0 2.8867 11 1 0 0 1 4.6506 12 1 0 1 1 4.4768 13 1 2 1 1 8.7521 14 1 1 2 1 13.8632 15 1 1 1 1 4.1777 16 1 1 0 1 3.0573 17 1 1 1 0 1.1443 18 1 1 0 0 2.5734 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3601 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.83 2 C002 has 27 9 9 11.13 3 C003 has 2646 882 882 0.00 4 C004 has 861 287 287 0.00 5 C005 has 840 280 280 0.00 6 C006 has 1224 408 408 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1266 422 422 0.00 9 C009 has 1263 421 421 0.00 Total of12709 atoms and 4229 groups and 4224 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3601 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3601 Number of groups = 1193 Number of bonds = 3595 Number of angles = 1297 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1191 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 = 3601 Number of groups = 1193 Number of bonds = 3595 Number of angles = 1297 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1191 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 <- "35.874" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1188" Evaluating: 1188-13 Parameter: NUMWAT <- "1175" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1175" Comparing "1075" and "1175". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.874" Parameter: BOX -> "35.874" Parameter: BOX -> "35.874" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.87400 B = 35.87400 C = 35.87400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7491 2 1 -1 -2 -1 13.8601 3 1 -1 -1 -1 4.1773 4 1 -1 0 -1 3.0572 5 1 0 -1 -1 4.4772 6 1 0 0 -1 4.6512 7 1 -1 -1 0 1.1444 8 1 -1 0 0 2.5725 9 1 0 -1 0 2.8851 10 1 0 1 0 2.8851 11 1 0 0 1 4.6512 12 1 0 1 1 4.4772 13 1 2 1 1 8.7491 14 1 1 2 1 13.8601 15 1 1 1 1 4.1773 16 1 1 0 1 3.0572 17 1 1 1 0 1.1444 18 1 1 0 0 2.5725 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3601 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.83 2 C002 has 27 9 9 11.13 3 C003 has 2646 882 882 0.00 4 C004 has 861 287 287 0.00 5 C005 has 840 280 280 0.00 6 C006 has 1224 408 408 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1266 422 422 0.00 9 C009 has 1263 421 421 0.00 Total of12709 atoms and 4229 groups and 4224 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3601 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3601 Number of groups = 1193 Number of bonds = 3595 Number of angles = 1297 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1191 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 = 3601 Number of groups = 1193 Number of bonds = 3595 Number of angles = 1297 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1191 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 <- "35.872" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1188" Evaluating: 1188-13 Parameter: NUMWAT <- "1175" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1175" Comparing "1075" and "1175". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.872" Parameter: BOX -> "35.872" Parameter: BOX -> "35.872" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.87200 B = 35.87200 C = 35.87200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7461 2 1 -1 -2 -1 13.8570 3 1 -1 -1 -1 4.1770 4 1 -1 0 -1 3.0572 5 1 0 -1 -1 4.4776 6 1 0 0 -1 4.6517 7 1 -1 -1 0 1.1445 8 1 -1 0 0 2.5716 9 1 0 -1 0 2.8834 10 1 0 1 0 2.8834 11 1 0 0 1 4.6517 12 1 0 1 1 4.4776 13 1 2 1 1 8.7461 14 1 1 2 1 13.8570 15 1 1 1 1 4.1770 16 1 1 0 1 3.0572 17 1 1 1 0 1.1445 18 1 1 0 0 2.5716 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3601 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.82 2 C002 has 27 9 9 11.13 3 C003 has 2646 882 882 0.00 4 C004 has 861 287 287 0.00 5 C005 has 840 280 280 0.00 6 C006 has 1224 408 408 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1266 422 422 0.00 9 C009 has 1263 421 421 0.00 Total of12709 atoms and 4229 groups and 4224 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3601 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3601 Number of groups = 1193 Number of bonds = 3595 Number of angles = 1297 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1191 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 = 3601 Number of groups = 1193 Number of bonds = 3595 Number of angles = 1297 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1191 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 <- "35.87" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1188" Evaluating: 1188-13 Parameter: NUMWAT <- "1175" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1175" Comparing "1075" and "1175". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.87" Parameter: BOX -> "35.87" Parameter: BOX -> "35.87" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.87000 B = 35.87000 C = 35.87000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7431 2 1 -1 -2 -1 13.8540 3 1 -1 -1 -1 4.1767 4 1 -1 0 -1 3.0572 5 1 0 -1 -1 4.4780 6 1 0 0 -1 4.6522 7 1 -1 -1 0 1.1446 8 1 -1 0 0 2.5707 9 1 0 -1 0 2.8818 10 1 0 1 0 2.8818 11 1 0 0 1 4.6522 12 1 0 1 1 4.4780 13 1 2 1 1 8.7431 14 1 1 2 1 13.8540 15 1 1 1 1 4.1767 16 1 1 0 1 3.0572 17 1 1 1 0 1.1446 18 1 1 0 0 2.5707 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3601 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 252 OPERATED ON BY TRANSFORMATION C012 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.82 2 C002 has 27 9 9 11.12 3 C003 has 2652 884 884 0.00 4 C004 has 864 288 288 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1227 409 409 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1263 421 421 0.00 9 C009 has 1266 422 422 0.00 Total of12712 atoms and 4230 groups and 4225 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3601 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 = 3598 Number of groups = 1192 Number of bonds = 3592 Number of angles = 1296 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1190 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 = 3598 Number of groups = 1192 Number of bonds = 3592 Number of angles = 1296 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1190 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 <- "35.868" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1187" Evaluating: 1187-13 Parameter: NUMWAT <- "1174" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1174" Comparing "1075" and "1174". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.868" Parameter: BOX -> "35.868" Parameter: BOX -> "35.868" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.86800 B = 35.86800 C = 35.86800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7400 2 1 -1 -2 -1 13.8509 3 1 -1 -1 -1 4.1764 4 1 -1 0 -1 3.0572 5 1 0 -1 -1 4.4785 6 1 0 0 -1 4.6527 7 1 -1 -1 0 1.1448 8 1 -1 0 0 2.5697 9 1 0 -1 0 2.8802 10 1 0 1 0 2.8802 11 1 0 0 1 4.6527 12 1 0 1 1 4.4785 13 1 2 1 1 8.7400 14 1 1 2 1 13.8509 15 1 1 1 1 4.1764 16 1 1 0 1 3.0572 17 1 1 1 0 1.1448 18 1 1 0 0 2.5697 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3598 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.82 2 C002 has 27 9 9 11.12 3 C003 has 2649 883 883 0.00 4 C004 has 864 288 288 0.00 5 C005 has 828 276 276 0.00 6 C006 has 1224 408 408 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1263 421 421 0.00 9 C009 has 1263 421 421 0.00 Total of12697 atoms and 4225 groups and 4220 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3598 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3598 Number of groups = 1192 Number of bonds = 3592 Number of angles = 1296 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1190 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 = 3598 Number of groups = 1192 Number of bonds = 3592 Number of angles = 1296 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1190 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 <- "35.866" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1187" Evaluating: 1187-13 Parameter: NUMWAT <- "1174" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1174" Comparing "1075" and "1174". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.866" Parameter: BOX -> "35.866" Parameter: BOX -> "35.866" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.86600 B = 35.86600 C = 35.86600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7370 2 1 -1 -2 -1 13.8478 3 1 -1 -1 -1 4.1761 4 1 -1 0 -1 3.0572 5 1 0 -1 -1 4.4789 6 1 0 0 -1 4.6532 7 1 -1 -1 0 1.1449 8 1 -1 0 0 2.5688 9 1 0 -1 0 2.8785 10 1 0 1 0 2.8785 11 1 0 0 1 4.6532 12 1 0 1 1 4.4789 13 1 2 1 1 8.7370 14 1 1 2 1 13.8478 15 1 1 1 1 4.1761 16 1 1 0 1 3.0572 17 1 1 1 0 1.1449 18 1 1 0 0 2.5688 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3598 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.82 2 C002 has 27 9 9 11.12 3 C003 has 2649 883 883 0.00 4 C004 has 864 288 288 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1224 408 408 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1263 421 421 0.00 9 C009 has 1263 421 421 0.00 Total of12700 atoms and 4226 groups and 4221 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3598 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3598 Number of groups = 1192 Number of bonds = 3592 Number of angles = 1296 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1190 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 = 3598 Number of groups = 1192 Number of bonds = 3592 Number of angles = 1296 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1190 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 <- "35.864" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1187" Evaluating: 1187-13 Parameter: NUMWAT <- "1174" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1174" Comparing "1075" and "1174". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.864" Parameter: BOX -> "35.864" Parameter: BOX -> "35.864" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.86400 B = 35.86400 C = 35.86400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7340 2 1 -1 -2 -1 13.8448 3 1 -1 -1 -1 4.1757 4 1 -1 0 -1 3.0572 5 1 0 -1 -1 4.4793 6 1 0 0 -1 4.6537 7 1 -1 -1 0 1.1450 8 1 -1 0 0 2.5679 9 1 0 -1 0 2.8769 10 1 0 1 0 2.8769 11 1 0 0 1 4.6537 12 1 0 1 1 4.4793 13 1 2 1 1 8.7340 14 1 1 2 1 13.8448 15 1 1 1 1 4.1757 16 1 1 0 1 3.0572 17 1 1 1 0 1.1450 18 1 1 0 0 2.5679 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3598 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.81 2 C002 has 27 9 9 11.11 3 C003 has 2649 883 883 0.00 4 C004 has 867 289 289 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1224 408 408 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1263 421 421 0.00 9 C009 has 1263 421 421 0.00 Total of12703 atoms and 4227 groups and 4222 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3598 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3598 Number of groups = 1192 Number of bonds = 3592 Number of angles = 1296 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1190 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 = 3598 Number of groups = 1192 Number of bonds = 3592 Number of angles = 1296 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1190 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 <- "35.862" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1187" Evaluating: 1187-13 Parameter: NUMWAT <- "1174" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1174" Comparing "1075" and "1174". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.862" Parameter: BOX -> "35.862" Parameter: BOX -> "35.862" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.86200 B = 35.86200 C = 35.86200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7309 2 1 -1 -2 -1 13.8417 3 1 -1 -1 -1 4.1754 4 1 -1 0 -1 3.0572 5 1 0 -1 -1 4.4798 6 1 0 0 -1 4.6542 7 1 -1 -1 0 1.1452 8 1 -1 0 0 2.5670 9 1 0 -1 0 2.8752 10 1 0 1 0 2.8752 11 1 0 0 1 4.6542 12 1 0 1 1 4.4798 13 1 2 1 1 8.7309 14 1 1 2 1 13.8417 15 1 1 1 1 4.1754 16 1 1 0 1 3.0572 17 1 1 1 0 1.1452 18 1 1 0 0 2.5670 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3598 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.81 2 C002 has 27 9 9 11.11 3 C003 has 2649 883 883 0.00 4 C004 has 867 289 289 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1224 408 408 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1263 421 421 0.00 9 C009 has 1263 421 421 0.00 Total of12703 atoms and 4227 groups and 4222 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3598 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3598 Number of groups = 1192 Number of bonds = 3592 Number of angles = 1296 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1190 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 = 3598 Number of groups = 1192 Number of bonds = 3592 Number of angles = 1296 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1190 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 <- "35.86" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1187" Evaluating: 1187-13 Parameter: NUMWAT <- "1174" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1174" Comparing "1075" and "1174". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.86" Parameter: BOX -> "35.86" Parameter: BOX -> "35.86" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.86000 B = 35.86000 C = 35.86000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7279 2 1 -1 -2 -1 13.8386 3 1 -1 -1 -1 4.1751 4 1 -1 0 -1 3.0572 5 1 0 -1 -1 4.4802 6 1 0 0 -1 4.6547 7 1 -1 -1 0 1.1453 8 1 -1 0 0 2.5661 9 1 0 -1 0 2.8736 10 1 0 1 0 2.8736 11 1 0 0 1 4.6547 12 1 0 1 1 4.4802 13 1 2 1 1 8.7279 14 1 1 2 1 13.8386 15 1 1 1 1 4.1751 16 1 1 0 1 3.0572 17 1 1 1 0 1.1453 18 1 1 0 0 2.5661 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3598 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.81 2 C002 has 27 9 9 11.11 3 C003 has 2649 883 883 0.00 4 C004 has 867 289 289 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1224 408 408 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1263 421 421 0.00 9 C009 has 1263 421 421 0.00 Total of12703 atoms and 4227 groups and 4222 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3598 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3598 Number of groups = 1192 Number of bonds = 3592 Number of angles = 1296 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1190 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 = 3598 Number of groups = 1192 Number of bonds = 3592 Number of angles = 1296 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1190 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 <- "35.858" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1187" Evaluating: 1187-13 Parameter: NUMWAT <- "1174" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1174" Comparing "1075" and "1174". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.858" Parameter: BOX -> "35.858" Parameter: BOX -> "35.858" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.85800 B = 35.85800 C = 35.85800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7249 2 1 -1 -2 -1 13.8356 3 1 -1 -1 -1 4.1748 4 1 -1 0 -1 3.0572 5 1 0 -1 -1 4.4806 6 1 0 0 -1 4.6552 7 1 -1 -1 0 1.1455 8 1 -1 0 0 2.5652 9 1 0 -1 0 2.8720 10 1 0 1 0 2.8720 11 1 0 0 1 4.6552 12 1 0 1 1 4.4806 13 1 2 1 1 8.7249 14 1 1 2 1 13.8356 15 1 1 1 1 4.1748 16 1 1 0 1 3.0572 17 1 1 1 0 1.1455 18 1 1 0 0 2.5652 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3598 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.80 2 C002 has 27 9 9 11.10 3 C003 has 2649 883 883 0.00 4 C004 has 870 290 290 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1224 408 408 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1263 421 421 0.00 9 C009 has 1263 421 421 0.00 Total of12706 atoms and 4228 groups and 4223 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3598 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3598 Number of groups = 1192 Number of bonds = 3592 Number of angles = 1296 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1190 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 = 3598 Number of groups = 1192 Number of bonds = 3592 Number of angles = 1296 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1190 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 <- "35.856" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1187" Evaluating: 1187-13 Parameter: NUMWAT <- "1174" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1174" Comparing "1075" and "1174". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.856" Parameter: BOX -> "35.856" Parameter: BOX -> "35.856" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.85600 B = 35.85600 C = 35.85600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7219 2 1 -1 -2 -1 13.8325 3 1 -1 -1 -1 4.1745 4 1 -1 0 -1 3.0572 5 1 0 -1 -1 4.4811 6 1 0 0 -1 4.6558 7 1 -1 -1 0 1.1456 8 1 -1 0 0 2.5643 9 1 0 -1 0 2.8703 10 1 0 1 0 2.8703 11 1 0 0 1 4.6558 12 1 0 1 1 4.4811 13 1 2 1 1 8.7219 14 1 1 2 1 13.8325 15 1 1 1 1 4.1745 16 1 1 0 1 3.0572 17 1 1 1 0 1.1456 18 1 1 0 0 2.5643 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3598 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.80 2 C002 has 27 9 9 11.10 3 C003 has 2649 883 883 0.00 4 C004 has 870 290 290 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1224 408 408 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1263 421 421 0.00 9 C009 has 1263 421 421 0.00 Total of12706 atoms and 4228 groups and 4223 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3598 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3598 Number of groups = 1192 Number of bonds = 3592 Number of angles = 1296 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1190 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 = 3598 Number of groups = 1192 Number of bonds = 3592 Number of angles = 1296 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1190 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 <- "35.854" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1187" Evaluating: 1187-13 Parameter: NUMWAT <- "1174" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1174" Comparing "1075" and "1174". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.854" Parameter: BOX -> "35.854" Parameter: BOX -> "35.854" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.85400 B = 35.85400 C = 35.85400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7188 2 1 -1 -2 -1 13.8294 3 1 -1 -1 -1 4.1741 4 1 -1 0 -1 3.0572 5 1 0 -1 -1 4.4815 6 1 0 0 -1 4.6563 7 1 -1 -1 0 1.1458 8 1 -1 0 0 2.5634 9 1 0 -1 0 2.8687 10 1 0 1 0 2.8687 11 1 0 0 1 4.6563 12 1 0 1 1 4.4815 13 1 2 1 1 8.7188 14 1 1 2 1 13.8294 15 1 1 1 1 4.1741 16 1 1 0 1 3.0572 17 1 1 1 0 1.1458 18 1 1 0 0 2.5634 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3598 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.80 2 C002 has 27 9 9 11.10 3 C003 has 2649 883 883 0.00 4 C004 has 870 290 290 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1224 408 408 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1263 421 421 0.00 9 C009 has 1263 421 421 0.00 Total of12706 atoms and 4228 groups and 4223 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3598 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3598 Number of groups = 1192 Number of bonds = 3592 Number of angles = 1296 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1190 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 = 3598 Number of groups = 1192 Number of bonds = 3592 Number of angles = 1296 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1190 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 <- "35.852" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1187" Evaluating: 1187-13 Parameter: NUMWAT <- "1174" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1174" Comparing "1075" and "1174". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.852" Parameter: BOX -> "35.852" Parameter: BOX -> "35.852" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.85200 B = 35.85200 C = 35.85200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7158 2 1 -1 -2 -1 13.8264 3 1 -1 -1 -1 4.1738 4 1 -1 0 -1 3.0572 5 1 0 -1 -1 4.4820 6 1 0 0 -1 4.6568 7 1 -1 -1 0 1.1459 8 1 -1 0 0 2.5625 9 1 0 -1 0 2.8670 10 1 0 1 0 2.8670 11 1 0 0 1 4.6568 12 1 0 1 1 4.4820 13 1 2 1 1 8.7158 14 1 1 2 1 13.8264 15 1 1 1 1 4.1738 16 1 1 0 1 3.0572 17 1 1 1 0 1.1459 18 1 1 0 0 2.5625 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3598 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.79 2 C002 has 30 10 10 11.10 3 C003 has 2649 883 883 0.00 4 C004 has 870 290 290 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1224 408 408 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1263 421 421 0.00 9 C009 has 1263 421 421 0.00 Total of12709 atoms and 4229 groups and 4224 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3598 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3598 Number of groups = 1192 Number of bonds = 3592 Number of angles = 1296 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1190 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 = 3598 Number of groups = 1192 Number of bonds = 3592 Number of angles = 1296 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1190 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 <- "35.85" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1187" Evaluating: 1187-13 Parameter: NUMWAT <- "1174" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1174" Comparing "1075" and "1174". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.85" Parameter: BOX -> "35.85" Parameter: BOX -> "35.85" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.85000 B = 35.85000 C = 35.85000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7128 2 1 -1 -2 -1 13.8233 3 1 -1 -1 -1 4.1735 4 1 -1 0 -1 3.0572 5 1 0 -1 -1 4.4824 6 1 0 0 -1 4.6573 7 1 -1 -1 0 1.1461 8 1 -1 0 0 2.5616 9 1 0 -1 0 2.8654 10 1 0 1 0 2.8654 11 1 0 0 1 4.6573 12 1 0 1 1 4.4824 13 1 2 1 1 8.7128 14 1 1 2 1 13.8233 15 1 1 1 1 4.1735 16 1 1 0 1 3.0572 17 1 1 1 0 1.1461 18 1 1 0 0 2.5616 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3598 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 293 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 156 52 52 6.79 2 C002 has 30 10 10 11.09 3 C003 has 2649 883 883 0.00 4 C004 has 867 289 289 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1227 409 409 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1272 424 424 0.00 9 C009 has 1263 421 421 0.00 Total of12718 atoms and 4232 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> 3 atoms have been selected out of 3598 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 = 3595 Number of groups = 1191 Number of bonds = 3589 Number of angles = 1295 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1189 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 = 3595 Number of groups = 1191 Number of bonds = 3589 Number of angles = 1295 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1189 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 <- "35.848" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1186" Evaluating: 1186-13 Parameter: NUMWAT <- "1173" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1173" Comparing "1075" and "1173". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.848" Parameter: BOX -> "35.848" Parameter: BOX -> "35.848" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.84800 B = 35.84800 C = 35.84800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7097 2 1 -1 -2 -1 13.8202 3 1 -1 -1 -1 4.1732 4 1 -1 0 -1 3.0572 5 1 0 -1 -1 4.4828 6 1 0 0 -1 4.6578 7 1 -1 -1 0 1.1463 8 1 -1 0 0 2.5607 9 1 0 -1 0 2.8638 10 1 0 1 0 2.8638 11 1 0 0 1 4.6578 12 1 0 1 1 4.4828 13 1 2 1 1 8.7097 14 1 1 2 1 13.8202 15 1 1 1 1 4.1732 16 1 1 0 1 3.0572 17 1 1 1 0 1.1463 18 1 1 0 0 2.5607 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3595 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 661 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 156 52 52 6.79 2 C002 has 30 10 10 11.09 3 C003 has 2649 883 883 0.00 4 C004 has 864 288 288 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1221 407 407 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1260 420 420 0.00 9 C009 has 1263 421 421 0.00 Total of12694 atoms and 4224 groups and 4219 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3595 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 = 3592 Number of groups = 1190 Number of bonds = 3586 Number of angles = 1294 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1188 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 = 3592 Number of groups = 1190 Number of bonds = 3586 Number of angles = 1294 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1188 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 <- "35.846" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1185" Evaluating: 1185-13 Parameter: NUMWAT <- "1172" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1172" Comparing "1075" and "1172". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.846" Parameter: BOX -> "35.846" Parameter: BOX -> "35.846" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.84600 B = 35.84600 C = 35.84600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7067 2 1 -1 -2 -1 13.8172 3 1 -1 -1 -1 4.1729 4 1 -1 0 -1 3.0572 5 1 0 -1 -1 4.4833 6 1 0 0 -1 4.6583 7 1 -1 -1 0 1.1464 8 1 -1 0 0 2.5598 9 1 0 -1 0 2.8621 10 1 0 1 0 2.8621 11 1 0 0 1 4.6583 12 1 0 1 1 4.4833 13 1 2 1 1 8.7067 14 1 1 2 1 13.8172 15 1 1 1 1 4.1729 16 1 1 0 1 3.0572 17 1 1 1 0 1.1464 18 1 1 0 0 2.5598 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3592 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 885 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.78 2 C002 has 30 10 10 11.09 3 C003 has 2646 882 882 0.00 4 C004 has 861 287 287 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1224 408 408 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1266 422 422 0.00 9 C009 has 1260 420 420 0.00 Total of12688 atoms and 4222 groups and 4217 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3592 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 = 3589 Number of groups = 1189 Number of bonds = 3583 Number of angles = 1293 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1187 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 = 3589 Number of groups = 1189 Number of bonds = 3583 Number of angles = 1293 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1187 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 <- "35.844" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1184" Evaluating: 1184-13 Parameter: NUMWAT <- "1171" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1171" Comparing "1075" and "1171". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.844" Parameter: BOX -> "35.844" Parameter: BOX -> "35.844" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.84400 B = 35.84400 C = 35.84400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7037 2 1 -1 -2 -1 13.8141 3 1 -1 -1 -1 4.1726 4 1 -1 0 -1 3.0573 5 1 0 -1 -1 4.4837 6 1 0 0 -1 4.6589 7 1 -1 -1 0 1.1466 8 1 -1 0 0 2.5589 9 1 0 -1 0 2.8605 10 1 0 1 0 2.8605 11 1 0 0 1 4.6589 12 1 0 1 1 4.4837 13 1 2 1 1 8.7037 14 1 1 2 1 13.8141 15 1 1 1 1 4.1726 16 1 1 0 1 3.0573 17 1 1 1 0 1.1466 18 1 1 0 0 2.5589 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3589 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.78 2 C002 has 30 10 10 11.08 3 C003 has 2643 881 881 0.00 4 C004 has 864 288 288 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1221 407 407 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1257 419 419 0.00 9 C009 has 1260 420 420 0.00 Total of12673 atoms and 4217 groups and 4212 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3589 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3589 Number of groups = 1189 Number of bonds = 3583 Number of angles = 1293 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1187 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 = 3589 Number of groups = 1189 Number of bonds = 3583 Number of angles = 1293 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1187 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 <- "35.842" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1184" Evaluating: 1184-13 Parameter: NUMWAT <- "1171" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1171" Comparing "1075" and "1171". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.842" Parameter: BOX -> "35.842" Parameter: BOX -> "35.842" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.84200 B = 35.84200 C = 35.84200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7007 2 1 -1 -2 -1 13.8110 3 1 -1 -1 -1 4.1723 4 1 -1 0 -1 3.0573 5 1 0 -1 -1 4.4842 6 1 0 0 -1 4.6594 7 1 -1 -1 0 1.1468 8 1 -1 0 0 2.5580 9 1 0 -1 0 2.8589 10 1 0 1 0 2.8589 11 1 0 0 1 4.6594 12 1 0 1 1 4.4842 13 1 2 1 1 8.7007 14 1 1 2 1 13.8110 15 1 1 1 1 4.1723 16 1 1 0 1 3.0573 17 1 1 1 0 1.1468 18 1 1 0 0 2.5580 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3589 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.78 2 C002 has 30 10 10 11.08 3 C003 has 2643 881 881 0.00 4 C004 has 864 288 288 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1221 407 407 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1257 419 419 0.00 9 C009 has 1260 420 420 0.00 Total of12673 atoms and 4217 groups and 4212 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3589 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3589 Number of groups = 1189 Number of bonds = 3583 Number of angles = 1293 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1187 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 = 3589 Number of groups = 1189 Number of bonds = 3583 Number of angles = 1293 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1187 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 <- "35.84" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1184" Evaluating: 1184-13 Parameter: NUMWAT <- "1171" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1171" Comparing "1075" and "1171". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.84" Parameter: BOX -> "35.84" Parameter: BOX -> "35.84" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.84000 B = 35.84000 C = 35.84000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6976 2 1 -1 -2 -1 13.8080 3 1 -1 -1 -1 4.1720 4 1 -1 0 -1 3.0573 5 1 0 -1 -1 4.4846 6 1 0 0 -1 4.6599 7 1 -1 -1 0 1.1470 8 1 -1 0 0 2.5571 9 1 0 -1 0 2.8572 10 1 0 1 0 2.8572 11 1 0 0 1 4.6599 12 1 0 1 1 4.4846 13 1 2 1 1 8.6976 14 1 1 2 1 13.8080 15 1 1 1 1 4.1720 16 1 1 0 1 3.0573 17 1 1 1 0 1.1470 18 1 1 0 0 2.5571 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3589 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.78 2 C002 has 30 10 10 11.08 3 C003 has 2643 881 881 0.00 4 C004 has 864 288 288 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1221 407 407 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1257 419 419 0.00 9 C009 has 1260 420 420 0.00 Total of12673 atoms and 4217 groups and 4212 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3589 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3589 Number of groups = 1189 Number of bonds = 3583 Number of angles = 1293 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1187 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 = 3589 Number of groups = 1189 Number of bonds = 3583 Number of angles = 1293 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1187 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 <- "35.838" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1184" Evaluating: 1184-13 Parameter: NUMWAT <- "1171" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1171" Comparing "1075" and "1171". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.838" Parameter: BOX -> "35.838" Parameter: BOX -> "35.838" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.83800 B = 35.83800 C = 35.83800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6946 2 1 -1 -2 -1 13.8049 3 1 -1 -1 -1 4.1717 4 1 -1 0 -1 3.0573 5 1 0 -1 -1 4.4851 6 1 0 0 -1 4.6604 7 1 -1 -1 0 1.1472 8 1 -1 0 0 2.5562 9 1 0 -1 0 2.8556 10 1 0 1 0 2.8556 11 1 0 0 1 4.6604 12 1 0 1 1 4.4851 13 1 2 1 1 8.6946 14 1 1 2 1 13.8049 15 1 1 1 1 4.1717 16 1 1 0 1 3.0573 17 1 1 1 0 1.1472 18 1 1 0 0 2.5562 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3589 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 592 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.77 2 C002 has 30 10 10 11.07 3 C003 has 2649 883 883 0.00 4 C004 has 867 289 289 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1212 404 404 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1254 418 418 0.00 9 C009 has 1257 419 419 0.00 Total of12670 atoms and 4216 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 3589 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 = 3586 Number of groups = 1188 Number of bonds = 3580 Number of angles = 1292 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1186 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 = 3586 Number of groups = 1188 Number of bonds = 3580 Number of angles = 1292 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1186 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 <- "35.836" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1183" Evaluating: 1183-13 Parameter: NUMWAT <- "1170" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1170" Comparing "1075" and "1170". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.836" Parameter: BOX -> "35.836" Parameter: BOX -> "35.836" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.83600 B = 35.83600 C = 35.83600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6916 2 1 -1 -2 -1 13.8018 3 1 -1 -1 -1 4.1713 4 1 -1 0 -1 3.0573 5 1 0 -1 -1 4.4855 6 1 0 0 -1 4.6609 7 1 -1 -1 0 1.1474 8 1 -1 0 0 2.5553 9 1 0 -1 0 2.8540 10 1 0 1 0 2.8540 11 1 0 0 1 4.6609 12 1 0 1 1 4.4855 13 1 2 1 1 8.6916 14 1 1 2 1 13.8018 15 1 1 1 1 4.1713 16 1 1 0 1 3.0573 17 1 1 1 0 1.1474 18 1 1 0 0 2.5553 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3586 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.77 2 C002 has 30 10 10 11.07 3 C003 has 2646 882 882 0.00 4 C004 has 867 289 289 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1209 403 403 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1254 418 418 0.00 9 C009 has 1257 419 419 0.00 Total of12658 atoms and 4212 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 3586 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3586 Number of groups = 1188 Number of bonds = 3580 Number of angles = 1292 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1186 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 = 3586 Number of groups = 1188 Number of bonds = 3580 Number of angles = 1292 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1186 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 <- "35.834" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1183" Evaluating: 1183-13 Parameter: NUMWAT <- "1170" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1170" Comparing "1075" and "1170". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.834" Parameter: BOX -> "35.834" Parameter: BOX -> "35.834" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.83400 B = 35.83400 C = 35.83400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6886 2 1 -1 -2 -1 13.7988 3 1 -1 -1 -1 4.1710 4 1 -1 0 -1 3.0574 5 1 0 -1 -1 4.4860 6 1 0 0 -1 4.6615 7 1 -1 -1 0 1.1476 8 1 -1 0 0 2.5544 9 1 0 -1 0 2.8523 10 1 0 1 0 2.8523 11 1 0 0 1 4.6615 12 1 0 1 1 4.4860 13 1 2 1 1 8.6886 14 1 1 2 1 13.7988 15 1 1 1 1 4.1710 16 1 1 0 1 3.0574 17 1 1 1 0 1.1476 18 1 1 0 0 2.5544 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3586 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.77 2 C002 has 30 10 10 11.07 3 C003 has 2646 882 882 0.00 4 C004 has 867 289 289 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1209 403 403 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1254 418 418 0.00 9 C009 has 1257 419 419 0.00 Total of12658 atoms and 4212 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 3586 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3586 Number of groups = 1188 Number of bonds = 3580 Number of angles = 1292 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1186 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 = 3586 Number of groups = 1188 Number of bonds = 3580 Number of angles = 1292 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1186 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 <- "35.832" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1183" Evaluating: 1183-13 Parameter: NUMWAT <- "1170" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1170" Comparing "1075" and "1170". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.832" Parameter: BOX -> "35.832" Parameter: BOX -> "35.832" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.83200 B = 35.83200 C = 35.83200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6855 2 1 -1 -2 -1 13.7957 3 1 -1 -1 -1 4.1707 4 1 -1 0 -1 3.0574 5 1 0 -1 -1 4.4864 6 1 0 0 -1 4.6620 7 1 -1 -1 0 1.1478 8 1 -1 0 0 2.5535 9 1 0 -1 0 2.8507 10 1 0 1 0 2.8507 11 1 0 0 1 4.6620 12 1 0 1 1 4.4864 13 1 2 1 1 8.6855 14 1 1 2 1 13.7957 15 1 1 1 1 4.1707 16 1 1 0 1 3.0574 17 1 1 1 0 1.1478 18 1 1 0 0 2.5535 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3586 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.76 2 C002 has 30 10 10 11.06 3 C003 has 2652 884 884 0.00 4 C004 has 867 289 289 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1209 403 403 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1254 418 418 0.00 9 C009 has 1257 419 419 0.00 Total of12664 atoms and 4214 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 3586 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3586 Number of groups = 1188 Number of bonds = 3580 Number of angles = 1292 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1186 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 = 3586 Number of groups = 1188 Number of bonds = 3580 Number of angles = 1292 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1186 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 <- "35.83" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1183" Evaluating: 1183-13 Parameter: NUMWAT <- "1170" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1170" Comparing "1075" and "1170". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.83" Parameter: BOX -> "35.83" Parameter: BOX -> "35.83" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.83000 B = 35.83000 C = 35.83000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6825 2 1 -1 -2 -1 13.7926 3 1 -1 -1 -1 4.1704 4 1 -1 0 -1 3.0574 5 1 0 -1 -1 4.4869 6 1 0 0 -1 4.6625 7 1 -1 -1 0 1.1480 8 1 -1 0 0 2.5526 9 1 0 -1 0 2.8491 10 1 0 1 0 2.8491 11 1 0 0 1 4.6625 12 1 0 1 1 4.4869 13 1 2 1 1 8.6825 14 1 1 2 1 13.7926 15 1 1 1 1 4.1704 16 1 1 0 1 3.0574 17 1 1 1 0 1.1480 18 1 1 0 0 2.5526 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3586 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.76 2 C002 has 30 10 10 11.06 3 C003 has 2652 884 884 0.00 4 C004 has 870 290 290 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1209 403 403 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1254 418 418 0.00 9 C009 has 1257 419 419 0.00 Total of12667 atoms and 4215 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 3586 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3586 Number of groups = 1188 Number of bonds = 3580 Number of angles = 1292 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1186 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 = 3586 Number of groups = 1188 Number of bonds = 3580 Number of angles = 1292 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1186 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 <- "35.828" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1183" Evaluating: 1183-13 Parameter: NUMWAT <- "1170" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1170" Comparing "1075" and "1170". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.828" Parameter: BOX -> "35.828" Parameter: BOX -> "35.828" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.82800 B = 35.82800 C = 35.82800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6795 2 1 -1 -2 -1 13.7896 3 1 -1 -1 -1 4.1701 4 1 -1 0 -1 3.0574 5 1 0 -1 -1 4.4873 6 1 0 0 -1 4.6630 7 1 -1 -1 0 1.1482 8 1 -1 0 0 2.5517 9 1 0 -1 0 2.8474 10 1 0 1 0 2.8474 11 1 0 0 1 4.6630 12 1 0 1 1 4.4873 13 1 2 1 1 8.6795 14 1 1 2 1 13.7896 15 1 1 1 1 4.1701 16 1 1 0 1 3.0574 17 1 1 1 0 1.1482 18 1 1 0 0 2.5517 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3586 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.76 2 C002 has 30 10 10 11.06 3 C003 has 2652 884 884 0.00 4 C004 has 870 290 290 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1209 403 403 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1254 418 418 0.00 9 C009 has 1257 419 419 0.00 Total of12667 atoms and 4215 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 3586 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3586 Number of groups = 1188 Number of bonds = 3580 Number of angles = 1292 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1186 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 = 3586 Number of groups = 1188 Number of bonds = 3580 Number of angles = 1292 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1186 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 <- "35.826" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1183" Evaluating: 1183-13 Parameter: NUMWAT <- "1170" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1170" Comparing "1075" and "1170". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.826" Parameter: BOX -> "35.826" Parameter: BOX -> "35.826" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.82600 B = 35.82600 C = 35.82600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6765 2 1 -1 -2 -1 13.7865 3 1 -1 -1 -1 4.1698 4 1 -1 0 -1 3.0575 5 1 0 -1 -1 4.4878 6 1 0 0 -1 4.6636 7 1 -1 -1 0 1.1485 8 1 -1 0 0 2.5508 9 1 0 -1 0 2.8458 10 1 0 1 0 2.8458 11 1 0 0 1 4.6636 12 1 0 1 1 4.4878 13 1 2 1 1 8.6765 14 1 1 2 1 13.7865 15 1 1 1 1 4.1698 16 1 1 0 1 3.0575 17 1 1 1 0 1.1485 18 1 1 0 0 2.5508 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3586 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 933 OPERATED ON BY TRANSFORMATION C018 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 156 52 52 6.75 2 C002 has 30 10 10 11.06 3 C003 has 2652 884 884 0.00 4 C004 has 873 291 291 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1206 402 402 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1251 417 417 0.00 9 C009 has 1257 419 419 0.00 Total of12667 atoms and 4215 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> 3 atoms have been selected out of 3586 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 = 3583 Number of groups = 1187 Number of bonds = 3577 Number of angles = 1291 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1185 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 = 3583 Number of groups = 1187 Number of bonds = 3577 Number of angles = 1291 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1185 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 <- "35.824" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1182" Evaluating: 1182-13 Parameter: NUMWAT <- "1169" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1169" Comparing "1075" and "1169". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.824" Parameter: BOX -> "35.824" Parameter: BOX -> "35.824" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.82400 B = 35.82400 C = 35.82400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6734 2 1 -1 -2 -1 13.7834 3 1 -1 -1 -1 4.1695 4 1 -1 0 -1 3.0575 5 1 0 -1 -1 4.4882 6 1 0 0 -1 4.6641 7 1 -1 -1 0 1.1487 8 1 -1 0 0 2.5499 9 1 0 -1 0 2.8442 10 1 0 1 0 2.8442 11 1 0 0 1 4.6641 12 1 0 1 1 4.4882 13 1 2 1 1 8.6734 14 1 1 2 1 13.7834 15 1 1 1 1 4.1695 16 1 1 0 1 3.0575 17 1 1 1 0 1.1487 18 1 1 0 0 2.5499 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3583 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.75 2 C002 has 30 10 10 11.05 3 C003 has 2649 883 883 0.00 4 C004 has 870 290 290 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1206 402 402 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1248 416 416 0.00 9 C009 has 1257 419 419 0.00 Total of12652 atoms and 4210 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 3583 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3583 Number of groups = 1187 Number of bonds = 3577 Number of angles = 1291 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1185 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 = 3583 Number of groups = 1187 Number of bonds = 3577 Number of angles = 1291 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1185 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 <- "35.822" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1182" Evaluating: 1182-13 Parameter: NUMWAT <- "1169" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1169" Comparing "1075" and "1169". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.822" Parameter: BOX -> "35.822" Parameter: BOX -> "35.822" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.82200 B = 35.82200 C = 35.82200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6704 2 1 -1 -2 -1 13.7804 3 1 -1 -1 -1 4.1692 4 1 -1 0 -1 3.0575 5 1 0 -1 -1 4.4887 6 1 0 0 -1 4.6646 7 1 -1 -1 0 1.1489 8 1 -1 0 0 2.5490 9 1 0 -1 0 2.8425 10 1 0 1 0 2.8425 11 1 0 0 1 4.6646 12 1 0 1 1 4.4887 13 1 2 1 1 8.6704 14 1 1 2 1 13.7804 15 1 1 1 1 4.1692 16 1 1 0 1 3.0575 17 1 1 1 0 1.1489 18 1 1 0 0 2.5490 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3583 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.75 2 C002 has 30 10 10 11.05 3 C003 has 2649 883 883 0.00 4 C004 has 870 290 290 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1206 402 402 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1248 416 416 0.00 9 C009 has 1257 419 419 0.00 Total of12652 atoms and 4210 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 3583 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3583 Number of groups = 1187 Number of bonds = 3577 Number of angles = 1291 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1185 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 = 3583 Number of groups = 1187 Number of bonds = 3577 Number of angles = 1291 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1185 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 <- "35.82" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1182" Evaluating: 1182-13 Parameter: NUMWAT <- "1169" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1169" Comparing "1075" and "1169". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.82" Parameter: BOX -> "35.82" Parameter: BOX -> "35.82" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.82000 B = 35.82000 C = 35.82000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6674 2 1 -1 -2 -1 13.7773 3 1 -1 -1 -1 4.1689 4 1 -1 0 -1 3.0576 5 1 0 -1 -1 4.4891 6 1 0 0 -1 4.6651 7 1 -1 -1 0 1.1492 8 1 -1 0 0 2.5481 9 1 0 -1 0 2.8409 10 1 0 1 0 2.8409 11 1 0 0 1 4.6651 12 1 0 1 1 4.4891 13 1 2 1 1 8.6674 14 1 1 2 1 13.7773 15 1 1 1 1 4.1689 16 1 1 0 1 3.0576 17 1 1 1 0 1.1492 18 1 1 0 0 2.5481 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3583 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 894 OPERATED ON BY TRANSFORMATION C006 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.74 2 C002 has 30 10 10 11.05 3 C003 has 2649 883 883 0.00 4 C004 has 870 290 290 0.00 5 C005 has 828 276 276 0.00 6 C006 has 1206 402 402 0.00 7 C007 has 828 276 276 0.00 8 C008 has 1248 416 416 0.00 9 C009 has 1260 420 420 0.00 Total of12655 atoms and 4211 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 3583 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 = 3580 Number of groups = 1186 Number of bonds = 3574 Number of angles = 1290 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1184 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 = 3580 Number of groups = 1186 Number of bonds = 3574 Number of angles = 1290 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1184 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 <- "35.818" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1181" Evaluating: 1181-13 Parameter: NUMWAT <- "1168" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1168" Comparing "1075" and "1168". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.818" Parameter: BOX -> "35.818" Parameter: BOX -> "35.818" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.81800 B = 35.81800 C = 35.81800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6644 2 1 -1 -2 -1 13.7742 3 1 -1 -1 -1 4.1686 4 1 -1 0 -1 3.0576 5 1 0 -1 -1 4.4896 6 1 0 0 -1 4.6657 7 1 -1 -1 0 1.1494 8 1 -1 0 0 2.5473 9 1 0 -1 0 2.8393 10 1 0 1 0 2.8393 11 1 0 0 1 4.6657 12 1 0 1 1 4.4896 13 1 2 1 1 8.6644 14 1 1 2 1 13.7742 15 1 1 1 1 4.1686 16 1 1 0 1 3.0576 17 1 1 1 0 1.1494 18 1 1 0 0 2.5473 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3580 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.74 2 C002 has 30 10 10 11.04 3 C003 has 2649 883 883 0.00 4 C004 has 870 290 290 0.00 5 C005 has 828 276 276 0.00 6 C006 has 1203 401 401 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1251 417 417 0.00 9 C009 has 1257 419 419 0.00 Total of12646 atoms and 4208 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 3580 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3580 Number of groups = 1186 Number of bonds = 3574 Number of angles = 1290 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1184 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 = 3580 Number of groups = 1186 Number of bonds = 3574 Number of angles = 1290 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1184 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 <- "35.816" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1181" Evaluating: 1181-13 Parameter: NUMWAT <- "1168" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1168" Comparing "1075" and "1168". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.816" Parameter: BOX -> "35.816" Parameter: BOX -> "35.816" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.81600 B = 35.81600 C = 35.81600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6613 2 1 -1 -2 -1 13.7712 3 1 -1 -1 -1 4.1683 4 1 -1 0 -1 3.0576 5 1 0 -1 -1 4.4901 6 1 0 0 -1 4.6662 7 1 -1 -1 0 1.1496 8 1 -1 0 0 2.5464 9 1 0 -1 0 2.8377 10 1 0 1 0 2.8377 11 1 0 0 1 4.6662 12 1 0 1 1 4.4901 13 1 2 1 1 8.6613 14 1 1 2 1 13.7712 15 1 1 1 1 4.1683 16 1 1 0 1 3.0576 17 1 1 1 0 1.1496 18 1 1 0 0 2.5464 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3580 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.74 2 C002 has 30 10 10 11.04 3 C003 has 2652 884 884 0.00 4 C004 has 870 290 290 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1203 401 401 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1251 417 417 0.00 9 C009 has 1257 419 419 0.00 Total of12652 atoms and 4210 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 3580 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3580 Number of groups = 1186 Number of bonds = 3574 Number of angles = 1290 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1184 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 = 3580 Number of groups = 1186 Number of bonds = 3574 Number of angles = 1290 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1184 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 <- "35.814" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1181" Evaluating: 1181-13 Parameter: NUMWAT <- "1168" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1168" Comparing "1075" and "1168". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.814" Parameter: BOX -> "35.814" Parameter: BOX -> "35.814" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.81400 B = 35.81400 C = 35.81400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6583 2 1 -1 -2 -1 13.7681 3 1 -1 -1 -1 4.1680 4 1 -1 0 -1 3.0577 5 1 0 -1 -1 4.4905 6 1 0 0 -1 4.6667 7 1 -1 -1 0 1.1499 8 1 -1 0 0 2.5455 9 1 0 -1 0 2.8360 10 1 0 1 0 2.8360 11 1 0 0 1 4.6667 12 1 0 1 1 4.4905 13 1 2 1 1 8.6583 14 1 1 2 1 13.7681 15 1 1 1 1 4.1680 16 1 1 0 1 3.0577 17 1 1 1 0 1.1499 18 1 1 0 0 2.5455 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3580 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.74 2 C002 has 30 10 10 11.04 3 C003 has 2652 884 884 0.00 4 C004 has 870 290 290 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1203 401 401 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1251 417 417 0.00 9 C009 has 1257 419 419 0.00 Total of12652 atoms and 4210 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 3580 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3580 Number of groups = 1186 Number of bonds = 3574 Number of angles = 1290 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1184 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 = 3580 Number of groups = 1186 Number of bonds = 3574 Number of angles = 1290 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1184 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 <- "35.812" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1181" Evaluating: 1181-13 Parameter: NUMWAT <- "1168" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1168" Comparing "1075" and "1168". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.812" Parameter: BOX -> "35.812" Parameter: BOX -> "35.812" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.81200 B = 35.81200 C = 35.81200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6553 2 1 -1 -2 -1 13.7650 3 1 -1 -1 -1 4.1677 4 1 -1 0 -1 3.0577 5 1 0 -1 -1 4.4910 6 1 0 0 -1 4.6673 7 1 -1 -1 0 1.1501 8 1 -1 0 0 2.5446 9 1 0 -1 0 2.8344 10 1 0 1 0 2.8344 11 1 0 0 1 4.6673 12 1 0 1 1 4.4910 13 1 2 1 1 8.6553 14 1 1 2 1 13.7650 15 1 1 1 1 4.1677 16 1 1 0 1 3.0577 17 1 1 1 0 1.1501 18 1 1 0 0 2.5446 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3580 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.73 2 C002 has 30 10 10 11.03 3 C003 has 2652 884 884 0.00 4 C004 has 870 290 290 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1203 401 401 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1251 417 417 0.00 9 C009 has 1257 419 419 0.00 Total of12652 atoms and 4210 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 3580 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3580 Number of groups = 1186 Number of bonds = 3574 Number of angles = 1290 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1184 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 = 3580 Number of groups = 1186 Number of bonds = 3574 Number of angles = 1290 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1184 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 <- "35.81" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1181" Evaluating: 1181-13 Parameter: NUMWAT <- "1168" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1168" Comparing "1075" and "1168". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.81" Parameter: BOX -> "35.81" Parameter: BOX -> "35.81" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.81000 B = 35.81000 C = 35.81000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6523 2 1 -1 -2 -1 13.7620 3 1 -1 -1 -1 4.1674 4 1 -1 0 -1 3.0577 5 1 0 -1 -1 4.4915 6 1 0 0 -1 4.6678 7 1 -1 -1 0 1.1504 8 1 -1 0 0 2.5437 9 1 0 -1 0 2.8328 10 1 0 1 0 2.8328 11 1 0 0 1 4.6678 12 1 0 1 1 4.4915 13 1 2 1 1 8.6523 14 1 1 2 1 13.7620 15 1 1 1 1 4.1674 16 1 1 0 1 3.0577 17 1 1 1 0 1.1504 18 1 1 0 0 2.5437 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3580 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.73 2 C002 has 30 10 10 11.03 3 C003 has 2652 884 884 0.00 4 C004 has 870 290 290 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1203 401 401 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1251 417 417 0.00 9 C009 has 1257 419 419 0.00 Total of12652 atoms and 4210 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 3580 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3580 Number of groups = 1186 Number of bonds = 3574 Number of angles = 1290 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1184 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 = 3580 Number of groups = 1186 Number of bonds = 3574 Number of angles = 1290 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1184 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 <- "35.808" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1181" Evaluating: 1181-13 Parameter: NUMWAT <- "1168" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1168" Comparing "1075" and "1168". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.808" Parameter: BOX -> "35.808" Parameter: BOX -> "35.808" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.80800 B = 35.80800 C = 35.80800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6493 2 1 -1 -2 -1 13.7589 3 1 -1 -1 -1 4.1671 4 1 -1 0 -1 3.0578 5 1 0 -1 -1 4.4919 6 1 0 0 -1 4.6683 7 1 -1 -1 0 1.1507 8 1 -1 0 0 2.5429 9 1 0 -1 0 2.8311 10 1 0 1 0 2.8311 11 1 0 0 1 4.6683 12 1 0 1 1 4.4919 13 1 2 1 1 8.6493 14 1 1 2 1 13.7589 15 1 1 1 1 4.1671 16 1 1 0 1 3.0578 17 1 1 1 0 1.1507 18 1 1 0 0 2.5429 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3580 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.73 2 C002 has 30 10 10 11.03 3 C003 has 2652 884 884 0.00 4 C004 has 870 290 290 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1203 401 401 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1251 417 417 0.00 9 C009 has 1257 419 419 0.00 Total of12652 atoms and 4210 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 3580 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3580 Number of groups = 1186 Number of bonds = 3574 Number of angles = 1290 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1184 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 = 3580 Number of groups = 1186 Number of bonds = 3574 Number of angles = 1290 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1184 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 <- "35.806" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1181" Evaluating: 1181-13 Parameter: NUMWAT <- "1168" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1168" Comparing "1075" and "1168". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.806" Parameter: BOX -> "35.806" Parameter: BOX -> "35.806" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.80600 B = 35.80600 C = 35.80600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6462 2 1 -1 -2 -1 13.7558 3 1 -1 -1 -1 4.1668 4 1 -1 0 -1 3.0578 5 1 0 -1 -1 4.4924 6 1 0 0 -1 4.6689 7 1 -1 -1 0 1.1509 8 1 -1 0 0 2.5420 9 1 0 -1 0 2.8295 10 1 0 1 0 2.8295 11 1 0 0 1 4.6689 12 1 0 1 1 4.4924 13 1 2 1 1 8.6462 14 1 1 2 1 13.7558 15 1 1 1 1 4.1668 16 1 1 0 1 3.0578 17 1 1 1 0 1.1509 18 1 1 0 0 2.5420 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3580 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.72 2 C002 has 30 10 10 11.02 3 C003 has 2652 884 884 0.00 4 C004 has 870 290 290 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1203 401 401 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1251 417 417 0.00 9 C009 has 1257 419 419 0.00 Total of12652 atoms and 4210 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 3580 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3580 Number of groups = 1186 Number of bonds = 3574 Number of angles = 1290 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1184 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 = 3580 Number of groups = 1186 Number of bonds = 3574 Number of angles = 1290 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1184 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 <- "35.804" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1181" Evaluating: 1181-13 Parameter: NUMWAT <- "1168" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1168" Comparing "1075" and "1168". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.804" Parameter: BOX -> "35.804" Parameter: BOX -> "35.804" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.80400 B = 35.80400 C = 35.80400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6432 2 1 -1 -2 -1 13.7528 3 1 -1 -1 -1 4.1666 4 1 -1 0 -1 3.0579 5 1 0 -1 -1 4.4929 6 1 0 0 -1 4.6694 7 1 -1 -1 0 1.1512 8 1 -1 0 0 2.5411 9 1 0 -1 0 2.8279 10 1 0 1 0 2.8279 11 1 0 0 1 4.6694 12 1 0 1 1 4.4929 13 1 2 1 1 8.6432 14 1 1 2 1 13.7528 15 1 1 1 1 4.1666 16 1 1 0 1 3.0579 17 1 1 1 0 1.1512 18 1 1 0 0 2.5411 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3580 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 290 OPERATED ON BY TRANSFORMATION C012 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.72 2 C002 has 30 10 10 11.02 3 C003 has 2655 885 885 0.00 4 C004 has 870 290 290 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1206 402 402 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1248 416 416 0.00 9 C009 has 1260 420 420 0.00 Total of12658 atoms and 4212 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> 3 atoms have been selected out of 3580 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 = 3577 Number of groups = 1185 Number of bonds = 3571 Number of angles = 1289 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1183 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 = 3577 Number of groups = 1185 Number of bonds = 3571 Number of angles = 1289 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1183 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 <- "35.802" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1180" Evaluating: 1180-13 Parameter: NUMWAT <- "1167" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1167" Comparing "1075" and "1167". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.802" Parameter: BOX -> "35.802" Parameter: BOX -> "35.802" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.80200 B = 35.80200 C = 35.80200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6402 2 1 -1 -2 -1 13.7497 3 1 -1 -1 -1 4.1663 4 1 -1 0 -1 3.0579 5 1 0 -1 -1 4.4933 6 1 0 0 -1 4.6699 7 1 -1 -1 0 1.1515 8 1 -1 0 0 2.5402 9 1 0 -1 0 2.8263 10 1 0 1 0 2.8263 11 1 0 0 1 4.6699 12 1 0 1 1 4.4933 13 1 2 1 1 8.6402 14 1 1 2 1 13.7497 15 1 1 1 1 4.1663 16 1 1 0 1 3.0579 17 1 1 1 0 1.1515 18 1 1 0 0 2.5402 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3577 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 441 OPERATED ON BY TRANSFORMATION C009 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.72 2 C002 has 30 10 10 11.02 3 C003 has 2649 883 883 0.00 4 C004 has 873 291 291 0.00 5 C005 has 825 275 275 0.00 6 C006 has 1206 402 402 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1248 416 416 0.00 9 C009 has 1257 419 419 0.00 Total of12643 atoms and 4207 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> 3 atoms have been selected out of 3577 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 = 1179 Number of atoms = 3574 Number of groups = 1184 Number of bonds = 3568 Number of angles = 1288 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1182 Number of HB donors = 2340 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1179 Number of atoms = 3574 Number of groups = 1184 Number of bonds = 3568 Number of angles = 1288 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1182 Number of HB donors = 2340 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.8" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1179" Evaluating: 1179-13 Parameter: NUMWAT <- "1166" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1166" Comparing "1075" and "1166". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.8" Parameter: BOX -> "35.8" Parameter: BOX -> "35.8" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.80000 B = 35.80000 C = 35.80000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6372 2 1 -1 -2 -1 13.7466 3 1 -1 -1 -1 4.1660 4 1 -1 0 -1 3.0580 5 1 0 -1 -1 4.4938 6 1 0 0 -1 4.6705 7 1 -1 -1 0 1.1518 8 1 -1 0 0 2.5394 9 1 0 -1 0 2.8246 10 1 0 1 0 2.8246 11 1 0 0 1 4.6705 12 1 0 1 1 4.4938 13 1 2 1 1 8.6372 14 1 1 2 1 13.7466 15 1 1 1 1 4.1660 16 1 1 0 1 3.0580 17 1 1 1 0 1.1518 18 1 1 0 0 2.5394 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3498 atoms have been selected out of 3574 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.71 2 C002 has 30 10 10 11.02 3 C003 has 2649 883 883 0.00 4 C004 has 870 290 290 0.00 5 C005 has 825 275 275 0.00 6 C006 has 1203 401 401 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1248 416 416 0.00 9 C009 has 1254 418 418 0.00 Total of12631 atoms and 4203 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 3574 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1179 Number of atoms = 3574 Number of groups = 1184 Number of bonds = 3568 Number of angles = 1288 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1182 Number of HB donors = 2340 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1179 Number of atoms = 3574 Number of groups = 1184 Number of bonds = 3568 Number of angles = 1288 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1182 Number of HB donors = 2340 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.798" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1179" Evaluating: 1179-13 Parameter: NUMWAT <- "1166" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1166" Comparing "1075" and "1166". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.798" Parameter: BOX -> "35.798" Parameter: BOX -> "35.798" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.79800 B = 35.79800 C = 35.79800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6341 2 1 -1 -2 -1 13.7436 3 1 -1 -1 -1 4.1657 4 1 -1 0 -1 3.0580 5 1 0 -1 -1 4.4943 6 1 0 0 -1 4.6710 7 1 -1 -1 0 1.1521 8 1 -1 0 0 2.5385 9 1 0 -1 0 2.8230 10 1 0 1 0 2.8230 11 1 0 0 1 4.6710 12 1 0 1 1 4.4943 13 1 2 1 1 8.6341 14 1 1 2 1 13.7436 15 1 1 1 1 4.1657 16 1 1 0 1 3.0580 17 1 1 1 0 1.1521 18 1 1 0 0 2.5385 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3498 atoms have been selected out of 3574 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 498 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.71 2 C002 has 30 10 10 11.01 3 C003 has 2652 884 884 0.00 4 C004 has 873 291 291 0.00 5 C005 has 825 275 275 0.00 6 C006 has 1191 397 397 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1245 415 415 0.00 9 C009 has 1254 418 418 0.00 Total of12619 atoms and 4199 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 3574 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 = 1178 Number of atoms = 3571 Number of groups = 1183 Number of bonds = 3565 Number of angles = 1287 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1181 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 = 3571 Number of groups = 1183 Number of bonds = 3565 Number of angles = 1287 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1181 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 <- "35.796" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1178" Evaluating: 1178-13 Parameter: NUMWAT <- "1165" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1165" Comparing "1075" and "1165". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.796" Parameter: BOX -> "35.796" Parameter: BOX -> "35.796" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.79600 B = 35.79600 C = 35.79600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6311 2 1 -1 -2 -1 13.7405 3 1 -1 -1 -1 4.1654 4 1 -1 0 -1 3.0581 5 1 0 -1 -1 4.4947 6 1 0 0 -1 4.6716 7 1 -1 -1 0 1.1523 8 1 -1 0 0 2.5376 9 1 0 -1 0 2.8214 10 1 0 1 0 2.8214 11 1 0 0 1 4.6716 12 1 0 1 1 4.4947 13 1 2 1 1 8.6311 14 1 1 2 1 13.7405 15 1 1 1 1 4.1654 16 1 1 0 1 3.0581 17 1 1 1 0 1.1523 18 1 1 0 0 2.5376 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3571 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 804 OPERATED ON BY TRANSFORMATION C004 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.71 2 C002 has 30 10 10 11.01 3 C003 has 2646 882 882 0.00 4 C004 has 867 289 289 0.00 5 C005 has 825 275 275 0.00 6 C006 has 1185 395 395 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1245 415 415 0.00 9 C009 has 1257 419 419 0.00 Total of12601 atoms and 4193 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 3571 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 = 1177 Number of atoms = 3568 Number of groups = 1182 Number of bonds = 3562 Number of angles = 1286 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2336 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1177 Number of atoms = 3568 Number of groups = 1182 Number of bonds = 3562 Number of angles = 1286 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2336 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.794" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1177" Evaluating: 1177-13 Parameter: NUMWAT <- "1164" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1164" Comparing "1075" and "1164". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.794" Parameter: BOX -> "35.794" Parameter: BOX -> "35.794" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.79400 B = 35.79400 C = 35.79400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6281 2 1 -1 -2 -1 13.7374 3 1 -1 -1 -1 4.1651 4 1 -1 0 -1 3.0582 5 1 0 -1 -1 4.4952 6 1 0 0 -1 4.6721 7 1 -1 -1 0 1.1526 8 1 -1 0 0 2.5367 9 1 0 -1 0 2.8198 10 1 0 1 0 2.8198 11 1 0 0 1 4.6721 12 1 0 1 1 4.4952 13 1 2 1 1 8.6281 14 1 1 2 1 13.7374 15 1 1 1 1 4.1651 16 1 1 0 1 3.0582 17 1 1 1 0 1.1526 18 1 1 0 0 2.5367 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3492 atoms have been selected out of 3568 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.70 2 C002 has 30 10 10 11.01 3 C003 has 2646 882 882 0.00 4 C004 has 867 289 289 0.00 5 C005 has 825 275 275 0.00 6 C006 has 1185 395 395 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1245 415 415 0.00 9 C009 has 1254 418 418 0.00 Total of12595 atoms and 4191 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 3568 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1177 Number of atoms = 3568 Number of groups = 1182 Number of bonds = 3562 Number of angles = 1286 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2336 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1177 Number of atoms = 3568 Number of groups = 1182 Number of bonds = 3562 Number of angles = 1286 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2336 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.792" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1177" Evaluating: 1177-13 Parameter: NUMWAT <- "1164" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1164" Comparing "1075" and "1164". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.792" Parameter: BOX -> "35.792" Parameter: BOX -> "35.792" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.79200 B = 35.79200 C = 35.79200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6251 2 1 -1 -2 -1 13.7344 3 1 -1 -1 -1 4.1648 4 1 -1 0 -1 3.0582 5 1 0 -1 -1 4.4957 6 1 0 0 -1 4.6726 7 1 -1 -1 0 1.1529 8 1 -1 0 0 2.5359 9 1 0 -1 0 2.8182 10 1 0 1 0 2.8182 11 1 0 0 1 4.6726 12 1 0 1 1 4.4957 13 1 2 1 1 8.6251 14 1 1 2 1 13.7344 15 1 1 1 1 4.1648 16 1 1 0 1 3.0582 17 1 1 1 0 1.1529 18 1 1 0 0 2.5359 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3492 atoms have been selected out of 3568 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.70 2 C002 has 30 10 10 11.00 3 C003 has 2646 882 882 0.00 4 C004 has 867 289 289 0.00 5 C005 has 825 275 275 0.00 6 C006 has 1185 395 395 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1245 415 415 0.00 9 C009 has 1254 418 418 0.00 Total of12595 atoms and 4191 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 3568 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1177 Number of atoms = 3568 Number of groups = 1182 Number of bonds = 3562 Number of angles = 1286 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2336 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1177 Number of atoms = 3568 Number of groups = 1182 Number of bonds = 3562 Number of angles = 1286 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2336 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.79" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1177" Evaluating: 1177-13 Parameter: NUMWAT <- "1164" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1164" Comparing "1075" and "1164". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.79" Parameter: BOX -> "35.79" Parameter: BOX -> "35.79" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.79000 B = 35.79000 C = 35.79000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6221 2 1 -1 -2 -1 13.7313 3 1 -1 -1 -1 4.1645 4 1 -1 0 -1 3.0583 5 1 0 -1 -1 4.4962 6 1 0 0 -1 4.6732 7 1 -1 -1 0 1.1533 8 1 -1 0 0 2.5350 9 1 0 -1 0 2.8165 10 1 0 1 0 2.8165 11 1 0 0 1 4.6732 12 1 0 1 1 4.4962 13 1 2 1 1 8.6221 14 1 1 2 1 13.7313 15 1 1 1 1 4.1645 16 1 1 0 1 3.0583 17 1 1 1 0 1.1533 18 1 1 0 0 2.5350 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3492 atoms have been selected out of 3568 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.70 2 C002 has 30 10 10 11.00 3 C003 has 2646 882 882 0.00 4 C004 has 867 289 289 0.00 5 C005 has 825 275 275 0.00 6 C006 has 1185 395 395 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1245 415 415 0.00 9 C009 has 1254 418 418 0.00 Total of12595 atoms and 4191 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 3568 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1177 Number of atoms = 3568 Number of groups = 1182 Number of bonds = 3562 Number of angles = 1286 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2336 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1177 Number of atoms = 3568 Number of groups = 1182 Number of bonds = 3562 Number of angles = 1286 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2336 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.788" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1177" Evaluating: 1177-13 Parameter: NUMWAT <- "1164" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1164" Comparing "1075" and "1164". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.788" Parameter: BOX -> "35.788" Parameter: BOX -> "35.788" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.78800 B = 35.78800 C = 35.78800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6190 2 1 -1 -2 -1 13.7283 3 1 -1 -1 -1 4.1643 4 1 -1 0 -1 3.0583 5 1 0 -1 -1 4.4966 6 1 0 0 -1 4.6737 7 1 -1 -1 0 1.1536 8 1 -1 0 0 2.5341 9 1 0 -1 0 2.8149 10 1 0 1 0 2.8149 11 1 0 0 1 4.6737 12 1 0 1 1 4.4966 13 1 2 1 1 8.6190 14 1 1 2 1 13.7283 15 1 1 1 1 4.1643 16 1 1 0 1 3.0583 17 1 1 1 0 1.1536 18 1 1 0 0 2.5341 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3492 atoms have been selected out of 3568 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.70 2 C002 has 30 10 10 11.00 3 C003 has 2646 882 882 0.00 4 C004 has 867 289 289 0.00 5 C005 has 825 275 275 0.00 6 C006 has 1185 395 395 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1245 415 415 0.00 9 C009 has 1254 418 418 0.00 Total of12595 atoms and 4191 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 3568 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1177 Number of atoms = 3568 Number of groups = 1182 Number of bonds = 3562 Number of angles = 1286 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2336 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1177 Number of atoms = 3568 Number of groups = 1182 Number of bonds = 3562 Number of angles = 1286 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2336 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.786" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1177" Evaluating: 1177-13 Parameter: NUMWAT <- "1164" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1164" Comparing "1075" and "1164". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.786" Parameter: BOX -> "35.786" Parameter: BOX -> "35.786" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.78600 B = 35.78600 C = 35.78600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6160 2 1 -1 -2 -1 13.7252 3 1 -1 -1 -1 4.1640 4 1 -1 0 -1 3.0584 5 1 0 -1 -1 4.4971 6 1 0 0 -1 4.6743 7 1 -1 -1 0 1.1539 8 1 -1 0 0 2.5333 9 1 0 -1 0 2.8133 10 1 0 1 0 2.8133 11 1 0 0 1 4.6743 12 1 0 1 1 4.4971 13 1 2 1 1 8.6160 14 1 1 2 1 13.7252 15 1 1 1 1 4.1640 16 1 1 0 1 3.0584 17 1 1 1 0 1.1539 18 1 1 0 0 2.5333 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3492 atoms have been selected out of 3568 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.69 2 C002 has 30 10 10 10.99 3 C003 has 2646 882 882 0.00 4 C004 has 867 289 289 0.00 5 C005 has 825 275 275 0.00 6 C006 has 1185 395 395 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1245 415 415 0.00 9 C009 has 1254 418 418 0.00 Total of12595 atoms and 4191 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 3568 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1177 Number of atoms = 3568 Number of groups = 1182 Number of bonds = 3562 Number of angles = 1286 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2336 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1177 Number of atoms = 3568 Number of groups = 1182 Number of bonds = 3562 Number of angles = 1286 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2336 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.784" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1177" Evaluating: 1177-13 Parameter: NUMWAT <- "1164" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1164" Comparing "1075" and "1164". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.784" Parameter: BOX -> "35.784" Parameter: BOX -> "35.784" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.78400 B = 35.78400 C = 35.78400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6130 2 1 -1 -2 -1 13.7221 3 1 -1 -1 -1 4.1637 4 1 -1 0 -1 3.0585 5 1 0 -1 -1 4.4976 6 1 0 0 -1 4.6748 7 1 -1 -1 0 1.1542 8 1 -1 0 0 2.5324 9 1 0 -1 0 2.8117 10 1 0 1 0 2.8117 11 1 0 0 1 4.6748 12 1 0 1 1 4.4976 13 1 2 1 1 8.6130 14 1 1 2 1 13.7221 15 1 1 1 1 4.1637 16 1 1 0 1 3.0585 17 1 1 1 0 1.1542 18 1 1 0 0 2.5324 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3492 atoms have been selected out of 3568 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.69 2 C002 has 30 10 10 10.99 3 C003 has 2649 883 883 0.00 4 C004 has 867 289 289 0.00 5 C005 has 828 276 276 0.00 6 C006 has 1185 395 395 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1245 415 415 0.00 9 C009 has 1254 418 418 0.00 Total of12601 atoms and 4193 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 3568 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1177 Number of atoms = 3568 Number of groups = 1182 Number of bonds = 3562 Number of angles = 1286 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2336 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1177 Number of atoms = 3568 Number of groups = 1182 Number of bonds = 3562 Number of angles = 1286 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2336 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.782" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1177" Evaluating: 1177-13 Parameter: NUMWAT <- "1164" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1164" Comparing "1075" and "1164". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.782" Parameter: BOX -> "35.782" Parameter: BOX -> "35.782" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.78200 B = 35.78200 C = 35.78200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6100 2 1 -1 -2 -1 13.7191 3 1 -1 -1 -1 4.1634 4 1 -1 0 -1 3.0585 5 1 0 -1 -1 4.4981 6 1 0 0 -1 4.6754 7 1 -1 -1 0 1.1545 8 1 -1 0 0 2.5316 9 1 0 -1 0 2.8100 10 1 0 1 0 2.8100 11 1 0 0 1 4.6754 12 1 0 1 1 4.4981 13 1 2 1 1 8.6100 14 1 1 2 1 13.7191 15 1 1 1 1 4.1634 16 1 1 0 1 3.0585 17 1 1 1 0 1.1545 18 1 1 0 0 2.5316 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3492 atoms have been selected out of 3568 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.69 2 C002 has 30 10 10 10.99 3 C003 has 2649 883 883 0.00 4 C004 has 867 289 289 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1185 395 395 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1245 415 415 0.00 9 C009 has 1254 418 418 0.00 Total of12607 atoms and 4195 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 3568 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1177 Number of atoms = 3568 Number of groups = 1182 Number of bonds = 3562 Number of angles = 1286 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2336 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1177 Number of atoms = 3568 Number of groups = 1182 Number of bonds = 3562 Number of angles = 1286 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2336 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.78" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1177" Evaluating: 1177-13 Parameter: NUMWAT <- "1164" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1164" Comparing "1075" and "1164". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.78" Parameter: BOX -> "35.78" Parameter: BOX -> "35.78" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.78000 B = 35.78000 C = 35.78000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6069 2 1 -1 -2 -1 13.7160 3 1 -1 -1 -1 4.1631 4 1 -1 0 -1 3.0586 5 1 0 -1 -1 4.4985 6 1 0 0 -1 4.6759 7 1 -1 -1 0 1.1548 8 1 -1 0 0 2.5307 9 1 0 -1 0 2.8084 10 1 0 1 0 2.8084 11 1 0 0 1 4.6759 12 1 0 1 1 4.4985 13 1 2 1 1 8.6069 14 1 1 2 1 13.7160 15 1 1 1 1 4.1631 16 1 1 0 1 3.0586 17 1 1 1 0 1.1548 18 1 1 0 0 2.5307 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3492 atoms have been selected out of 3568 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.68 2 C002 has 33 11 11 10.98 3 C003 has 2649 883 883 0.00 4 C004 has 867 289 289 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1185 395 395 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1248 416 416 0.00 9 C009 has 1254 418 418 0.00 Total of12613 atoms and 4197 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 3568 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1177 Number of atoms = 3568 Number of groups = 1182 Number of bonds = 3562 Number of angles = 1286 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2336 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1177 Number of atoms = 3568 Number of groups = 1182 Number of bonds = 3562 Number of angles = 1286 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2336 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.778" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1177" Evaluating: 1177-13 Parameter: NUMWAT <- "1164" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1164" Comparing "1075" and "1164". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.778" Parameter: BOX -> "35.778" Parameter: BOX -> "35.778" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.77800 B = 35.77800 C = 35.77800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6039 2 1 -1 -2 -1 13.7129 3 1 -1 -1 -1 4.1628 4 1 -1 0 -1 3.0587 5 1 0 -1 -1 4.4990 6 1 0 0 -1 4.6764 7 1 -1 -1 0 1.1552 8 1 -1 0 0 2.5298 9 1 0 -1 0 2.8068 10 1 0 1 0 2.8068 11 1 0 0 1 4.6764 12 1 0 1 1 4.4990 13 1 2 1 1 8.6039 14 1 1 2 1 13.7129 15 1 1 1 1 4.1628 16 1 1 0 1 3.0587 17 1 1 1 0 1.1552 18 1 1 0 0 2.5298 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3492 atoms have been selected out of 3568 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.68 2 C002 has 33 11 11 10.98 3 C003 has 2649 883 883 0.00 4 C004 has 867 289 289 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1185 395 395 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1248 416 416 0.00 9 C009 has 1254 418 418 0.00 Total of12613 atoms and 4197 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 3568 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1177 Number of atoms = 3568 Number of groups = 1182 Number of bonds = 3562 Number of angles = 1286 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2336 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1177 Number of atoms = 3568 Number of groups = 1182 Number of bonds = 3562 Number of angles = 1286 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2336 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.776" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1177" Evaluating: 1177-13 Parameter: NUMWAT <- "1164" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1164" Comparing "1075" and "1164". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.776" Parameter: BOX -> "35.776" Parameter: BOX -> "35.776" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.77600 B = 35.77600 C = 35.77600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.6009 2 1 -1 -2 -1 13.7099 3 1 -1 -1 -1 4.1626 4 1 -1 0 -1 3.0587 5 1 0 -1 -1 4.4995 6 1 0 0 -1 4.6770 7 1 -1 -1 0 1.1555 8 1 -1 0 0 2.5290 9 1 0 -1 0 2.8052 10 1 0 1 0 2.8052 11 1 0 0 1 4.6770 12 1 0 1 1 4.4995 13 1 2 1 1 8.6009 14 1 1 2 1 13.7099 15 1 1 1 1 4.1626 16 1 1 0 1 3.0587 17 1 1 1 0 1.1555 18 1 1 0 0 2.5290 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3492 atoms have been selected out of 3568 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.68 2 C002 has 33 11 11 10.98 3 C003 has 2649 883 883 0.00 4 C004 has 867 289 289 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1185 395 395 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1248 416 416 0.00 9 C009 has 1254 418 418 0.00 Total of12613 atoms and 4197 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 3568 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1177 Number of atoms = 3568 Number of groups = 1182 Number of bonds = 3562 Number of angles = 1286 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2336 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1177 Number of atoms = 3568 Number of groups = 1182 Number of bonds = 3562 Number of angles = 1286 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2336 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.774" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1177" Evaluating: 1177-13 Parameter: NUMWAT <- "1164" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1164" Comparing "1075" and "1164". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.774" Parameter: BOX -> "35.774" Parameter: BOX -> "35.774" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.77400 B = 35.77400 C = 35.77400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.5979 2 1 -1 -2 -1 13.7068 3 1 -1 -1 -1 4.1623 4 1 -1 0 -1 3.0588 5 1 0 -1 -1 4.5000 6 1 0 0 -1 4.6775 7 1 -1 -1 0 1.1559 8 1 -1 0 0 2.5281 9 1 0 -1 0 2.8036 10 1 0 1 0 2.8036 11 1 0 0 1 4.6775 12 1 0 1 1 4.5000 13 1 2 1 1 8.5979 14 1 1 2 1 13.7068 15 1 1 1 1 4.1623 16 1 1 0 1 3.0588 17 1 1 1 0 1.1559 18 1 1 0 0 2.5281 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3492 atoms have been selected out of 3568 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.67 2 C002 has 33 11 11 10.98 3 C003 has 2649 883 883 0.00 4 C004 has 867 289 289 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1185 395 395 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1248 416 416 0.00 9 C009 has 1254 418 418 0.00 Total of12613 atoms and 4197 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 3568 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1177 Number of atoms = 3568 Number of groups = 1182 Number of bonds = 3562 Number of angles = 1286 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2336 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1177 Number of atoms = 3568 Number of groups = 1182 Number of bonds = 3562 Number of angles = 1286 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2336 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.772" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1177" Evaluating: 1177-13 Parameter: NUMWAT <- "1164" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1164" Comparing "1075" and "1164". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.772" Parameter: BOX -> "35.772" Parameter: BOX -> "35.772" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.77200 B = 35.77200 C = 35.77200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.5949 2 1 -1 -2 -1 13.7037 3 1 -1 -1 -1 4.1620 4 1 -1 0 -1 3.0589 5 1 0 -1 -1 4.5005 6 1 0 0 -1 4.6781 7 1 -1 -1 0 1.1562 8 1 -1 0 0 2.5273 9 1 0 -1 0 2.8020 10 1 0 1 0 2.8020 11 1 0 0 1 4.6781 12 1 0 1 1 4.5005 13 1 2 1 1 8.5949 14 1 1 2 1 13.7037 15 1 1 1 1 4.1620 16 1 1 0 1 3.0589 17 1 1 1 0 1.1562 18 1 1 0 0 2.5273 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3492 atoms have been selected out of 3568 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.67 2 C002 has 33 11 11 10.97 3 C003 has 2649 883 883 0.00 4 C004 has 867 289 289 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1185 395 395 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1248 416 416 0.00 9 C009 has 1254 418 418 0.00 Total of12616 atoms and 4198 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 3568 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1177 Number of atoms = 3568 Number of groups = 1182 Number of bonds = 3562 Number of angles = 1286 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2336 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1177 Number of atoms = 3568 Number of groups = 1182 Number of bonds = 3562 Number of angles = 1286 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1180 Number of HB donors = 2336 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.77" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1177" Evaluating: 1177-13 Parameter: NUMWAT <- "1164" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1164" Comparing "1075" and "1164". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.77" Parameter: BOX -> "35.77" Parameter: BOX -> "35.77" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.77000 B = 35.77000 C = 35.77000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.5918 2 1 -1 -2 -1 13.7007 3 1 -1 -1 -1 4.1617 4 1 -1 0 -1 3.0590 5 1 0 -1 -1 4.5010 6 1 0 0 -1 4.6786 7 1 -1 -1 0 1.1565 8 1 -1 0 0 2.5264 9 1 0 -1 0 2.8003 10 1 0 1 0 2.8003 11 1 0 0 1 4.6786 12 1 0 1 1 4.5010 13 1 2 1 1 8.5918 14 1 1 2 1 13.7007 15 1 1 1 1 4.1617 16 1 1 0 1 3.0590 17 1 1 1 0 1.1565 18 1 1 0 0 2.5264 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3492 atoms have been selected out of 3568 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 C004 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.67 2 C002 has 33 11 11 10.97 3 C003 has 2649 883 883 0.00 4 C004 has 882 294 294 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1191 397 397 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1245 415 415 0.00 9 C009 has 1257 419 419 0.00 Total of12637 atoms and 4205 groups and 4200 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3568 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 = 1176 Number of atoms = 3565 Number of groups = 1181 Number of bonds = 3559 Number of angles = 1285 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1179 Number of HB donors = 2334 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1176 Number of atoms = 3565 Number of groups = 1181 Number of bonds = 3559 Number of angles = 1285 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1179 Number of HB donors = 2334 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.768" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1176" Evaluating: 1176-13 Parameter: NUMWAT <- "1163" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1163" Comparing "1075" and "1163". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.768" Parameter: BOX -> "35.768" Parameter: BOX -> "35.768" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.76800 B = 35.76800 C = 35.76800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.5888 2 1 -1 -2 -1 13.6976 3 1 -1 -1 -1 4.1615 4 1 -1 0 -1 3.0590 5 1 0 -1 -1 4.5015 6 1 0 0 -1 4.6792 7 1 -1 -1 0 1.1569 8 1 -1 0 0 6.5527 9 1 0 -1 0 2.7987 10 1 0 1 0 2.7987 11 1 0 0 1 4.6792 12 1 0 1 1 4.5015 13 1 2 1 1 8.5888 14 1 1 2 1 13.6976 15 1 1 1 1 4.1615 16 1 1 0 1 3.0590 17 1 1 1 0 1.1569 18 1 1 0 0 6.5527 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3489 atoms have been selected out of 3565 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.66 2 C002 has 33 11 11 10.97 3 C003 has 2646 882 882 0.00 4 C004 has 864 288 288 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1182 394 394 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1245 415 415 0.00 9 C009 has 1254 418 418 0.00 Total of12601 atoms and 4193 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 3565 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1176 Number of atoms = 3565 Number of groups = 1181 Number of bonds = 3559 Number of angles = 1285 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1179 Number of HB donors = 2334 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1176 Number of atoms = 3565 Number of groups = 1181 Number of bonds = 3559 Number of angles = 1285 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1179 Number of HB donors = 2334 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.766" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1176" Evaluating: 1176-13 Parameter: NUMWAT <- "1163" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1163" Comparing "1075" and "1163". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.766" Parameter: BOX -> "35.766" Parameter: BOX -> "35.766" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.76600 B = 35.76600 C = 35.76600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.5858 2 1 -1 -2 -1 13.6946 3 1 -1 -1 -1 4.1612 4 1 -1 0 -1 3.0591 5 1 0 -1 -1 4.5019 6 1 0 0 -1 4.6797 7 1 -1 -1 0 1.1573 8 1 -1 0 0 6.5511 9 1 0 -1 0 2.7971 10 1 0 1 0 2.7971 11 1 0 0 1 4.6797 12 1 0 1 1 4.5019 13 1 2 1 1 8.5858 14 1 1 2 1 13.6946 15 1 1 1 1 4.1612 16 1 1 0 1 3.0591 17 1 1 1 0 1.1573 18 1 1 0 0 6.5511 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3489 atoms have been selected out of 3565 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.66 2 C002 has 33 11 11 10.96 3 C003 has 2646 882 882 0.00 4 C004 has 864 288 288 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1185 395 395 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1245 415 415 0.00 9 C009 has 1254 418 418 0.00 Total of12607 atoms and 4195 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 3565 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1176 Number of atoms = 3565 Number of groups = 1181 Number of bonds = 3559 Number of angles = 1285 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1179 Number of HB donors = 2334 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1176 Number of atoms = 3565 Number of groups = 1181 Number of bonds = 3559 Number of angles = 1285 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1179 Number of HB donors = 2334 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.764" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1176" Evaluating: 1176-13 Parameter: NUMWAT <- "1163" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1163" Comparing "1075" and "1163". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.764" Parameter: BOX -> "35.764" Parameter: BOX -> "35.764" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.76400 B = 35.76400 C = 35.76400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.5828 2 1 -1 -2 -1 13.6915 3 1 -1 -1 -1 4.1609 4 1 -1 0 -1 3.0592 5 1 0 -1 -1 4.5024 6 1 0 0 -1 4.6803 7 1 -1 -1 0 1.1576 8 1 -1 0 0 6.5495 9 1 0 -1 0 2.7955 10 1 0 1 0 2.7955 11 1 0 0 1 4.6803 12 1 0 1 1 4.5024 13 1 2 1 1 8.5828 14 1 1 2 1 13.6915 15 1 1 1 1 4.1609 16 1 1 0 1 3.0592 17 1 1 1 0 1.1576 18 1 1 0 0 6.5495 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3489 atoms have been selected out of 3565 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.66 2 C002 has 33 11 11 10.96 3 C003 has 2646 882 882 0.00 4 C004 has 864 288 288 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1185 395 395 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1245 415 415 0.00 9 C009 has 1254 418 418 0.00 Total of12607 atoms and 4195 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 3565 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1176 Number of atoms = 3565 Number of groups = 1181 Number of bonds = 3559 Number of angles = 1285 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1179 Number of HB donors = 2334 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1176 Number of atoms = 3565 Number of groups = 1181 Number of bonds = 3559 Number of angles = 1285 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1179 Number of HB donors = 2334 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.762" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1176" Evaluating: 1176-13 Parameter: NUMWAT <- "1163" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1163" Comparing "1075" and "1163". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.762" Parameter: BOX -> "35.762" Parameter: BOX -> "35.762" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.76200 B = 35.76200 C = 35.76200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.5798 2 1 -1 -2 -1 13.6884 3 1 -1 -1 -1 4.1606 4 1 -1 0 -1 3.0593 5 1 0 -1 -1 4.5029 6 1 0 0 -1 4.6808 7 1 -1 -1 0 1.1580 8 1 -1 0 0 6.5478 9 1 0 -1 0 2.7939 10 1 0 1 0 2.7939 11 1 0 0 1 4.6808 12 1 0 1 1 4.5029 13 1 2 1 1 8.5798 14 1 1 2 1 13.6884 15 1 1 1 1 4.1606 16 1 1 0 1 3.0593 17 1 1 1 0 1.1580 18 1 1 0 0 6.5478 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3489 atoms have been selected out of 3565 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 716 OPERATED ON BY TRANSFORMATION C006 RESIDUE 783 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.66 2 C002 has 36 12 12 10.96 3 C003 has 2646 882 882 0.00 4 C004 has 861 287 287 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1206 402 402 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1242 414 414 0.00 9 C009 has 1254 418 418 0.00 Total of12616 atoms and 4198 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> 6 atoms have been selected out of 3565 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 = 1174 Number of atoms = 3559 Number of groups = 1179 Number of bonds = 3553 Number of angles = 1283 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1177 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 = 3559 Number of groups = 1179 Number of bonds = 3553 Number of angles = 1283 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1177 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 <- "35.76" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1174" Evaluating: 1174-13 Parameter: NUMWAT <- "1161" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1161" Comparing "1075" and "1161". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.76" Parameter: BOX -> "35.76" Parameter: BOX -> "35.76" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.76000 B = 35.76000 C = 35.76000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.5768 2 1 -1 -2 -1 13.6854 3 1 -1 -1 -1 4.1604 4 1 -1 0 -1 3.0594 5 1 0 -1 -1 4.5034 6 1 0 0 -1 5.3524 7 1 -1 -1 0 4.5302 8 1 -1 0 0 6.5462 9 1 0 -1 0 2.7923 10 1 0 1 0 2.7923 11 1 0 0 1 5.3524 12 1 0 1 1 4.5034 13 1 2 1 1 8.5768 14 1 1 2 1 13.6854 15 1 1 1 1 4.1604 16 1 1 0 1 3.0594 17 1 1 1 0 4.5302 18 1 1 0 0 6.5462 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3559 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.65 2 C002 has 33 11 11 10.95 3 C003 has 2643 881 881 0.00 4 C004 has 861 287 287 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1182 394 394 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1242 414 414 0.00 9 C009 has 1251 417 417 0.00 Total of12574 atoms and 4184 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 3559 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3559 Number of groups = 1179 Number of bonds = 3553 Number of angles = 1283 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1177 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 = 3559 Number of groups = 1179 Number of bonds = 3553 Number of angles = 1283 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1177 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 <- "35.758" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1174" Evaluating: 1174-13 Parameter: NUMWAT <- "1161" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1161" Comparing "1075" and "1161". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.758" Parameter: BOX -> "35.758" Parameter: BOX -> "35.758" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.75800 B = 35.75800 C = 35.75800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.5737 2 1 -1 -2 -1 13.6823 3 1 -1 -1 -1 4.1601 4 1 -1 0 -1 3.0595 5 1 0 -1 -1 4.5039 6 1 0 0 -1 5.3506 7 1 -1 -1 0 4.5300 8 1 -1 0 0 6.5445 9 1 0 -1 0 2.7906 10 1 0 1 0 2.7906 11 1 0 0 1 5.3506 12 1 0 1 1 4.5039 13 1 2 1 1 8.5737 14 1 1 2 1 13.6823 15 1 1 1 1 4.1601 16 1 1 0 1 3.0595 17 1 1 1 0 4.5300 18 1 1 0 0 6.5445 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3559 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.65 2 C002 has 33 11 11 10.95 3 C003 has 2643 881 881 0.00 4 C004 has 864 288 288 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1182 394 394 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1242 414 414 0.00 9 C009 has 1251 417 417 0.00 Total of12577 atoms and 4185 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 3559 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3559 Number of groups = 1179 Number of bonds = 3553 Number of angles = 1283 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1177 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 = 3559 Number of groups = 1179 Number of bonds = 3553 Number of angles = 1283 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1177 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 <- "35.756" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1174" Evaluating: 1174-13 Parameter: NUMWAT <- "1161" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1161" Comparing "1075" and "1161". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.756" Parameter: BOX -> "35.756" Parameter: BOX -> "35.756" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.75600 B = 35.75600 C = 35.75600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.5707 2 1 -1 -2 -1 13.6792 3 1 -1 -1 -1 4.1598 4 1 -1 0 -1 3.0596 5 1 0 -1 -1 4.5044 6 1 0 0 -1 5.3488 7 1 -1 -1 0 4.5298 8 1 -1 0 0 6.5429 9 1 0 -1 0 2.7890 10 1 0 1 0 2.7890 11 1 0 0 1 5.3488 12 1 0 1 1 4.5044 13 1 2 1 1 8.5707 14 1 1 2 1 13.6792 15 1 1 1 1 4.1598 16 1 1 0 1 3.0596 17 1 1 1 0 4.5298 18 1 1 0 0 6.5429 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3559 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.65 2 C002 has 33 11 11 10.95 3 C003 has 2643 881 881 0.00 4 C004 has 864 288 288 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1182 394 394 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1242 414 414 0.00 9 C009 has 1251 417 417 0.00 Total of12577 atoms and 4185 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 3559 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3559 Number of groups = 1179 Number of bonds = 3553 Number of angles = 1283 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1177 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 = 3559 Number of groups = 1179 Number of bonds = 3553 Number of angles = 1283 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1177 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 <- "35.754" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1174" Evaluating: 1174-13 Parameter: NUMWAT <- "1161" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1161" Comparing "1075" and "1161". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.754" Parameter: BOX -> "35.754" Parameter: BOX -> "35.754" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.75400 B = 35.75400 C = 35.75400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.5677 2 1 -1 -2 -1 13.6762 3 1 -1 -1 -1 4.1596 4 1 -1 0 -1 3.0597 5 1 0 -1 -1 4.5049 6 1 0 0 -1 5.3470 7 1 -1 -1 0 4.5296 8 1 -1 0 0 6.5413 9 1 0 -1 0 2.7874 10 1 0 1 0 2.7874 11 1 0 0 1 5.3470 12 1 0 1 1 4.5049 13 1 2 1 1 8.5677 14 1 1 2 1 13.6762 15 1 1 1 1 4.1596 16 1 1 0 1 3.0597 17 1 1 1 0 4.5296 18 1 1 0 0 6.5413 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3559 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 219 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.64 2 C002 has 33 11 11 10.94 3 C003 has 2643 881 881 0.00 4 C004 has 864 288 288 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1182 394 394 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1239 413 413 0.00 9 C009 has 1251 417 417 0.00 Total of12580 atoms and 4186 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 3559 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 = 3556 Number of groups = 1178 Number of bonds = 3550 Number of angles = 1282 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1176 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 = 3556 Number of groups = 1178 Number of bonds = 3550 Number of angles = 1282 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1176 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 <- "35.752" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1173" Evaluating: 1173-13 Parameter: NUMWAT <- "1160" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1160" Comparing "1075" and "1160". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.752" Parameter: BOX -> "35.752" Parameter: BOX -> "35.752" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.75200 B = 35.75200 C = 35.75200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.5647 2 1 -1 -2 -1 13.6731 3 1 -1 -1 -1 4.1593 4 1 -1 0 -1 3.0597 5 1 0 -1 -1 4.5054 6 1 0 0 -1 5.3452 7 1 -1 -1 0 4.5294 8 1 -1 0 0 6.5396 9 1 0 -1 0 2.7858 10 1 0 1 0 2.7858 11 1 0 0 1 5.3452 12 1 0 1 1 4.5054 13 1 2 1 1 8.5647 14 1 1 2 1 13.6731 15 1 1 1 1 4.1593 16 1 1 0 1 3.0597 17 1 1 1 0 4.5294 18 1 1 0 0 6.5396 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3556 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.64 2 C002 has 33 11 11 10.94 3 C003 has 2643 881 881 0.00 4 C004 has 867 289 289 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1182 394 394 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1239 413 413 0.00 9 C009 has 1251 417 417 0.00 Total of12577 atoms and 4185 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 3556 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3556 Number of groups = 1178 Number of bonds = 3550 Number of angles = 1282 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1176 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 = 3556 Number of groups = 1178 Number of bonds = 3550 Number of angles = 1282 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1176 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 <- "35.75" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1173" Evaluating: 1173-13 Parameter: NUMWAT <- "1160" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1160" Comparing "1075" and "1160". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.75" Parameter: BOX -> "35.75" Parameter: BOX -> "35.75" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.75000 B = 35.75000 C = 35.75000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.5617 2 1 -1 -2 -1 13.6700 3 1 -1 -1 -1 4.1590 4 1 -1 0 -1 3.0598 5 1 0 -1 -1 4.5059 6 1 0 0 -1 5.3434 7 1 -1 -1 0 4.5292 8 1 -1 0 0 6.5380 9 1 0 -1 0 2.7842 10 1 0 1 0 2.7842 11 1 0 0 1 5.3434 12 1 0 1 1 4.5059 13 1 2 1 1 8.5617 14 1 1 2 1 13.6700 15 1 1 1 1 4.1590 16 1 1 0 1 3.0598 17 1 1 1 0 4.5292 18 1 1 0 0 6.5380 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3556 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.64 2 C002 has 33 11 11 10.94 3 C003 has 2643 881 881 0.00 4 C004 has 867 289 289 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1182 394 394 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1239 413 413 0.00 9 C009 has 1251 417 417 0.00 Total of12577 atoms and 4185 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 3556 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3556 Number of groups = 1178 Number of bonds = 3550 Number of angles = 1282 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1176 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 = 3556 Number of groups = 1178 Number of bonds = 3550 Number of angles = 1282 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1176 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 <- "35.748" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1173" Evaluating: 1173-13 Parameter: NUMWAT <- "1160" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1160" Comparing "1075" and "1160". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.748" Parameter: BOX -> "35.748" Parameter: BOX -> "35.748" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.74800 B = 35.74800 C = 35.74800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.5586 2 1 -1 -2 -1 13.6670 3 1 -1 -1 -1 4.1588 4 1 -1 0 -1 3.0599 5 1 0 -1 -1 4.5064 6 1 0 0 -1 5.3416 7 1 -1 -1 0 4.5291 8 1 -1 0 0 6.5363 9 1 0 -1 0 2.7826 10 1 0 1 0 2.7826 11 1 0 0 1 5.3416 12 1 0 1 1 4.5064 13 1 2 1 1 8.5586 14 1 1 2 1 13.6670 15 1 1 1 1 4.1588 16 1 1 0 1 3.0599 17 1 1 1 0 4.5291 18 1 1 0 0 6.5363 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3556 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.63 2 C002 has 33 11 11 10.94 3 C003 has 2643 881 881 0.00 4 C004 has 867 289 289 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1182 394 394 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1239 413 413 0.00 9 C009 has 1251 417 417 0.00 Total of12577 atoms and 4185 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 3556 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3556 Number of groups = 1178 Number of bonds = 3550 Number of angles = 1282 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1176 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 = 3556 Number of groups = 1178 Number of bonds = 3550 Number of angles = 1282 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1176 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 <- "35.746" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1173" Evaluating: 1173-13 Parameter: NUMWAT <- "1160" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1160" Comparing "1075" and "1160". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.746" Parameter: BOX -> "35.746" Parameter: BOX -> "35.746" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.74600 B = 35.74600 C = 35.74600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.5556 2 1 -1 -2 -1 13.9975 3 1 -1 -1 -1 4.1585 4 1 -1 0 -1 3.0600 5 1 0 -1 -1 4.5069 6 1 0 0 -1 5.3398 7 1 -1 -1 0 4.5289 8 1 -1 0 0 6.5347 9 1 0 -1 0 2.7810 10 1 0 1 0 2.7810 11 1 0 0 1 5.3398 12 1 0 1 1 4.5069 13 1 2 1 1 8.5556 14 1 1 2 1 13.9975 15 1 1 1 1 4.1585 16 1 1 0 1 3.0600 17 1 1 1 0 4.5289 18 1 1 0 0 6.5347 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3556 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.63 2 C002 has 33 11 11 10.93 3 C003 has 2643 881 881 0.00 4 C004 has 867 289 289 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1182 394 394 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1239 413 413 0.00 9 C009 has 1251 417 417 0.00 Total of12577 atoms and 4185 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 3556 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3556 Number of groups = 1178 Number of bonds = 3550 Number of angles = 1282 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1176 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 = 3556 Number of groups = 1178 Number of bonds = 3550 Number of angles = 1282 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1176 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 <- "35.744" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1173" Evaluating: 1173-13 Parameter: NUMWAT <- "1160" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1160" Comparing "1075" and "1160". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.744" Parameter: BOX -> "35.744" Parameter: BOX -> "35.744" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.74400 B = 35.74400 C = 35.74400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.5526 2 1 -1 -2 -1 13.9945 3 1 -1 -1 -1 4.1582 4 1 -1 0 -1 3.0601 5 1 0 -1 -1 4.5074 6 1 0 0 -1 5.3381 7 1 -1 -1 0 4.5287 8 1 -1 0 0 6.5331 9 1 0 -1 0 2.7794 10 1 0 1 0 2.7794 11 1 0 0 1 5.3381 12 1 0 1 1 4.5074 13 1 2 1 1 8.5526 14 1 1 2 1 13.9945 15 1 1 1 1 4.1582 16 1 1 0 1 3.0601 17 1 1 1 0 4.5287 18 1 1 0 0 6.5331 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3556 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.63 2 C002 has 33 11 11 10.93 3 C003 has 2643 881 881 0.00 4 C004 has 867 289 289 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1182 394 394 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1239 413 413 0.00 9 C009 has 1251 417 417 0.00 Total of12577 atoms and 4185 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 3556 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3556 Number of groups = 1178 Number of bonds = 3550 Number of angles = 1282 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1176 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 = 3556 Number of groups = 1178 Number of bonds = 3550 Number of angles = 1282 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1176 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 <- "35.742" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1173" Evaluating: 1173-13 Parameter: NUMWAT <- "1160" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1160" Comparing "1075" and "1160". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.742" Parameter: BOX -> "35.742" Parameter: BOX -> "35.742" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.74200 B = 35.74200 C = 35.74200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.5496 2 1 -1 -2 -1 13.9914 3 1 -1 -1 -1 4.1580 4 1 -1 0 -1 3.0602 5 1 0 -1 -1 4.5079 6 1 0 0 -1 5.3363 7 1 -1 -1 0 4.5285 8 1 -1 0 0 6.5314 9 1 0 -1 0 2.7777 10 1 0 1 0 2.7777 11 1 0 0 1 5.3363 12 1 0 1 1 4.5079 13 1 2 1 1 8.5496 14 1 1 2 1 13.9914 15 1 1 1 1 4.1580 16 1 1 0 1 3.0602 17 1 1 1 0 4.5285 18 1 1 0 0 6.5314 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3556 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.62 2 C002 has 33 11 11 10.93 3 C003 has 2643 881 881 0.00 4 C004 has 867 289 289 0.00 5 C005 has 840 280 280 0.00 6 C006 has 1182 394 394 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1239 413 413 0.00 9 C009 has 1251 417 417 0.00 Total of12580 atoms and 4186 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 3556 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3556 Number of groups = 1178 Number of bonds = 3550 Number of angles = 1282 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1176 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 = 3556 Number of groups = 1178 Number of bonds = 3550 Number of angles = 1282 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1176 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 <- "35.74" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1173" Evaluating: 1173-13 Parameter: NUMWAT <- "1160" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1160" Comparing "1075" and "1160". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.74" Parameter: BOX -> "35.74" Parameter: BOX -> "35.74" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.74000 B = 35.74000 C = 35.74000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.5466 2 1 -1 -2 -1 13.9883 3 1 -1 -1 -1 4.1577 4 1 -1 0 -1 3.0603 5 1 0 -1 -1 4.5084 6 1 0 0 -1 5.3345 7 1 -1 -1 0 4.5283 8 1 -1 0 0 6.5298 9 1 0 -1 0 2.7761 10 1 0 1 0 2.7761 11 1 0 0 1 5.3345 12 1 0 1 1 4.5084 13 1 2 1 1 8.5466 14 1 1 2 1 13.9883 15 1 1 1 1 4.1577 16 1 1 0 1 3.0603 17 1 1 1 0 4.5283 18 1 1 0 0 6.5298 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3556 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.62 2 C002 has 33 11 11 10.92 3 C003 has 2643 881 881 0.00 4 C004 has 867 289 289 0.00 5 C005 has 840 280 280 0.00 6 C006 has 1182 394 394 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1239 413 413 0.00 9 C009 has 1251 417 417 0.00 Total of12580 atoms and 4186 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 3556 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3556 Number of groups = 1178 Number of bonds = 3550 Number of angles = 1282 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1176 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 = 3556 Number of groups = 1178 Number of bonds = 3550 Number of angles = 1282 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1176 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 <- "35.738" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1173" Evaluating: 1173-13 Parameter: NUMWAT <- "1160" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1160" Comparing "1075" and "1160". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.738" Parameter: BOX -> "35.738" Parameter: BOX -> "35.738" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.73800 B = 35.73800 C = 35.73800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.5436 2 1 -1 -2 -1 13.9852 3 1 -1 -1 -1 4.1574 4 1 -1 0 -1 3.0604 5 1 0 -1 -1 4.5089 6 1 0 0 -1 5.3327 7 1 -1 -1 0 4.5281 8 1 -1 0 0 6.5282 9 1 0 -1 0 2.7745 10 1 0 1 0 2.7745 11 1 0 0 1 5.3327 12 1 0 1 1 4.5089 13 1 2 1 1 8.5436 14 1 1 2 1 13.9852 15 1 1 1 1 4.1574 16 1 1 0 1 3.0604 17 1 1 1 0 4.5281 18 1 1 0 0 6.5282 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3556 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.62 2 C002 has 33 11 11 10.92 3 C003 has 2643 881 881 0.00 4 C004 has 867 289 289 0.00 5 C005 has 840 280 280 0.00 6 C006 has 1182 394 394 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1239 413 413 0.00 9 C009 has 1251 417 417 0.00 Total of12580 atoms and 4186 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 3556 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3556 Number of groups = 1178 Number of bonds = 3550 Number of angles = 1282 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1176 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 = 3556 Number of groups = 1178 Number of bonds = 3550 Number of angles = 1282 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1176 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 <- "35.736" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1173" Evaluating: 1173-13 Parameter: NUMWAT <- "1160" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1160" Comparing "1075" and "1160". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.736" Parameter: BOX -> "35.736" Parameter: BOX -> "35.736" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.73600 B = 35.73600 C = 35.73600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.5405 2 1 -1 -2 -1 13.9821 3 1 -1 -1 -1 4.1572 4 1 -1 0 -1 3.0606 5 1 0 -1 -1 4.5094 6 1 0 0 -1 5.3309 7 1 -1 -1 0 4.5279 8 1 -1 0 0 6.5265 9 1 0 -1 0 2.7729 10 1 0 1 0 2.7729 11 1 0 0 1 5.3309 12 1 0 1 1 4.5094 13 1 2 1 1 8.5405 14 1 1 2 1 13.9821 15 1 1 1 1 4.1572 16 1 1 0 1 3.0606 17 1 1 1 0 4.5279 18 1 1 0 0 6.5265 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3556 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 395 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.62 2 C002 has 33 11 11 10.92 3 C003 has 2646 882 882 0.00 4 C004 has 864 288 288 0.00 5 C005 has 840 280 280 0.00 6 C006 has 1185 395 395 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1242 414 414 0.00 9 C009 has 1248 416 416 0.00 Total of12583 atoms and 4187 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 3556 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 = 3553 Number of groups = 1177 Number of bonds = 3547 Number of angles = 1281 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1175 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 = 3553 Number of groups = 1177 Number of bonds = 3547 Number of angles = 1281 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1175 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 <- "35.734" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1172" Evaluating: 1172-13 Parameter: NUMWAT <- "1159" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1159" Comparing "1075" and "1159". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.734" Parameter: BOX -> "35.734" Parameter: BOX -> "35.734" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.73400 B = 35.73400 C = 35.73400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.5375 2 1 -1 -2 -1 13.9790 3 1 -1 -1 -1 4.1569 4 1 -1 0 -1 3.0607 5 1 0 -1 -1 4.5099 6 1 0 0 -1 5.3291 7 1 -1 -1 0 4.5277 8 1 -1 0 0 6.5249 9 1 0 -1 0 2.7713 10 1 0 1 0 2.7713 11 1 0 0 1 5.3291 12 1 0 1 1 4.5099 13 1 2 1 1 8.5375 14 1 1 2 1 13.9790 15 1 1 1 1 4.1569 16 1 1 0 1 3.0607 17 1 1 1 0 4.5277 18 1 1 0 0 6.5249 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3553 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.61 2 C002 has 33 11 11 10.91 3 C003 has 2643 881 881 0.00 4 C004 has 861 287 287 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1182 394 394 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1239 413 413 0.00 9 C009 has 1248 416 416 0.00 Total of12571 atoms and 4183 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 3553 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3553 Number of groups = 1177 Number of bonds = 3547 Number of angles = 1281 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1175 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 = 3553 Number of groups = 1177 Number of bonds = 3547 Number of angles = 1281 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1175 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 <- "35.732" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1172" Evaluating: 1172-13 Parameter: NUMWAT <- "1159" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1159" Comparing "1075" and "1159". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.732" Parameter: BOX -> "35.732" Parameter: BOX -> "35.732" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.73200 B = 35.73200 C = 35.73200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.5345 2 1 -1 -2 -1 13.9760 3 1 -1 -1 -1 4.1567 4 1 -1 0 -1 3.0608 5 1 0 -1 -1 4.5104 6 1 0 0 -1 5.3273 7 1 -1 -1 0 4.5276 8 1 -1 0 0 6.5232 9 1 0 -1 0 2.7697 10 1 0 1 0 2.7697 11 1 0 0 1 5.3273 12 1 0 1 1 4.5104 13 1 2 1 1 8.5345 14 1 1 2 1 13.9760 15 1 1 1 1 4.1567 16 1 1 0 1 3.0608 17 1 1 1 0 4.5276 18 1 1 0 0 6.5232 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3553 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 387 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 156 52 52 6.61 2 C002 has 33 11 11 10.91 3 C003 has 2649 883 883 0.00 4 C004 has 849 283 283 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1185 395 395 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1239 413 413 0.00 9 C009 has 1245 415 415 0.00 Total of12568 atoms and 4182 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 3553 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 = 1171 Number of atoms = 3550 Number of groups = 1176 Number of bonds = 3544 Number of angles = 1280 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1174 Number of HB donors = 2324 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1171 Number of atoms = 3550 Number of groups = 1176 Number of bonds = 3544 Number of angles = 1280 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1174 Number of HB donors = 2324 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.73" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1171" Evaluating: 1171-13 Parameter: NUMWAT <- "1158" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1158" Comparing "1075" and "1158". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.73" Parameter: BOX -> "35.73" Parameter: BOX -> "35.73" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.73000 B = 35.73000 C = 35.73000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.5315 2 1 -1 -2 -1 13.9729 3 1 -1 -1 -1 4.1564 4 1 -1 0 -1 3.0609 5 1 0 -1 -1 4.5109 6 1 0 0 -1 5.3256 7 1 -1 -1 0 4.5274 8 1 -1 0 0 6.5216 9 1 0 -1 0 2.7681 10 1 0 1 0 2.7681 11 1 0 0 1 5.3256 12 1 0 1 1 4.5109 13 1 2 1 1 8.5315 14 1 1 2 1 13.9729 15 1 1 1 1 4.1564 16 1 1 0 1 3.0609 17 1 1 1 0 4.5274 18 1 1 0 0 6.5216 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3474 atoms have been selected out of 3550 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 1039 OPERATED ON BY TRANSFORMATION C003 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 156 52 52 6.61 2 C002 has 33 11 11 10.91 3 C003 has 2643 881 881 0.00 4 C004 has 843 281 281 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1179 393 393 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1233 411 411 0.00 9 C009 has 1245 415 415 0.00 Total of12541 atoms and 4173 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> 3 atoms have been selected out of 3550 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 = 1170 Number of atoms = 3547 Number of groups = 1175 Number of bonds = 3541 Number of angles = 1279 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1173 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 = 3547 Number of groups = 1175 Number of bonds = 3541 Number of angles = 1279 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1173 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 <- "35.728" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1170" Evaluating: 1170-13 Parameter: NUMWAT <- "1157" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1157" Comparing "1075" and "1157". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.728" Parameter: BOX -> "35.728" Parameter: BOX -> "35.728" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.72800 B = 35.72800 C = 35.72800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.5285 2 1 -1 -2 -1 13.9698 3 1 -1 -1 -1 4.1561 4 1 -1 0 -1 3.0610 5 1 0 -1 -1 4.5114 6 1 0 0 -1 5.3238 7 1 -1 -1 0 4.5272 8 1 -1 0 0 6.5200 9 1 0 -1 0 2.7665 10 1 0 1 0 2.7665 11 1 0 0 1 5.3238 12 1 0 1 1 4.5114 13 1 2 1 1 8.5285 14 1 1 2 1 13.9698 15 1 1 1 1 4.1561 16 1 1 0 1 3.0610 17 1 1 1 0 4.5272 18 1 1 0 0 6.5200 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3547 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 597 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.60 2 C002 has 33 11 11 10.90 3 C003 has 2643 881 881 0.00 4 C004 has 840 280 280 0.00 5 C005 has 846 282 282 0.00 6 C006 has 1182 394 394 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1236 412 412 0.00 9 C009 has 1248 416 416 0.00 Total of12541 atoms and 4173 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> 3 atoms have been selected out of 3547 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 = 3544 Number of groups = 1174 Number of bonds = 3538 Number of angles = 1278 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1172 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 = 3544 Number of groups = 1174 Number of bonds = 3538 Number of angles = 1278 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1172 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 <- "35.726" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1169" Evaluating: 1169-13 Parameter: NUMWAT <- "1156" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1156" Comparing "1075" and "1156". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.726" Parameter: BOX -> "35.726" Parameter: BOX -> "35.726" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.72600 B = 35.72600 C = 35.72600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.5220 2 1 -1 -2 -1 13.9667 3 1 -1 -1 -1 4.1559 4 1 -1 0 -1 3.0611 5 1 0 -1 -1 4.5119 6 1 0 0 -1 5.3220 7 1 -1 -1 0 4.5270 8 1 -1 0 0 6.5183 9 1 0 -1 0 2.7649 10 1 0 1 0 2.7649 11 1 0 0 1 5.3220 12 1 0 1 1 4.5119 13 1 2 1 1 10.5220 14 1 1 2 1 13.9667 15 1 1 1 1 4.1559 16 1 1 0 1 3.0611 17 1 1 1 0 4.5270 18 1 1 0 0 6.5183 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3544 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.60 2 C002 has 33 11 11 10.90 3 C003 has 2640 880 880 0.00 4 C004 has 840 280 280 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1179 393 393 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1233 411 411 0.00 9 C009 has 1245 415 415 0.00 Total of12523 atoms and 4167 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 3544 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3544 Number of groups = 1174 Number of bonds = 3538 Number of angles = 1278 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1172 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 = 3544 Number of groups = 1174 Number of bonds = 3538 Number of angles = 1278 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1172 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 <- "35.724" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1169" Evaluating: 1169-13 Parameter: NUMWAT <- "1156" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1156" Comparing "1075" and "1156". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.724" Parameter: BOX -> "35.724" Parameter: BOX -> "35.724" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.72400 B = 35.72400 C = 35.72400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.5194 2 1 -1 -2 -1 13.9636 3 1 -1 -1 -1 4.1556 4 1 -1 0 -1 3.0612 5 1 0 -1 -1 4.5125 6 1 0 0 -1 5.3202 7 1 -1 -1 0 4.5268 8 1 -1 0 0 6.5167 9 1 0 -1 0 2.7633 10 1 0 1 0 2.7633 11 1 0 0 1 5.3202 12 1 0 1 1 4.5125 13 1 2 1 1 10.5194 14 1 1 2 1 13.9636 15 1 1 1 1 4.1556 16 1 1 0 1 3.0612 17 1 1 1 0 4.5268 18 1 1 0 0 6.5167 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3544 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.60 2 C002 has 33 11 11 10.90 3 C003 has 2640 880 880 0.00 4 C004 has 840 280 280 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1179 393 393 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1233 411 411 0.00 9 C009 has 1245 415 415 0.00 Total of12523 atoms and 4167 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 3544 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3544 Number of groups = 1174 Number of bonds = 3538 Number of angles = 1278 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1172 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 = 3544 Number of groups = 1174 Number of bonds = 3538 Number of angles = 1278 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1172 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 <- "35.722" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1169" Evaluating: 1169-13 Parameter: NUMWAT <- "1156" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1156" Comparing "1075" and "1156". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.722" Parameter: BOX -> "35.722" Parameter: BOX -> "35.722" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.72200 B = 35.72200 C = 35.72200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.5168 2 1 -1 -2 -1 13.9606 3 1 -1 -1 -1 4.1554 4 1 -1 0 -1 3.0614 5 1 0 -1 -1 4.5130 6 1 0 0 -1 5.3184 7 1 -1 -1 0 4.5267 8 1 -1 0 0 6.5151 9 1 0 -1 0 2.7617 10 1 0 1 0 2.7617 11 1 0 0 1 5.3184 12 1 0 1 1 4.5130 13 1 2 1 1 10.5168 14 1 1 2 1 13.9606 15 1 1 1 1 4.1554 16 1 1 0 1 3.0614 17 1 1 1 0 4.5267 18 1 1 0 0 6.5151 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3544 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 405 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.59 2 C002 has 33 11 11 10.90 3 C003 has 2643 881 881 0.00 4 C004 has 837 279 279 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1182 394 394 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1236 412 412 0.00 9 C009 has 1242 414 414 0.00 Total of12526 atoms and 4168 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> 3 atoms have been selected out of 3544 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 = 3541 Number of groups = 1173 Number of bonds = 3535 Number of angles = 1277 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1171 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 = 3541 Number of groups = 1173 Number of bonds = 3535 Number of angles = 1277 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1171 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 <- "35.72" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1168" Evaluating: 1168-13 Parameter: NUMWAT <- "1155" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1155" Comparing "1075" and "1155". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.72" Parameter: BOX -> "35.72" Parameter: BOX -> "35.72" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.72000 B = 35.72000 C = 35.72000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.5142 2 1 -1 -2 -1 13.9575 3 1 -1 -1 -1 4.1551 4 1 -1 0 -1 3.0615 5 1 0 -1 -1 4.5135 6 1 0 0 -1 5.3166 7 1 -1 -1 0 4.5265 8 1 -1 0 0 6.5134 9 1 0 -1 0 2.7601 10 1 0 1 0 2.7601 11 1 0 0 1 5.3166 12 1 0 1 1 4.5135 13 1 2 1 1 10.5142 14 1 1 2 1 13.9575 15 1 1 1 1 4.1551 16 1 1 0 1 3.0615 17 1 1 1 0 4.5265 18 1 1 0 0 6.5134 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3541 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.59 2 C002 has 33 11 11 10.89 3 C003 has 2640 880 880 0.00 4 C004 has 834 278 278 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1179 393 393 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1233 411 411 0.00 9 C009 has 1242 414 414 0.00 Total of12511 atoms and 4163 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 3541 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3541 Number of groups = 1173 Number of bonds = 3535 Number of angles = 1277 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1171 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 = 3541 Number of groups = 1173 Number of bonds = 3535 Number of angles = 1277 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1171 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 <- "35.718" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1168" Evaluating: 1168-13 Parameter: NUMWAT <- "1155" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1155" Comparing "1075" and "1155". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.718" Parameter: BOX -> "35.718" Parameter: BOX -> "35.718" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.71800 B = 35.71800 C = 35.71800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.5117 2 1 -1 -2 -1 13.9544 3 1 -1 -1 -1 4.1549 4 1 -1 0 -1 3.0616 5 1 0 -1 -1 4.5140 6 1 0 0 -1 5.3148 7 1 -1 -1 0 4.5263 8 1 -1 0 0 6.5118 9 1 0 -1 0 2.7585 10 1 0 1 0 2.7585 11 1 0 0 1 5.3148 12 1 0 1 1 4.5140 13 1 2 1 1 10.5117 14 1 1 2 1 13.9544 15 1 1 1 1 4.1549 16 1 1 0 1 3.0616 17 1 1 1 0 4.5263 18 1 1 0 0 6.5118 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3541 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.59 2 C002 has 33 11 11 10.89 3 C003 has 2640 880 880 0.00 4 C004 has 834 278 278 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1179 393 393 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1233 411 411 0.00 9 C009 has 1242 414 414 0.00 Total of12511 atoms and 4163 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 3541 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3541 Number of groups = 1173 Number of bonds = 3535 Number of angles = 1277 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1171 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 = 3541 Number of groups = 1173 Number of bonds = 3535 Number of angles = 1277 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1171 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 <- "35.716" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1168" Evaluating: 1168-13 Parameter: NUMWAT <- "1155" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1155" Comparing "1075" and "1155". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.716" Parameter: BOX -> "35.716" Parameter: BOX -> "35.716" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.71600 B = 35.71600 C = 35.71600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.5091 2 1 -1 -2 -1 13.9971 3 1 -1 -1 -1 4.1546 4 1 -1 0 -1 3.0617 5 1 0 -1 -1 4.5145 6 1 0 0 -1 5.3131 7 1 -1 -1 0 4.5261 8 1 -1 0 0 6.5102 9 1 0 -1 0 2.7569 10 1 0 1 0 2.7569 11 1 0 0 1 5.3131 12 1 0 1 1 4.5145 13 1 2 1 1 10.5091 14 1 1 2 1 13.9971 15 1 1 1 1 4.1546 16 1 1 0 1 3.0617 17 1 1 1 0 4.5261 18 1 1 0 0 6.5102 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3541 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.58 2 C002 has 33 11 11 10.89 3 C003 has 2640 880 880 0.00 4 C004 has 834 278 278 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1179 393 393 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1233 411 411 0.00 9 C009 has 1242 414 414 0.00 Total of12511 atoms and 4163 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 3541 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3541 Number of groups = 1173 Number of bonds = 3535 Number of angles = 1277 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1171 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 = 3541 Number of groups = 1173 Number of bonds = 3535 Number of angles = 1277 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1171 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 <- "35.714" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1168" Evaluating: 1168-13 Parameter: NUMWAT <- "1155" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1155" Comparing "1075" and "1155". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.714" Parameter: BOX -> "35.714" Parameter: BOX -> "35.714" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.71400 B = 35.71400 C = 35.71400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.5065 2 1 -1 -2 -1 13.9938 3 1 -1 -1 -1 4.1544 4 1 -1 0 -1 3.0618 5 1 0 -1 -1 4.5150 6 1 0 0 -1 5.3113 7 1 -1 -1 0 4.5260 8 1 -1 0 0 6.5085 9 1 0 -1 0 2.7553 10 1 0 1 0 2.7553 11 1 0 0 1 5.3113 12 1 0 1 1 4.5150 13 1 2 1 1 10.5065 14 1 1 2 1 13.9938 15 1 1 1 1 4.1544 16 1 1 0 1 3.0618 17 1 1 1 0 4.5260 18 1 1 0 0 6.5085 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3541 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 137 OPERATED ON BY TRANSFORMATION C015 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.58 2 C002 has 33 11 11 10.88 3 C003 has 2643 881 881 0.00 4 C004 has 837 279 279 0.00 5 C005 has 846 282 282 0.00 6 C006 has 1182 394 394 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1233 411 411 0.00 9 C009 has 1242 414 414 0.00 Total of12523 atoms and 4167 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> 3 atoms have been selected out of 3541 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 = 3538 Number of groups = 1172 Number of bonds = 3532 Number of angles = 1276 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1170 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 = 3538 Number of groups = 1172 Number of bonds = 3532 Number of angles = 1276 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1170 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 <- "35.712" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1167" Evaluating: 1167-13 Parameter: NUMWAT <- "1154" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1154" Comparing "1075" and "1154". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.712" Parameter: BOX -> "35.712" Parameter: BOX -> "35.712" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.71200 B = 35.71200 C = 35.71200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.5039 2 1 -1 -2 -1 13.9906 3 1 -1 -1 -1 4.1541 4 1 -1 0 -1 3.0620 5 1 0 -1 -1 4.5156 6 1 0 0 -1 5.3095 7 1 -1 -1 0 4.5258 8 1 -1 0 0 6.5069 9 1 0 -1 0 2.7536 10 1 0 1 0 2.7536 11 1 0 0 1 5.3095 12 1 0 1 1 4.5156 13 1 2 1 1 10.5039 14 1 1 2 1 13.9906 15 1 1 1 1 4.1541 16 1 1 0 1 3.0620 17 1 1 1 0 4.5258 18 1 1 0 0 6.5069 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3538 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 276 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.58 2 C002 has 33 11 11 10.88 3 C003 has 2640 880 880 0.00 4 C004 has 834 278 278 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1179 393 393 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1239 413 413 0.00 9 C009 has 1245 415 415 0.00 Total of12514 atoms and 4164 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> 3 atoms have been selected out of 3538 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 = 1166 Number of atoms = 3535 Number of groups = 1171 Number of bonds = 3529 Number of angles = 1275 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2314 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1166 Number of atoms = 3535 Number of groups = 1171 Number of bonds = 3529 Number of angles = 1275 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2314 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.71" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1166" Evaluating: 1166-13 Parameter: NUMWAT <- "1153" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1153" Comparing "1075" and "1153". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.71" Parameter: BOX -> "35.71" Parameter: BOX -> "35.71" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.71000 B = 35.71000 C = 35.71000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.5013 2 1 -1 -2 -1 13.9874 3 1 -1 -1 -1 4.1539 4 1 -1 0 -1 3.0621 5 1 0 -1 -1 4.5161 6 1 0 0 -1 5.3077 7 1 -1 -1 0 4.5256 8 1 -1 0 0 6.5053 9 1 0 -1 0 2.7520 10 1 0 1 0 2.7520 11 1 0 0 1 5.3077 12 1 0 1 1 4.5161 13 1 2 1 1 10.5013 14 1 1 2 1 13.9874 15 1 1 1 1 4.1539 16 1 1 0 1 3.0621 17 1 1 1 0 4.5256 18 1 1 0 0 6.5053 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3459 atoms have been selected out of 3535 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.57 2 C002 has 33 11 11 10.88 3 C003 has 2640 880 880 0.00 4 C004 has 837 279 279 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1179 393 393 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1242 414 414 0.00 Total of12502 atoms and 4160 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 3535 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1166 Number of atoms = 3535 Number of groups = 1171 Number of bonds = 3529 Number of angles = 1275 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2314 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1166 Number of atoms = 3535 Number of groups = 1171 Number of bonds = 3529 Number of angles = 1275 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2314 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.708" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1166" Evaluating: 1166-13 Parameter: NUMWAT <- "1153" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1153" Comparing "1075" and "1153". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.708" Parameter: BOX -> "35.708" Parameter: BOX -> "35.708" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.70800 B = 35.70800 C = 35.70800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4987 2 1 -1 -2 -1 13.9841 3 1 -1 -1 -1 4.1536 4 1 -1 0 -1 3.0622 5 1 0 -1 -1 4.5166 6 1 0 0 -1 5.3059 7 1 -1 -1 0 4.5254 8 1 -1 0 0 6.5036 9 1 0 -1 0 2.7504 10 1 0 1 0 2.7504 11 1 0 0 1 5.3059 12 1 0 1 1 4.5166 13 1 2 1 1 10.4987 14 1 1 2 1 13.9841 15 1 1 1 1 4.1536 16 1 1 0 1 3.0622 17 1 1 1 0 4.5254 18 1 1 0 0 6.5036 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3459 atoms have been selected out of 3535 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.57 2 C002 has 33 11 11 10.87 3 C003 has 2640 880 880 0.00 4 C004 has 837 279 279 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1179 393 393 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1242 414 414 0.00 Total of12502 atoms and 4160 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 3535 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1166 Number of atoms = 3535 Number of groups = 1171 Number of bonds = 3529 Number of angles = 1275 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2314 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1166 Number of atoms = 3535 Number of groups = 1171 Number of bonds = 3529 Number of angles = 1275 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2314 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.706" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1166" Evaluating: 1166-13 Parameter: NUMWAT <- "1153" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1153" Comparing "1075" and "1153". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.706" Parameter: BOX -> "35.706" Parameter: BOX -> "35.706" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.70600 B = 35.70600 C = 35.70600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4961 2 1 -1 -2 -1 13.9809 3 1 -1 -1 -1 4.1534 4 1 -1 0 -1 3.0624 5 1 0 -1 -1 4.5171 6 1 0 0 -1 5.3041 7 1 -1 -1 0 4.5253 8 1 -1 0 0 6.5020 9 1 0 -1 0 2.7488 10 1 0 1 0 2.7488 11 1 0 0 1 5.3041 12 1 0 1 1 4.5171 13 1 2 1 1 10.4961 14 1 1 2 1 13.9809 15 1 1 1 1 4.1534 16 1 1 0 1 3.0624 17 1 1 1 0 4.5253 18 1 1 0 0 6.5020 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3459 atoms have been selected out of 3535 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.57 2 C002 has 33 11 11 10.87 3 C003 has 2640 880 880 0.00 4 C004 has 837 279 279 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1179 393 393 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1242 414 414 0.00 Total of12502 atoms and 4160 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 3535 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1166 Number of atoms = 3535 Number of groups = 1171 Number of bonds = 3529 Number of angles = 1275 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2314 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1166 Number of atoms = 3535 Number of groups = 1171 Number of bonds = 3529 Number of angles = 1275 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2314 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.704" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1166" Evaluating: 1166-13 Parameter: NUMWAT <- "1153" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1153" Comparing "1075" and "1153". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.704" Parameter: BOX -> "35.704" Parameter: BOX -> "35.704" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.70400 B = 35.70400 C = 35.70400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4935 2 1 -1 -2 -1 13.9777 3 1 -1 -1 -1 4.1531 4 1 -1 0 -1 3.0625 5 1 0 -1 -1 4.5176 6 1 0 0 -1 5.3024 7 1 -1 -1 0 4.5251 8 1 -1 0 0 6.5004 9 1 0 -1 0 2.7472 10 1 0 1 0 2.7472 11 1 0 0 1 5.3024 12 1 0 1 1 4.5176 13 1 2 1 1 10.4935 14 1 1 2 1 13.9777 15 1 1 1 1 4.1531 16 1 1 0 1 3.0625 17 1 1 1 0 4.5251 18 1 1 0 0 6.5004 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3459 atoms have been selected out of 3535 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.57 2 C002 has 33 11 11 10.87 3 C003 has 2640 880 880 0.00 4 C004 has 837 279 279 0.00 5 C005 has 846 282 282 0.00 6 C006 has 1179 393 393 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1242 414 414 0.00 Total of12505 atoms and 4161 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 3535 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1166 Number of atoms = 3535 Number of groups = 1171 Number of bonds = 3529 Number of angles = 1275 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2314 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1166 Number of atoms = 3535 Number of groups = 1171 Number of bonds = 3529 Number of angles = 1275 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2314 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.702" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1166" Evaluating: 1166-13 Parameter: NUMWAT <- "1153" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1153" Comparing "1075" and "1153". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.702" Parameter: BOX -> "35.702" Parameter: BOX -> "35.702" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.70200 B = 35.70200 C = 35.70200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4909 2 1 -1 -2 -1 13.9745 3 1 -1 -1 -1 4.1529 4 1 -1 0 -1 3.0626 5 1 0 -1 -1 4.5182 6 1 0 0 -1 5.3006 7 1 -1 -1 0 4.5249 8 1 -1 0 0 6.4987 9 1 0 -1 0 2.7456 10 1 0 1 0 2.7456 11 1 0 0 1 5.3006 12 1 0 1 1 4.5182 13 1 2 1 1 10.4909 14 1 1 2 1 13.9745 15 1 1 1 1 4.1529 16 1 1 0 1 3.0626 17 1 1 1 0 4.5249 18 1 1 0 0 6.4987 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3459 atoms have been selected out of 3535 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.56 2 C002 has 33 11 11 10.86 3 C003 has 2640 880 880 0.00 4 C004 has 840 280 280 0.00 5 C005 has 846 282 282 0.00 6 C006 has 1179 393 393 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1242 414 414 0.00 Total of12508 atoms and 4162 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 3535 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1166 Number of atoms = 3535 Number of groups = 1171 Number of bonds = 3529 Number of angles = 1275 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2314 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1166 Number of atoms = 3535 Number of groups = 1171 Number of bonds = 3529 Number of angles = 1275 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2314 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.7" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1166" Evaluating: 1166-13 Parameter: NUMWAT <- "1153" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1153" Comparing "1075" and "1153". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.7" Parameter: BOX -> "35.7" Parameter: BOX -> "35.7" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.70000 B = 35.70000 C = 35.70000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4883 2 1 -1 -2 -1 13.9712 3 1 -1 -1 -1 4.1527 4 1 -1 0 -1 3.0628 5 1 0 -1 -1 4.5187 6 1 0 0 -1 5.2988 7 1 -1 -1 0 4.5248 8 1 -1 0 0 6.4971 9 1 0 -1 0 2.7440 10 1 0 1 0 2.7440 11 1 0 0 1 5.2988 12 1 0 1 1 4.5187 13 1 2 1 1 10.4883 14 1 1 2 1 13.9712 15 1 1 1 1 4.1527 16 1 1 0 1 3.0628 17 1 1 1 0 4.5248 18 1 1 0 0 6.4971 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3459 atoms have been selected out of 3535 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.56 2 C002 has 33 11 11 10.86 3 C003 has 2640 880 880 0.00 4 C004 has 840 280 280 0.00 5 C005 has 846 282 282 0.00 6 C006 has 1179 393 393 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1245 415 415 0.00 Total of12511 atoms and 4163 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 3535 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1166 Number of atoms = 3535 Number of groups = 1171 Number of bonds = 3529 Number of angles = 1275 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2314 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1166 Number of atoms = 3535 Number of groups = 1171 Number of bonds = 3529 Number of angles = 1275 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2314 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.698" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1166" Evaluating: 1166-13 Parameter: NUMWAT <- "1153" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1153" Comparing "1075" and "1153". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.698" Parameter: BOX -> "35.698" Parameter: BOX -> "35.698" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.69800 B = 35.69800 C = 35.69800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4857 2 1 -1 -2 -1 13.9680 3 1 -1 -1 -1 4.1524 4 1 -1 0 -1 3.0629 5 1 0 -1 -1 4.5192 6 1 0 0 -1 5.2970 7 1 -1 -1 0 4.5246 8 1 -1 0 0 6.4955 9 1 0 -1 0 2.7424 10 1 0 1 0 2.7424 11 1 0 0 1 5.2970 12 1 0 1 1 4.5192 13 1 2 1 1 10.4857 14 1 1 2 1 13.9680 15 1 1 1 1 4.1524 16 1 1 0 1 3.0629 17 1 1 1 0 4.5246 18 1 1 0 0 6.4955 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3459 atoms have been selected out of 3535 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.56 2 C002 has 33 11 11 10.86 3 C003 has 2640 880 880 0.00 4 C004 has 840 280 280 0.00 5 C005 has 846 282 282 0.00 6 C006 has 1179 393 393 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1245 415 415 0.00 Total of12511 atoms and 4163 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 3535 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1166 Number of atoms = 3535 Number of groups = 1171 Number of bonds = 3529 Number of angles = 1275 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2314 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1166 Number of atoms = 3535 Number of groups = 1171 Number of bonds = 3529 Number of angles = 1275 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2314 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.696" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1166" Evaluating: 1166-13 Parameter: NUMWAT <- "1153" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1153" Comparing "1075" and "1153". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.696" Parameter: BOX -> "35.696" Parameter: BOX -> "35.696" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.69600 B = 35.69600 C = 35.69600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4831 2 1 -1 -2 -1 13.9648 3 1 -1 -1 -1 4.1522 4 1 -1 0 -1 3.0631 5 1 0 -1 -1 4.5197 6 1 0 0 -1 5.2952 7 1 -1 -1 0 4.5245 8 1 -1 0 0 6.4938 9 1 0 -1 0 2.7408 10 1 0 1 0 2.7408 11 1 0 0 1 5.2952 12 1 0 1 1 4.5197 13 1 2 1 1 10.4831 14 1 1 2 1 13.9648 15 1 1 1 1 4.1522 16 1 1 0 1 3.0631 17 1 1 1 0 4.5245 18 1 1 0 0 6.4938 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3459 atoms have been selected out of 3535 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.55 2 C002 has 33 11 11 10.86 3 C003 has 2640 880 880 0.00 4 C004 has 840 280 280 0.00 5 C005 has 846 282 282 0.00 6 C006 has 1179 393 393 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1245 415 415 0.00 Total of12511 atoms and 4163 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 3535 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1166 Number of atoms = 3535 Number of groups = 1171 Number of bonds = 3529 Number of angles = 1275 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2314 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1166 Number of atoms = 3535 Number of groups = 1171 Number of bonds = 3529 Number of angles = 1275 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2314 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.694" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1166" Evaluating: 1166-13 Parameter: NUMWAT <- "1153" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1153" Comparing "1075" and "1153". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.694" Parameter: BOX -> "35.694" Parameter: BOX -> "35.694" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.69400 B = 35.69400 C = 35.69400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4805 2 1 -1 -2 -1 13.9616 3 1 -1 -1 -1 4.1519 4 1 -1 0 -1 3.0632 5 1 0 -1 -1 4.5203 6 1 0 0 -1 5.2934 7 1 -1 -1 0 4.5243 8 1 -1 0 0 6.4922 9 1 0 -1 0 2.7392 10 1 0 1 0 2.7392 11 1 0 0 1 5.2934 12 1 0 1 1 4.5203 13 1 2 1 1 10.4805 14 1 1 2 1 13.9616 15 1 1 1 1 4.1519 16 1 1 0 1 3.0632 17 1 1 1 0 4.5243 18 1 1 0 0 6.4922 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3459 atoms have been selected out of 3535 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.55 2 C002 has 33 11 11 10.85 3 C003 has 2643 881 881 0.00 4 C004 has 840 280 280 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1179 393 393 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1248 416 416 0.00 Total of12520 atoms and 4166 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 3535 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1166 Number of atoms = 3535 Number of groups = 1171 Number of bonds = 3529 Number of angles = 1275 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2314 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1166 Number of atoms = 3535 Number of groups = 1171 Number of bonds = 3529 Number of angles = 1275 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2314 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.692" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1166" Evaluating: 1166-13 Parameter: NUMWAT <- "1153" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1153" Comparing "1075" and "1153". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.692" Parameter: BOX -> "35.692" Parameter: BOX -> "35.692" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.69200 B = 35.69200 C = 35.69200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4779 2 1 -1 -2 -1 13.9583 3 1 -1 -1 -1 4.1517 4 1 -1 0 -1 3.0633 5 1 0 -1 -1 4.5208 6 1 0 0 -1 5.2917 7 1 -1 -1 0 4.5241 8 1 -1 0 0 6.4906 9 1 0 -1 0 2.7376 10 1 0 1 0 2.7376 11 1 0 0 1 5.2917 12 1 0 1 1 4.5208 13 1 2 1 1 10.4779 14 1 1 2 1 13.9583 15 1 1 1 1 4.1517 16 1 1 0 1 3.0633 17 1 1 1 0 4.5241 18 1 1 0 0 6.4906 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3459 atoms have been selected out of 3535 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.55 2 C002 has 33 11 11 10.85 3 C003 has 2643 881 881 0.00 4 C004 has 840 280 280 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1179 393 393 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1248 416 416 0.00 Total of12523 atoms and 4167 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 3535 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1166 Number of atoms = 3535 Number of groups = 1171 Number of bonds = 3529 Number of angles = 1275 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2314 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1166 Number of atoms = 3535 Number of groups = 1171 Number of bonds = 3529 Number of angles = 1275 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1169 Number of HB donors = 2314 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.69" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1166" Evaluating: 1166-13 Parameter: NUMWAT <- "1153" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1153" Comparing "1075" and "1153". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.69" Parameter: BOX -> "35.69" Parameter: BOX -> "35.69" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.69000 B = 35.69000 C = 35.69000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4754 2 1 -1 -2 -1 13.9551 3 1 -1 -1 -1 4.1515 4 1 -1 0 -1 3.0635 5 1 0 -1 -1 4.5213 6 1 0 0 -1 5.2899 7 1 -1 -1 0 4.5240 8 1 -1 0 0 6.4889 9 1 0 -1 0 2.7361 10 1 0 1 0 2.7361 11 1 0 0 1 5.2899 12 1 0 1 1 4.5213 13 1 2 1 1 10.4754 14 1 1 2 1 13.9551 15 1 1 1 1 4.1515 16 1 1 0 1 3.0635 17 1 1 1 0 4.5240 18 1 1 0 0 6.4889 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3459 atoms have been selected out of 3535 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 C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.54 2 C002 has 36 12 12 10.85 3 C003 has 2643 881 881 0.00 4 C004 has 837 279 279 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1176 392 392 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1248 416 416 0.00 Total of12523 atoms and 4167 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> 3 atoms have been selected out of 3535 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 = 1165 Number of atoms = 3532 Number of groups = 1170 Number of bonds = 3526 Number of angles = 1274 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1168 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 = 3532 Number of groups = 1170 Number of bonds = 3526 Number of angles = 1274 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1168 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 <- "35.688" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1165" Evaluating: 1165-13 Parameter: NUMWAT <- "1152" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1152" Comparing "1075" and "1152". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.688" Parameter: BOX -> "35.688" Parameter: BOX -> "35.688" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.68800 B = 35.68800 C = 35.68800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4728 2 1 -1 -2 -1 13.9519 3 1 -1 -1 -1 4.1512 4 1 -1 0 -1 3.0636 5 1 0 -1 -1 4.5219 6 1 0 0 -1 5.2881 7 1 -1 -1 0 4.5238 8 1 -1 0 0 6.4873 9 1 0 -1 0 2.7345 10 1 0 1 0 2.7345 11 1 0 0 1 5.2881 12 1 0 1 1 4.5219 13 1 2 1 1 10.4728 14 1 1 2 1 13.9519 15 1 1 1 1 4.1512 16 1 1 0 1 3.0636 17 1 1 1 0 4.5238 18 1 1 0 0 6.4873 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3532 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 153 51 51 6.54 2 C002 has 33 11 11 10.84 3 C003 has 2640 880 880 0.00 4 C004 has 837 279 279 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1176 392 392 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1248 416 416 0.00 Total of12511 atoms and 4163 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 3532 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3532 Number of groups = 1170 Number of bonds = 3526 Number of angles = 1274 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1168 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 = 3532 Number of groups = 1170 Number of bonds = 3526 Number of angles = 1274 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1168 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 <- "35.686" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1165" Evaluating: 1165-13 Parameter: NUMWAT <- "1152" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1152" Comparing "1075" and "1152". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.686" Parameter: BOX -> "35.686" Parameter: BOX -> "35.686" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.68600 B = 35.68600 C = 35.68600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4702 2 1 -1 -2 -1 13.9486 3 1 -1 -1 -1 4.1510 4 1 -1 0 -1 3.0638 5 1 0 -1 -1 4.5224 6 1 0 0 -1 5.2863 7 1 -1 -1 0 4.5237 8 1 -1 0 0 6.4857 9 1 0 -1 0 2.7329 10 1 0 1 0 2.7329 11 1 0 0 1 5.2863 12 1 0 1 1 4.5224 13 1 2 1 1 10.4702 14 1 1 2 1 13.9486 15 1 1 1 1 4.1510 16 1 1 0 1 3.0638 17 1 1 1 0 4.5237 18 1 1 0 0 6.4857 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3532 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 433 OPERATED ON BY TRANSFORMATION C009 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 156 52 52 6.54 2 C002 has 33 11 11 10.84 3 C003 has 2643 881 881 0.00 4 C004 has 816 272 272 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1173 391 391 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1248 416 416 0.00 Total of12502 atoms and 4160 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> 3 atoms have been selected out of 3532 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 = 3529 Number of groups = 1169 Number of bonds = 3523 Number of angles = 1273 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1167 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 = 3529 Number of groups = 1169 Number of bonds = 3523 Number of angles = 1273 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1167 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 <- "35.684" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1164" Evaluating: 1164-13 Parameter: NUMWAT <- "1151" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1151" Comparing "1075" and "1151". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.684" Parameter: BOX -> "35.684" Parameter: BOX -> "35.684" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.68400 B = 35.68400 C = 35.68400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4676 2 1 -1 -2 -1 13.9454 3 1 -1 -1 -1 4.1507 4 1 -1 0 -1 3.0639 5 1 0 -1 -1 4.5229 6 1 0 0 -1 6.7403 7 1 -1 -1 0 4.5235 8 1 -1 0 0 6.4840 9 1 0 -1 0 2.7313 10 1 0 1 0 2.7313 11 1 0 0 1 6.7403 12 1 0 1 1 4.5229 13 1 2 1 1 10.4676 14 1 1 2 1 13.9454 15 1 1 1 1 4.1507 16 1 1 0 1 3.0639 17 1 1 1 0 4.5235 18 1 1 0 0 6.4840 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3529 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 156 52 52 6.53 2 C002 has 33 11 11 10.84 3 C003 has 2643 881 881 0.00 4 C004 has 816 272 272 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1173 391 391 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1245 415 415 0.00 Total of12487 atoms and 4155 groups and 4150 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3529 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3529 Number of groups = 1169 Number of bonds = 3523 Number of angles = 1273 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1167 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 = 3529 Number of groups = 1169 Number of bonds = 3523 Number of angles = 1273 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1167 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 <- "35.682" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1164" Evaluating: 1164-13 Parameter: NUMWAT <- "1151" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1151" Comparing "1075" and "1151". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.682" Parameter: BOX -> "35.682" Parameter: BOX -> "35.682" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.68200 B = 35.68200 C = 35.68200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4650 2 1 -1 -2 -1 13.9422 3 1 -1 -1 -1 4.1505 4 1 -1 0 -1 3.0641 5 1 0 -1 -1 4.5235 6 1 0 0 -1 6.7398 7 1 -1 -1 0 4.5234 8 1 -1 0 0 6.4824 9 1 0 -1 0 2.7297 10 1 0 1 0 2.7297 11 1 0 0 1 6.7398 12 1 0 1 1 4.5235 13 1 2 1 1 10.4650 14 1 1 2 1 13.9422 15 1 1 1 1 4.1505 16 1 1 0 1 3.0641 17 1 1 1 0 4.5234 18 1 1 0 0 6.4824 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3529 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.53 2 C002 has 33 11 11 10.83 3 C003 has 2643 881 881 0.00 4 C004 has 816 272 272 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1173 391 391 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1245 415 415 0.00 Total of12490 atoms and 4156 groups and 4151 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3529 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3529 Number of groups = 1169 Number of bonds = 3523 Number of angles = 1273 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1167 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 = 3529 Number of groups = 1169 Number of bonds = 3523 Number of angles = 1273 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1167 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 <- "35.68" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1164" Evaluating: 1164-13 Parameter: NUMWAT <- "1151" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1151" Comparing "1075" and "1151". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.68" Parameter: BOX -> "35.68" Parameter: BOX -> "35.68" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.68000 B = 35.68000 C = 35.68000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4624 2 1 -1 -2 -1 13.9390 3 1 -1 -1 -1 4.1503 4 1 -1 0 -1 3.0643 5 1 0 -1 -1 4.5240 6 1 0 0 -1 6.7394 7 1 -1 -1 0 4.5232 8 1 -1 0 0 6.4808 9 1 0 -1 0 2.7281 10 1 0 1 0 2.7281 11 1 0 0 1 6.7394 12 1 0 1 1 4.5240 13 1 2 1 1 10.4624 14 1 1 2 1 13.9390 15 1 1 1 1 4.1503 16 1 1 0 1 3.0643 17 1 1 1 0 4.5232 18 1 1 0 0 6.4808 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3529 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.53 2 C002 has 33 11 11 10.83 3 C003 has 2643 881 881 0.00 4 C004 has 816 272 272 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1173 391 391 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1248 416 416 0.00 Total of12493 atoms and 4157 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 3529 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3529 Number of groups = 1169 Number of bonds = 3523 Number of angles = 1273 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1167 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 = 3529 Number of groups = 1169 Number of bonds = 3523 Number of angles = 1273 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1167 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 <- "35.678" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1164" Evaluating: 1164-13 Parameter: NUMWAT <- "1151" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1151" Comparing "1075" and "1151". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.678" Parameter: BOX -> "35.678" Parameter: BOX -> "35.678" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.67800 B = 35.67800 C = 35.67800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4598 2 1 -1 -2 -1 13.9357 3 1 -1 -1 -1 4.1500 4 1 -1 0 -1 3.0644 5 1 0 -1 -1 4.5246 6 1 0 0 -1 6.7390 7 1 -1 -1 0 4.5230 8 1 -1 0 0 6.4791 9 1 0 -1 0 2.7265 10 1 0 1 0 2.7265 11 1 0 0 1 6.7390 12 1 0 1 1 4.5246 13 1 2 1 1 10.4598 14 1 1 2 1 13.9357 15 1 1 1 1 4.1500 16 1 1 0 1 3.0644 17 1 1 1 0 4.5230 18 1 1 0 0 6.4791 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3529 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.53 2 C002 has 33 11 11 10.83 3 C003 has 2643 881 881 0.00 4 C004 has 816 272 272 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1179 393 393 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1248 416 416 0.00 Total of12499 atoms and 4159 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 3529 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3529 Number of groups = 1169 Number of bonds = 3523 Number of angles = 1273 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1167 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 = 3529 Number of groups = 1169 Number of bonds = 3523 Number of angles = 1273 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1167 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 <- "35.676" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1164" Evaluating: 1164-13 Parameter: NUMWAT <- "1151" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1151" Comparing "1075" and "1151". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.676" Parameter: BOX -> "35.676" Parameter: BOX -> "35.676" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.67600 B = 35.67600 C = 35.67600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4572 2 1 -1 -2 -1 13.9325 3 1 -1 -1 -1 4.1498 4 1 -1 0 -1 3.0646 5 1 0 -1 -1 4.5251 6 1 0 0 -1 6.7386 7 1 -1 -1 0 4.5229 8 1 -1 0 0 6.4775 9 1 0 -1 0 2.7249 10 1 0 1 0 2.7249 11 1 0 0 1 6.7386 12 1 0 1 1 4.5251 13 1 2 1 1 10.4572 14 1 1 2 1 13.9325 15 1 1 1 1 4.1498 16 1 1 0 1 3.0646 17 1 1 1 0 4.5229 18 1 1 0 0 6.4775 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3529 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.52 2 C002 has 33 11 11 10.82 3 C003 has 2643 881 881 0.00 4 C004 has 816 272 272 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1179 393 393 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1248 416 416 0.00 Total of12499 atoms and 4159 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 3529 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3529 Number of groups = 1169 Number of bonds = 3523 Number of angles = 1273 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1167 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 = 3529 Number of groups = 1169 Number of bonds = 3523 Number of angles = 1273 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1167 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 <- "35.674" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1164" Evaluating: 1164-13 Parameter: NUMWAT <- "1151" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1151" Comparing "1075" and "1151". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.674" Parameter: BOX -> "35.674" Parameter: BOX -> "35.674" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.67400 B = 35.67400 C = 35.67400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4546 2 1 -1 -2 -1 13.9293 3 1 -1 -1 -1 4.1496 4 1 -1 0 -1 3.0647 5 1 0 -1 -1 4.5256 6 1 0 0 -1 6.7382 7 1 -1 -1 0 4.5227 8 1 -1 0 0 6.4759 9 1 0 -1 0 2.7233 10 1 0 1 0 2.7233 11 1 0 0 1 6.7382 12 1 0 1 1 4.5256 13 1 2 1 1 10.4546 14 1 1 2 1 13.9293 15 1 1 1 1 4.1496 16 1 1 0 1 3.0647 17 1 1 1 0 4.5227 18 1 1 0 0 6.4759 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3529 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 C015 RESIDUE 358 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.52 2 C002 has 33 11 11 10.82 3 C003 has 2649 883 883 0.00 4 C004 has 816 272 272 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1179 393 393 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1248 416 416 0.00 Total of12508 atoms and 4162 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> 6 atoms have been selected out of 3529 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 = 1162 Number of atoms = 3523 Number of groups = 1167 Number of bonds = 3517 Number of angles = 1271 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1165 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 = 3523 Number of groups = 1167 Number of bonds = 3517 Number of angles = 1271 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1165 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 <- "35.672" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1162" Evaluating: 1162-13 Parameter: NUMWAT <- "1149" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1149" Comparing "1075" and "1149". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.672" Parameter: BOX -> "35.672" Parameter: BOX -> "35.672" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.67200 B = 35.67200 C = 35.67200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4521 2 1 -1 -2 -1 13.9260 3 1 -1 -1 -1 4.1493 4 1 -1 0 -1 3.0649 5 1 0 -1 -1 4.5262 6 1 0 0 -1 6.7378 7 1 -1 -1 0 4.5226 8 1 -1 0 0 6.4742 9 1 0 -1 0 2.7217 10 1 0 1 0 2.7217 11 1 0 0 1 6.7378 12 1 0 1 1 4.5262 13 1 2 1 1 10.4521 14 1 1 2 1 13.9260 15 1 1 1 1 4.1493 16 1 1 0 1 3.0649 17 1 1 1 0 4.5226 18 1 1 0 0 6.4742 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3523 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.52 2 C002 has 33 11 11 10.82 3 C003 has 2643 881 881 0.00 4 C004 has 813 271 271 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1173 391 391 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1245 415 415 0.00 Total of12478 atoms and 4152 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> 0 atoms have been selected out of 3523 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3523 Number of groups = 1167 Number of bonds = 3517 Number of angles = 1271 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1165 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 = 3523 Number of groups = 1167 Number of bonds = 3517 Number of angles = 1271 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1165 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 <- "35.67" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1162" Evaluating: 1162-13 Parameter: NUMWAT <- "1149" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1149" Comparing "1075" and "1149". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.67" Parameter: BOX -> "35.67" Parameter: BOX -> "35.67" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.67000 B = 35.67000 C = 35.67000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4495 2 1 -1 -2 -1 13.9228 3 1 -1 -1 -1 4.1491 4 1 -1 0 -1 3.0651 5 1 0 -1 -1 4.5267 6 1 0 0 -1 6.7374 7 1 -1 -1 0 4.5225 8 1 -1 0 0 6.4726 9 1 0 -1 0 2.7201 10 1 0 1 0 2.7201 11 1 0 0 1 6.7374 12 1 0 1 1 4.5267 13 1 2 1 1 10.4495 14 1 1 2 1 13.9228 15 1 1 1 1 4.1491 16 1 1 0 1 3.0651 17 1 1 1 0 4.5225 18 1 1 0 0 6.4726 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3523 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.51 2 C002 has 33 11 11 10.82 3 C003 has 2643 881 881 0.00 4 C004 has 813 271 271 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1173 391 391 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1245 415 415 0.00 Total of12478 atoms and 4152 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> 0 atoms have been selected out of 3523 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3523 Number of groups = 1167 Number of bonds = 3517 Number of angles = 1271 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1165 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 = 3523 Number of groups = 1167 Number of bonds = 3517 Number of angles = 1271 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1165 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 <- "35.668" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1162" Evaluating: 1162-13 Parameter: NUMWAT <- "1149" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1149" Comparing "1075" and "1149". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.668" Parameter: BOX -> "35.668" Parameter: BOX -> "35.668" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.66800 B = 35.66800 C = 35.66800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4469 2 1 -1 -2 -1 13.9196 3 1 -1 -1 -1 4.1489 4 1 -1 0 -1 3.0652 5 1 0 -1 -1 4.5273 6 1 0 0 -1 6.7370 7 1 -1 -1 0 4.5223 8 1 -1 0 0 6.4710 9 1 0 -1 0 2.7185 10 1 0 1 0 2.7185 11 1 0 0 1 6.7370 12 1 0 1 1 4.5273 13 1 2 1 1 10.4469 14 1 1 2 1 13.9196 15 1 1 1 1 4.1489 16 1 1 0 1 3.0652 17 1 1 1 0 4.5223 18 1 1 0 0 6.4710 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3523 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.51 2 C002 has 33 11 11 10.81 3 C003 has 2643 881 881 0.00 4 C004 has 813 271 271 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1173 391 391 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1245 415 415 0.00 Total of12481 atoms and 4153 groups and 4148 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3523 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3523 Number of groups = 1167 Number of bonds = 3517 Number of angles = 1271 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1165 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 = 3523 Number of groups = 1167 Number of bonds = 3517 Number of angles = 1271 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1165 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 <- "35.666" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1162" Evaluating: 1162-13 Parameter: NUMWAT <- "1149" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1149" Comparing "1075" and "1149". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.666" Parameter: BOX -> "35.666" Parameter: BOX -> "35.666" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.66600 B = 35.66600 C = 35.66600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4443 2 1 -1 -2 -1 13.9164 3 1 -1 -1 -1 4.1487 4 1 -1 0 -1 3.0654 5 1 0 -1 -1 4.5278 6 1 0 0 -1 6.7366 7 1 -1 -1 0 4.5222 8 1 -1 0 0 6.4694 9 1 0 -1 0 2.7169 10 1 0 1 0 2.7169 11 1 0 0 1 6.7366 12 1 0 1 1 4.5278 13 1 2 1 1 10.4443 14 1 1 2 1 13.9164 15 1 1 1 1 4.1487 16 1 1 0 1 3.0654 17 1 1 1 0 4.5222 18 1 1 0 0 6.4694 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3523 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.51 2 C002 has 33 11 11 10.81 3 C003 has 2643 881 881 0.00 4 C004 has 813 271 271 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1173 391 391 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1245 415 415 0.00 Total of12481 atoms and 4153 groups and 4148 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3523 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3523 Number of groups = 1167 Number of bonds = 3517 Number of angles = 1271 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1165 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 = 3523 Number of groups = 1167 Number of bonds = 3517 Number of angles = 1271 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1165 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 <- "35.664" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1162" Evaluating: 1162-13 Parameter: NUMWAT <- "1149" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1149" Comparing "1075" and "1149". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.664" Parameter: BOX -> "35.664" Parameter: BOX -> "35.664" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.66400 B = 35.66400 C = 35.66400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4417 2 1 -1 -2 -1 13.9131 3 1 -1 -1 -1 4.1484 4 1 -1 0 -1 3.0656 5 1 0 -1 -1 4.5283 6 1 0 0 -1 6.7362 7 1 -1 -1 0 4.5220 8 1 -1 0 0 6.4677 9 1 0 -1 0 2.7153 10 1 0 1 0 2.7153 11 1 0 0 1 6.7362 12 1 0 1 1 4.5283 13 1 2 1 1 10.4417 14 1 1 2 1 13.9131 15 1 1 1 1 4.1484 16 1 1 0 1 3.0656 17 1 1 1 0 4.5220 18 1 1 0 0 6.4677 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3523 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 C007 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.50 2 C002 has 33 11 11 10.81 3 C003 has 2640 880 880 0.00 4 C004 has 813 271 271 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1176 392 392 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1242 414 414 0.00 Total of12478 atoms and 4152 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 3523 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 = 3520 Number of groups = 1166 Number of bonds = 3514 Number of angles = 1270 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1164 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 = 3520 Number of groups = 1166 Number of bonds = 3514 Number of angles = 1270 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1164 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 <- "35.662" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1161" Evaluating: 1161-13 Parameter: NUMWAT <- "1148" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1148" Comparing "1075" and "1148". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.662" Parameter: BOX -> "35.662" Parameter: BOX -> "35.662" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.66200 B = 35.66200 C = 35.66200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4391 2 1 -1 -2 -1 13.9099 3 1 -1 -1 -1 4.1482 4 1 -1 0 -1 3.0657 5 1 0 -1 -1 4.5289 6 1 0 0 -1 6.7358 7 1 -1 -1 0 4.5219 8 1 -1 0 0 6.4661 9 1 0 -1 0 2.7138 10 1 0 1 0 2.7138 11 1 0 0 1 6.7358 12 1 0 1 1 4.5289 13 1 2 1 1 10.4391 14 1 1 2 1 13.9099 15 1 1 1 1 4.1482 16 1 1 0 1 3.0657 17 1 1 1 0 4.5219 18 1 1 0 0 6.4661 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3520 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 602 OPERATED ON BY TRANSFORMATION C006 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.50 2 C002 has 33 11 11 10.80 3 C003 has 2640 880 880 0.00 4 C004 has 810 270 270 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1182 394 394 0.00 7 C007 has 807 269 269 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1242 414 414 0.00 Total of12481 atoms and 4153 groups and 4148 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3520 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 = 3517 Number of groups = 1165 Number of bonds = 3511 Number of angles = 1269 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1163 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 = 3517 Number of groups = 1165 Number of bonds = 3511 Number of angles = 1269 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1163 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 <- "35.66" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1160" Evaluating: 1160-13 Parameter: NUMWAT <- "1147" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1147" Comparing "1075" and "1147". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.66" Parameter: BOX -> "35.66" Parameter: BOX -> "35.66" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.66000 B = 35.66000 C = 35.66000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4365 2 1 -1 -2 -1 13.9067 3 1 -1 -1 -1 4.1480 4 1 -1 0 -1 3.0659 5 1 0 -1 -1 4.5294 6 1 0 0 -1 6.7354 7 1 -1 -1 0 4.5217 8 1 -1 0 0 6.4645 9 1 0 -1 0 2.7122 10 1 0 1 0 2.7122 11 1 0 0 1 6.7354 12 1 0 1 1 4.5294 13 1 2 1 1 10.4365 14 1 1 2 1 13.9067 15 1 1 1 1 4.1480 16 1 1 0 1 3.0659 17 1 1 1 0 4.5217 18 1 1 0 0 6.4645 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3517 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.50 2 C002 has 36 12 12 10.80 3 C003 has 2640 880 880 0.00 4 C004 has 810 270 270 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1170 390 390 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1242 414 414 0.00 Total of12463 atoms and 4147 groups and 4142 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3517 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3517 Number of groups = 1165 Number of bonds = 3511 Number of angles = 1269 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1163 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 = 3517 Number of groups = 1165 Number of bonds = 3511 Number of angles = 1269 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1163 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 <- "35.658" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1160" Evaluating: 1160-13 Parameter: NUMWAT <- "1147" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1147" Comparing "1075" and "1147". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.658" Parameter: BOX -> "35.658" Parameter: BOX -> "35.658" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.65800 B = 35.65800 C = 35.65800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4340 2 1 -1 -2 -1 13.9035 3 1 -1 -1 -1 4.1478 4 1 -1 0 -1 3.0661 5 1 0 -1 -1 4.5300 6 1 0 0 -1 6.7349 7 1 -1 -1 0 4.5216 8 1 -1 0 0 6.4628 9 1 0 -1 0 2.7106 10 1 0 1 0 2.7106 11 1 0 0 1 6.7349 12 1 0 1 1 4.5300 13 1 2 1 1 10.4340 14 1 1 2 1 13.9035 15 1 1 1 1 4.1478 16 1 1 0 1 3.0661 17 1 1 1 0 4.5216 18 1 1 0 0 6.4628 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3517 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.49 2 C002 has 36 12 12 10.80 3 C003 has 2640 880 880 0.00 4 C004 has 810 270 270 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1170 390 390 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1242 414 414 0.00 Total of12469 atoms and 4149 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 3517 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3517 Number of groups = 1165 Number of bonds = 3511 Number of angles = 1269 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1163 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 = 3517 Number of groups = 1165 Number of bonds = 3511 Number of angles = 1269 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1163 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 <- "35.656" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1160" Evaluating: 1160-13 Parameter: NUMWAT <- "1147" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1147" Comparing "1075" and "1147". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.656" Parameter: BOX -> "35.656" Parameter: BOX -> "35.656" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.65600 B = 35.65600 C = 35.65600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4314 2 1 -1 -2 -1 13.9002 3 1 -1 -1 -1 4.1475 4 1 -1 0 -1 3.0663 5 1 0 -1 -1 4.5305 6 1 0 0 -1 6.7345 7 1 -1 -1 0 4.5215 8 1 -1 0 0 6.4612 9 1 0 -1 0 2.7090 10 1 0 1 0 2.7090 11 1 0 0 1 6.7345 12 1 0 1 1 4.5305 13 1 2 1 1 10.4314 14 1 1 2 1 13.9002 15 1 1 1 1 4.1475 16 1 1 0 1 3.0663 17 1 1 1 0 4.5215 18 1 1 0 0 6.4612 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3517 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.49 2 C002 has 39 13 13 10.79 3 C003 has 2640 880 880 0.00 4 C004 has 810 270 270 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1170 390 390 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1242 414 414 0.00 Total of12472 atoms and 4150 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 3517 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3517 Number of groups = 1165 Number of bonds = 3511 Number of angles = 1269 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1163 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 = 3517 Number of groups = 1165 Number of bonds = 3511 Number of angles = 1269 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1163 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 <- "35.654" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1160" Evaluating: 1160-13 Parameter: NUMWAT <- "1147" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1147" Comparing "1075" and "1147". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.654" Parameter: BOX -> "35.654" Parameter: BOX -> "35.654" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.65400 B = 35.65400 C = 35.65400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4288 2 1 -1 -2 -1 13.8970 3 1 -1 -1 -1 4.1473 4 1 -1 0 -1 3.0664 5 1 0 -1 -1 4.5311 6 1 0 0 -1 6.7341 7 1 -1 -1 0 4.5213 8 1 -1 0 0 6.4596 9 1 0 -1 0 2.7074 10 1 0 1 0 2.7074 11 1 0 0 1 6.7341 12 1 0 1 1 4.5311 13 1 2 1 1 10.4288 14 1 1 2 1 13.8970 15 1 1 1 1 4.1473 16 1 1 0 1 3.0664 17 1 1 1 0 4.5213 18 1 1 0 0 6.4596 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3517 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.49 2 C002 has 39 13 13 10.79 3 C003 has 2640 880 880 0.00 4 C004 has 810 270 270 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1170 390 390 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1242 414 414 0.00 Total of12472 atoms and 4150 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 3517 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3517 Number of groups = 1165 Number of bonds = 3511 Number of angles = 1269 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1163 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 = 3517 Number of groups = 1165 Number of bonds = 3511 Number of angles = 1269 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1163 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 <- "35.652" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1160" Evaluating: 1160-13 Parameter: NUMWAT <- "1147" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1147" Comparing "1075" and "1147". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.652" Parameter: BOX -> "35.652" Parameter: BOX -> "35.652" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.65200 B = 35.65200 C = 35.65200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4262 2 1 -1 -2 -1 13.8938 3 1 -1 -1 -1 4.1471 4 1 -1 0 -1 3.0666 5 1 0 -1 -1 4.5316 6 1 0 0 -1 6.7337 7 1 -1 -1 0 4.5212 8 1 -1 0 0 6.4580 9 1 0 -1 0 2.7058 10 1 0 1 0 2.7058 11 1 0 0 1 6.7337 12 1 0 1 1 4.5316 13 1 2 1 1 10.4262 14 1 1 2 1 13.8938 15 1 1 1 1 4.1471 16 1 1 0 1 3.0666 17 1 1 1 0 4.5212 18 1 1 0 0 6.4580 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3517 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.49 2 C002 has 39 13 13 10.79 3 C003 has 2640 880 880 0.00 4 C004 has 810 270 270 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1170 390 390 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1242 414 414 0.00 Total of12472 atoms and 4150 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 3517 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3517 Number of groups = 1165 Number of bonds = 3511 Number of angles = 1269 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1163 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 = 3517 Number of groups = 1165 Number of bonds = 3511 Number of angles = 1269 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1163 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 <- "35.65" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1160" Evaluating: 1160-13 Parameter: NUMWAT <- "1147" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1147" Comparing "1075" and "1147". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.65" Parameter: BOX -> "35.65" Parameter: BOX -> "35.65" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.65000 B = 35.65000 C = 35.65000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4236 2 1 -1 -2 -1 13.8905 3 1 -1 -1 -1 4.1469 4 1 -1 0 -1 3.0668 5 1 0 -1 -1 4.5322 6 1 0 0 -1 6.7333 7 1 -1 -1 0 4.5210 8 1 -1 0 0 6.4563 9 1 0 -1 0 2.7042 10 1 0 1 0 2.7042 11 1 0 0 1 6.7333 12 1 0 1 1 4.5322 13 1 2 1 1 10.4236 14 1 1 2 1 13.8905 15 1 1 1 1 4.1469 16 1 1 0 1 3.0668 17 1 1 1 0 4.5210 18 1 1 0 0 6.4563 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3517 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.48 2 C002 has 39 13 13 10.78 3 C003 has 2640 880 880 0.00 4 C004 has 810 270 270 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1170 390 390 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1242 414 414 0.00 Total of12472 atoms and 4150 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 3517 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3517 Number of groups = 1165 Number of bonds = 3511 Number of angles = 1269 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1163 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 = 3517 Number of groups = 1165 Number of bonds = 3511 Number of angles = 1269 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1163 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 <- "35.648" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1160" Evaluating: 1160-13 Parameter: NUMWAT <- "1147" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1147" Comparing "1075" and "1147". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.648" Parameter: BOX -> "35.648" Parameter: BOX -> "35.648" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.64800 B = 35.64800 C = 35.64800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4210 2 1 -1 -2 -1 13.8873 3 1 -1 -1 -1 4.1467 4 1 -1 0 -1 3.0670 5 1 0 -1 -1 4.5328 6 1 0 0 -1 6.7329 7 1 -1 -1 0 4.5209 8 1 -1 0 0 6.4547 9 1 0 -1 0 2.7026 10 1 0 1 0 2.7026 11 1 0 0 1 6.7329 12 1 0 1 1 4.5328 13 1 2 1 1 10.4210 14 1 1 2 1 13.8873 15 1 1 1 1 4.1467 16 1 1 0 1 3.0670 17 1 1 1 0 4.5209 18 1 1 0 0 6.4547 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3517 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.48 2 C002 has 39 13 13 10.78 3 C003 has 2640 880 880 0.00 4 C004 has 810 270 270 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1170 390 390 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1242 414 414 0.00 Total of12472 atoms and 4150 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 3517 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3517 Number of groups = 1165 Number of bonds = 3511 Number of angles = 1269 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1163 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 = 3517 Number of groups = 1165 Number of bonds = 3511 Number of angles = 1269 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1163 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 <- "35.646" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1160" Evaluating: 1160-13 Parameter: NUMWAT <- "1147" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1147" Comparing "1075" and "1147". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.646" Parameter: BOX -> "35.646" Parameter: BOX -> "35.646" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.64600 B = 35.64600 C = 35.64600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4185 2 1 -1 -2 -1 13.8841 3 1 -1 -1 -1 4.1464 4 1 -1 0 -1 3.0672 5 1 0 -1 -1 4.5333 6 1 0 0 -1 6.7325 7 1 -1 -1 0 4.5208 8 1 -1 0 0 6.4531 9 1 0 -1 0 2.7011 10 1 0 1 0 2.7011 11 1 0 0 1 6.7325 12 1 0 1 1 4.5333 13 1 2 1 1 10.4185 14 1 1 2 1 13.8841 15 1 1 1 1 4.1464 16 1 1 0 1 3.0672 17 1 1 1 0 4.5208 18 1 1 0 0 6.4531 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3517 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.48 2 C002 has 39 13 13 10.78 3 C003 has 2640 880 880 0.00 4 C004 has 810 270 270 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1170 390 390 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1242 414 414 0.00 Total of12472 atoms and 4150 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 3517 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3517 Number of groups = 1165 Number of bonds = 3511 Number of angles = 1269 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1163 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 = 3517 Number of groups = 1165 Number of bonds = 3511 Number of angles = 1269 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1163 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 <- "35.644" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1160" Evaluating: 1160-13 Parameter: NUMWAT <- "1147" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1147" Comparing "1075" and "1147". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.644" Parameter: BOX -> "35.644" Parameter: BOX -> "35.644" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.64400 B = 35.64400 C = 35.64400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4159 2 1 -1 -2 -1 13.8809 3 1 -1 -1 -1 4.1462 4 1 -1 0 -1 3.0674 5 1 0 -1 -1 4.5339 6 1 0 0 -1 6.7321 7 1 -1 -1 0 4.5207 8 1 -1 0 0 6.4514 9 1 0 -1 0 2.6995 10 1 0 1 0 2.6995 11 1 0 0 1 6.7321 12 1 0 1 1 4.5339 13 1 2 1 1 10.4159 14 1 1 2 1 13.8809 15 1 1 1 1 4.1462 16 1 1 0 1 3.0674 17 1 1 1 0 4.5207 18 1 1 0 0 6.4514 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3517 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 263 OPERATED ON BY TRANSFORMATION C012 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.47 2 C002 has 39 13 13 10.78 3 C003 has 2643 881 881 0.00 4 C004 has 810 270 270 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1173 391 391 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1245 415 415 0.00 Total of12472 atoms and 4150 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 3517 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 = 3514 Number of groups = 1164 Number of bonds = 3508 Number of angles = 1268 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1162 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 = 3514 Number of groups = 1164 Number of bonds = 3508 Number of angles = 1268 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1162 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 <- "35.642" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1159" Evaluating: 1159-13 Parameter: NUMWAT <- "1146" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1146" Comparing "1075" and "1146". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.642" Parameter: BOX -> "35.642" Parameter: BOX -> "35.642" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.64200 B = 35.64200 C = 35.64200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4133 2 1 -1 -2 -1 13.8776 3 1 -1 -1 -1 4.1460 4 1 -1 0 -1 3.0675 5 1 0 -1 -1 5.0747 6 1 0 0 -1 6.7317 7 1 -1 -1 0 4.5205 8 1 -1 0 0 6.4498 9 1 0 -1 0 2.6979 10 1 0 1 0 2.6979 11 1 0 0 1 6.7317 12 1 0 1 1 5.0747 13 1 2 1 1 10.4133 14 1 1 2 1 13.8776 15 1 1 1 1 4.1460 16 1 1 0 1 3.0675 17 1 1 1 0 4.5205 18 1 1 0 0 6.4498 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3514 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.47 2 C002 has 39 13 13 10.77 3 C003 has 2640 880 880 0.00 4 C004 has 810 270 270 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1170 390 390 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1242 414 414 0.00 Total of12457 atoms and 4145 groups and 4140 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3514 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3514 Number of groups = 1164 Number of bonds = 3508 Number of angles = 1268 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1162 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 = 3514 Number of groups = 1164 Number of bonds = 3508 Number of angles = 1268 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1162 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 <- "35.64" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1159" Evaluating: 1159-13 Parameter: NUMWAT <- "1146" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1146" Comparing "1075" and "1146". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.64" Parameter: BOX -> "35.64" Parameter: BOX -> "35.64" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.64000 B = 35.64000 C = 35.64000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4107 2 1 -1 -2 -1 13.8744 3 1 -1 -1 -1 4.1458 4 1 -1 0 -1 3.0677 5 1 0 -1 -1 5.0751 6 1 0 0 -1 6.7313 7 1 -1 -1 0 4.5204 8 1 -1 0 0 6.4482 9 1 0 -1 0 2.6963 10 1 0 1 0 2.6963 11 1 0 0 1 6.7313 12 1 0 1 1 5.0751 13 1 2 1 1 10.4107 14 1 1 2 1 13.8744 15 1 1 1 1 4.1458 16 1 1 0 1 3.0677 17 1 1 1 0 4.5204 18 1 1 0 0 6.4482 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3514 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 124 OPERATED ON BY TRANSFORMATION C015 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.47 2 C002 has 42 14 14 10.77 3 C003 has 2643 881 881 0.00 4 C004 has 810 270 270 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1170 390 390 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1245 415 415 0.00 Total of12475 atoms and 4151 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 3514 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 = 3511 Number of groups = 1163 Number of bonds = 3505 Number of angles = 1267 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1161 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 = 3511 Number of groups = 1163 Number of bonds = 3505 Number of angles = 1267 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1161 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 <- "35.638" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1158" Evaluating: 1158-13 Parameter: NUMWAT <- "1145" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1145" Comparing "1075" and "1145". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.638" Parameter: BOX -> "35.638" Parameter: BOX -> "35.638" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.63800 B = 35.63800 C = 35.63800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4081 2 1 -1 -2 -1 13.8712 3 1 -1 -1 -1 4.1456 4 1 -1 0 -1 3.0679 5 1 0 -1 -1 5.0754 6 1 0 0 -1 6.7309 7 1 -1 -1 0 4.5203 8 1 -1 0 0 6.4466 9 1 0 -1 0 2.6947 10 1 0 1 0 2.6947 11 1 0 0 1 6.7309 12 1 0 1 1 5.0754 13 1 2 1 1 10.4081 14 1 1 2 1 13.8712 15 1 1 1 1 4.1456 16 1 1 0 1 3.0679 17 1 1 1 0 4.5203 18 1 1 0 0 6.4466 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3511 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 159 53 53 6.46 2 C002 has 42 14 14 10.77 3 C003 has 2640 880 880 0.00 4 C004 has 813 271 271 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1170 390 390 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1245 415 415 0.00 Total of12466 atoms and 4148 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 3511 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3511 Number of groups = 1163 Number of bonds = 3505 Number of angles = 1267 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1161 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 = 3511 Number of groups = 1163 Number of bonds = 3505 Number of angles = 1267 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1161 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 <- "35.636" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1158" Evaluating: 1158-13 Parameter: NUMWAT <- "1145" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1145" Comparing "1075" and "1145". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.636" Parameter: BOX -> "35.636" Parameter: BOX -> "35.636" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.63600 B = 35.63600 C = 35.63600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4056 2 1 -1 -2 -1 13.8680 3 1 -1 -1 -1 4.1454 4 1 -1 0 -1 3.0681 5 1 0 -1 -1 5.0758 6 1 0 0 -1 6.7305 7 1 -1 -1 0 4.5201 8 1 -1 0 0 6.4449 9 1 0 -1 0 2.6931 10 1 0 1 0 2.6931 11 1 0 0 1 6.7305 12 1 0 1 1 5.0758 13 1 2 1 1 10.4056 14 1 1 2 1 13.8680 15 1 1 1 1 4.1454 16 1 1 0 1 3.0681 17 1 1 1 0 4.5201 18 1 1 0 0 6.4449 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3511 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 162 54 54 6.46 2 C002 has 42 14 14 10.76 3 C003 has 2640 880 880 0.00 4 C004 has 813 271 271 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1170 390 390 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1245 415 415 0.00 Total of12469 atoms and 4149 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 3511 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3511 Number of groups = 1163 Number of bonds = 3505 Number of angles = 1267 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1161 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 = 3511 Number of groups = 1163 Number of bonds = 3505 Number of angles = 1267 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1161 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 <- "35.634" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1158" Evaluating: 1158-13 Parameter: NUMWAT <- "1145" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1145" Comparing "1075" and "1145". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.634" Parameter: BOX -> "35.634" Parameter: BOX -> "35.634" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.63400 B = 35.63400 C = 35.63400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4030 2 1 -1 -2 -1 13.8647 3 1 -1 -1 -1 4.1452 4 1 -1 0 -1 3.0683 5 1 0 -1 -1 5.0762 6 1 0 0 -1 6.7301 7 1 -1 -1 0 4.5200 8 1 -1 0 0 6.4433 9 1 0 -1 0 2.6916 10 1 0 1 0 2.6916 11 1 0 0 1 6.7301 12 1 0 1 1 5.0762 13 1 2 1 1 10.4030 14 1 1 2 1 13.8647 15 1 1 1 1 4.1452 16 1 1 0 1 3.0683 17 1 1 1 0 4.5200 18 1 1 0 0 6.4433 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3511 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 162 54 54 6.46 2 C002 has 42 14 14 10.76 3 C003 has 2643 881 881 0.00 4 C004 has 813 271 271 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1170 390 390 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1245 415 415 0.00 Total of12475 atoms and 4151 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> 0 atoms have been selected out of 3511 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3511 Number of groups = 1163 Number of bonds = 3505 Number of angles = 1267 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1161 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 = 3511 Number of groups = 1163 Number of bonds = 3505 Number of angles = 1267 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1161 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 <- "35.632" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1158" Evaluating: 1158-13 Parameter: NUMWAT <- "1145" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1145" Comparing "1075" and "1145". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.632" Parameter: BOX -> "35.632" Parameter: BOX -> "35.632" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.63200 B = 35.63200 C = 35.63200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.4004 2 1 -1 -2 -1 13.8615 3 1 -1 -1 -1 4.1449 4 1 -1 0 -1 3.0685 5 1 0 -1 -1 5.0765 6 1 0 0 -1 6.7297 7 1 -1 -1 0 4.5199 8 1 -1 0 0 6.4417 9 1 0 -1 0 2.6900 10 1 0 1 0 2.6900 11 1 0 0 1 6.7297 12 1 0 1 1 5.0765 13 1 2 1 1 10.4004 14 1 1 2 1 13.8615 15 1 1 1 1 4.1449 16 1 1 0 1 3.0685 17 1 1 1 0 4.5199 18 1 1 0 0 6.4417 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3511 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 162 54 54 6.45 2 C002 has 42 14 14 10.76 3 C003 has 2643 881 881 0.00 4 C004 has 813 271 271 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1170 390 390 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1248 416 416 0.00 Total of12481 atoms and 4153 groups and 4148 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3511 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3511 Number of groups = 1163 Number of bonds = 3505 Number of angles = 1267 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1161 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 = 3511 Number of groups = 1163 Number of bonds = 3505 Number of angles = 1267 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1161 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 <- "35.63" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1158" Evaluating: 1158-13 Parameter: NUMWAT <- "1145" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1145" Comparing "1075" and "1145". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.63" Parameter: BOX -> "35.63" Parameter: BOX -> "35.63" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.63000 B = 35.63000 C = 35.63000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3978 2 1 -1 -2 -1 13.8583 3 1 -1 -1 -1 4.1447 4 1 -1 0 -1 3.0687 5 1 0 -1 -1 5.0769 6 1 0 0 -1 6.7293 7 1 -1 -1 0 4.5198 8 1 -1 0 0 6.4401 9 1 0 -1 0 2.6884 10 1 0 1 0 2.6884 11 1 0 0 1 6.7293 12 1 0 1 1 5.0769 13 1 2 1 1 10.3978 14 1 1 2 1 13.8583 15 1 1 1 1 4.1447 16 1 1 0 1 3.0687 17 1 1 1 0 4.5198 18 1 1 0 0 6.4401 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3511 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 162 54 54 6.45 2 C002 has 42 14 14 10.75 3 C003 has 2643 881 881 0.00 4 C004 has 813 271 271 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1170 390 390 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1248 416 416 0.00 Total of12484 atoms and 4154 groups and 4149 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3511 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3511 Number of groups = 1163 Number of bonds = 3505 Number of angles = 1267 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1161 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 = 3511 Number of groups = 1163 Number of bonds = 3505 Number of angles = 1267 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1161 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 <- "35.628" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1158" Evaluating: 1158-13 Parameter: NUMWAT <- "1145" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1145" Comparing "1075" and "1145". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.628" Parameter: BOX -> "35.628" Parameter: BOX -> "35.628" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.62800 B = 35.62800 C = 35.62800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3952 2 1 -1 -2 -1 13.8550 3 1 -1 -1 -1 4.1445 4 1 -1 0 -1 3.0689 5 1 0 -1 -1 5.0773 6 1 0 0 -1 6.7289 7 1 -1 -1 0 4.5196 8 1 -1 0 0 6.4384 9 1 0 -1 0 2.6868 10 1 0 1 0 2.6868 11 1 0 0 1 6.7289 12 1 0 1 1 5.0773 13 1 2 1 1 10.3952 14 1 1 2 1 13.8550 15 1 1 1 1 4.1445 16 1 1 0 1 3.0689 17 1 1 1 0 4.5196 18 1 1 0 0 6.4384 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3511 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 850 OPERATED ON BY TRANSFORMATION C004 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 162 54 54 6.45 2 C002 has 42 14 14 10.75 3 C003 has 2640 880 880 0.00 4 C004 has 810 270 270 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1167 389 389 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1251 417 417 0.00 Total of12475 atoms and 4151 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 3511 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 = 3508 Number of groups = 1162 Number of bonds = 3502 Number of angles = 1266 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1160 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 = 3508 Number of groups = 1162 Number of bonds = 3502 Number of angles = 1266 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1160 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 <- "35.626" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1157" Evaluating: 1157-13 Parameter: NUMWAT <- "1144" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1144" Comparing "1075" and "1144". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.626" Parameter: BOX -> "35.626" Parameter: BOX -> "35.626" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.62600 B = 35.62600 C = 35.62600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3927 2 1 -1 -2 -1 13.8518 3 1 -1 -1 -1 4.1443 4 1 -1 0 -1 3.0691 5 1 0 -1 -1 5.0777 6 1 0 0 -1 6.7285 7 1 -1 -1 0 4.5195 8 1 -1 0 0 6.4368 9 1 0 -1 0 2.6852 10 1 0 1 0 2.6852 11 1 0 0 1 6.7285 12 1 0 1 1 5.0777 13 1 2 1 1 10.3927 14 1 1 2 1 13.8518 15 1 1 1 1 4.1443 16 1 1 0 1 3.0691 17 1 1 1 0 4.5195 18 1 1 0 0 6.4368 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3508 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 162 54 54 6.45 2 C002 has 42 14 14 10.75 3 C003 has 2640 880 880 0.00 4 C004 has 810 270 270 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1167 389 389 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1248 416 416 0.00 Total of12469 atoms and 4149 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 3508 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3508 Number of groups = 1162 Number of bonds = 3502 Number of angles = 1266 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1160 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 = 3508 Number of groups = 1162 Number of bonds = 3502 Number of angles = 1266 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1160 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 <- "35.624" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1157" Evaluating: 1157-13 Parameter: NUMWAT <- "1144" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1144" Comparing "1075" and "1144". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.624" Parameter: BOX -> "35.624" Parameter: BOX -> "35.624" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.62400 B = 35.62400 C = 35.62400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3901 2 1 -1 -2 -1 13.8486 3 1 -1 -1 -1 4.1441 4 1 -1 0 -1 3.0693 5 1 0 -1 -1 5.0780 6 1 0 0 -1 6.7282 7 1 -1 -1 0 4.5194 8 1 -1 0 0 6.4352 9 1 0 -1 0 2.6837 10 1 0 1 0 2.6837 11 1 0 0 1 6.7282 12 1 0 1 1 5.0780 13 1 2 1 1 10.3901 14 1 1 2 1 13.8486 15 1 1 1 1 4.1441 16 1 1 0 1 3.0693 17 1 1 1 0 4.5194 18 1 1 0 0 6.4352 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3508 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 162 54 54 6.44 2 C002 has 42 14 14 10.74 3 C003 has 2640 880 880 0.00 4 C004 has 813 271 271 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1170 390 390 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1248 416 416 0.00 Total of12475 atoms and 4151 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> 0 atoms have been selected out of 3508 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3508 Number of groups = 1162 Number of bonds = 3502 Number of angles = 1266 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1160 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 = 3508 Number of groups = 1162 Number of bonds = 3502 Number of angles = 1266 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1160 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 <- "35.622" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1157" Evaluating: 1157-13 Parameter: NUMWAT <- "1144" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1144" Comparing "1075" and "1144". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.622" Parameter: BOX -> "35.622" Parameter: BOX -> "35.622" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.62200 B = 35.62200 C = 35.62200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3875 2 1 -1 -2 -1 13.8454 3 1 -1 -1 -1 4.1439 4 1 -1 0 -1 3.0695 5 1 0 -1 -1 5.0784 6 1 0 0 -1 6.7278 7 1 -1 -1 0 4.5193 8 1 -1 0 0 6.4336 9 1 0 -1 0 2.6821 10 1 0 1 0 2.6821 11 1 0 0 1 6.7278 12 1 0 1 1 5.0784 13 1 2 1 1 10.3875 14 1 1 2 1 13.8454 15 1 1 1 1 4.1439 16 1 1 0 1 3.0695 17 1 1 1 0 4.5193 18 1 1 0 0 6.4336 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3508 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 162 54 54 6.44 2 C002 has 42 14 14 10.74 3 C003 has 2640 880 880 0.00 4 C004 has 813 271 271 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1170 390 390 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1248 416 416 0.00 Total of12478 atoms and 4152 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> 0 atoms have been selected out of 3508 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3508 Number of groups = 1162 Number of bonds = 3502 Number of angles = 1266 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1160 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 = 3508 Number of groups = 1162 Number of bonds = 3502 Number of angles = 1266 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1160 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 <- "35.62" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1157" Evaluating: 1157-13 Parameter: NUMWAT <- "1144" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1144" Comparing "1075" and "1144". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.62" Parameter: BOX -> "35.62" Parameter: BOX -> "35.62" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.62000 B = 35.62000 C = 35.62000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3849 2 1 -1 -2 -1 13.8421 3 1 -1 -1 -1 4.1437 4 1 -1 0 -1 3.0697 5 1 0 -1 -1 5.0788 6 1 0 0 -1 6.7274 7 1 -1 -1 0 4.5192 8 1 -1 0 0 6.4319 9 1 0 -1 0 2.6805 10 1 0 1 0 2.6805 11 1 0 0 1 6.7274 12 1 0 1 1 5.0788 13 1 2 1 1 10.3849 14 1 1 2 1 13.8421 15 1 1 1 1 4.1437 16 1 1 0 1 3.0697 17 1 1 1 0 4.5192 18 1 1 0 0 6.4319 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3508 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 131 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.44 2 C002 has 42 14 14 10.74 3 C003 has 2640 880 880 0.00 4 C004 has 813 271 271 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1248 416 416 0.00 Total of12466 atoms and 4148 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> 3 atoms have been selected out of 3508 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 = 3505 Number of groups = 1161 Number of bonds = 3499 Number of angles = 1265 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1159 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 = 3505 Number of groups = 1161 Number of bonds = 3499 Number of angles = 1265 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1159 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 <- "35.618" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1156" Evaluating: 1156-13 Parameter: NUMWAT <- "1143" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1143" Comparing "1075" and "1143". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.618" Parameter: BOX -> "35.618" Parameter: BOX -> "35.618" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.61800 B = 35.61800 C = 35.61800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3824 2 1 -1 -2 -1 13.8389 3 1 -1 -1 -1 4.1435 4 1 -1 0 -1 3.0699 5 1 0 -1 -1 5.0792 6 1 0 0 -1 4.0983 7 1 -1 -1 0 4.5190 8 1 -1 0 0 6.4303 9 1 0 -1 0 2.6789 10 1 0 1 0 2.6789 11 1 0 0 1 4.0983 12 1 0 1 1 5.0792 13 1 2 1 1 10.3824 14 1 1 2 1 13.8389 15 1 1 1 1 4.1435 16 1 1 0 1 3.0699 17 1 1 1 0 4.5190 18 1 1 0 0 6.4303 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3505 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 315 OPERATED ON BY TRANSFORMATION C009 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.43 2 C002 has 39 13 13 10.74 3 C003 has 2640 880 880 0.00 4 C004 has 816 272 272 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1245 415 415 0.00 Total of12457 atoms and 4145 groups and 4140 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3505 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 = 3502 Number of groups = 1160 Number of bonds = 3496 Number of angles = 1264 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1158 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 = 3502 Number of groups = 1160 Number of bonds = 3496 Number of angles = 1264 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1158 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 <- "35.616" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1155" Evaluating: 1155-13 Parameter: NUMWAT <- "1142" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1142" Comparing "1075" and "1142". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.616" Parameter: BOX -> "35.616" Parameter: BOX -> "35.616" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.61600 B = 35.61600 C = 35.61600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3798 2 1 -1 -2 -1 13.8457 3 1 -1 -1 -1 4.1433 4 1 -1 0 -1 3.0702 5 1 0 -1 -1 5.0795 6 1 0 0 -1 4.0973 7 1 -1 -1 0 4.5189 8 1 -1 0 0 6.4287 9 1 0 -1 0 2.6773 10 1 0 1 0 2.6773 11 1 0 0 1 4.0973 12 1 0 1 1 5.0795 13 1 2 1 1 10.3798 14 1 1 2 1 13.8457 15 1 1 1 1 4.1433 16 1 1 0 1 3.0702 17 1 1 1 0 4.5189 18 1 1 0 0 6.4287 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3502 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 464 OPERATED ON BY TRANSFORMATION C009 RESIDUE 777 OPERATED ON BY TRANSFORMATION C006 RESIDUE 1013 OPERATED ON BY TRANSFORMATION C009 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.43 2 C002 has 36 12 12 11.56 3 C003 has 2631 877 877 0.00 4 C004 has 816 272 272 0.00 5 C005 has 846 282 282 0.00 6 C006 has 1158 386 386 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1236 412 412 0.00 9 C009 has 1245 415 415 0.00 Total of12445 atoms and 4141 groups and 4136 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3502 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 = 1152 Number of atoms = 3493 Number of groups = 1157 Number of bonds = 3487 Number of angles = 1261 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1155 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 = 3493 Number of groups = 1157 Number of bonds = 3487 Number of angles = 1261 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1155 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 <- "35.614" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1152" Evaluating: 1152-13 Parameter: NUMWAT <- "1139" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1139" Comparing "1075" and "1139". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.614" Parameter: BOX -> "35.614" Parameter: BOX -> "35.614" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.61400 B = 35.61400 C = 35.61400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3772 2 1 -1 -2 -1 13.8426 3 1 -1 -1 -1 4.1431 4 1 -1 0 -1 3.0704 5 1 0 -1 -1 5.0799 6 1 0 0 -1 2.6458 7 1 -1 -1 0 4.5188 8 1 -1 0 0 6.4271 9 1 0 -1 0 2.6758 10 1 0 1 0 2.6758 11 1 0 0 1 2.6458 12 1 0 1 1 5.0799 13 1 2 1 1 10.3772 14 1 1 2 1 13.8426 15 1 1 1 1 4.1431 16 1 1 0 1 3.0704 17 1 1 1 0 4.5188 18 1 1 0 0 6.4271 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3493 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.43 2 C002 has 36 12 12 11.55 3 C003 has 2628 876 876 0.00 4 C004 has 810 270 270 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 807 269 269 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1239 413 413 0.00 Total of12403 atoms and 4127 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 3493 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3493 Number of groups = 1157 Number of bonds = 3487 Number of angles = 1261 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1155 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 = 3493 Number of groups = 1157 Number of bonds = 3487 Number of angles = 1261 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1155 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 <- "35.612" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1152" Evaluating: 1152-13 Parameter: NUMWAT <- "1139" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1139" Comparing "1075" and "1139". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.612" Parameter: BOX -> "35.612" Parameter: BOX -> "35.612" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.61200 B = 35.61200 C = 35.61200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3746 2 1 -1 -2 -1 13.8394 3 1 -1 -1 -1 4.1429 4 1 -1 0 -1 3.0706 5 1 0 -1 -1 5.0803 6 1 0 0 -1 2.6446 7 1 -1 -1 0 4.5187 8 1 -1 0 0 6.4254 9 1 0 -1 0 2.6742 10 1 0 1 0 2.6742 11 1 0 0 1 2.6446 12 1 0 1 1 5.0803 13 1 2 1 1 10.3746 14 1 1 2 1 13.8394 15 1 1 1 1 4.1429 16 1 1 0 1 3.0706 17 1 1 1 0 4.5187 18 1 1 0 0 6.4254 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3493 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.42 2 C002 has 36 12 12 11.55 3 C003 has 2628 876 876 0.00 4 C004 has 810 270 270 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 807 269 269 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1239 413 413 0.00 Total of12403 atoms and 4127 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 3493 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3493 Number of groups = 1157 Number of bonds = 3487 Number of angles = 1261 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1155 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 = 3493 Number of groups = 1157 Number of bonds = 3487 Number of angles = 1261 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1155 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 <- "35.61" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1152" Evaluating: 1152-13 Parameter: NUMWAT <- "1139" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1139" Comparing "1075" and "1139". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.61" Parameter: BOX -> "35.61" Parameter: BOX -> "35.61" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.61000 B = 35.61000 C = 35.61000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3721 2 1 -1 -2 -1 13.8363 3 1 -1 -1 -1 4.1427 4 1 -1 0 -1 3.0708 5 1 0 -1 -1 5.0807 6 1 0 0 -1 2.6433 7 1 -1 -1 0 4.5186 8 1 -1 0 0 6.4238 9 1 0 -1 0 2.6726 10 1 0 1 0 2.6726 11 1 0 0 1 2.6433 12 1 0 1 1 5.0807 13 1 2 1 1 10.3721 14 1 1 2 1 13.8363 15 1 1 1 1 4.1427 16 1 1 0 1 3.0708 17 1 1 1 0 4.5186 18 1 1 0 0 6.4238 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3493 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.42 2 C002 has 36 12 12 11.55 3 C003 has 2628 876 876 0.00 4 C004 has 810 270 270 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 807 269 269 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1239 413 413 0.00 Total of12403 atoms and 4127 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 3493 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3493 Number of groups = 1157 Number of bonds = 3487 Number of angles = 1261 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1155 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 = 3493 Number of groups = 1157 Number of bonds = 3487 Number of angles = 1261 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1155 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 <- "35.608" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1152" Evaluating: 1152-13 Parameter: NUMWAT <- "1139" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1139" Comparing "1075" and "1139". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.608" Parameter: BOX -> "35.608" Parameter: BOX -> "35.608" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.60800 B = 35.60800 C = 35.60800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3695 2 1 -1 -2 -1 13.8332 3 1 -1 -1 -1 4.1425 4 1 -1 0 -1 3.0710 5 1 0 -1 -1 5.0810 6 1 0 0 -1 2.6421 7 1 -1 -1 0 4.5185 8 1 -1 0 0 6.4222 9 1 0 -1 0 2.6710 10 1 0 1 0 2.6710 11 1 0 0 1 2.6421 12 1 0 1 1 5.0810 13 1 2 1 1 10.3695 14 1 1 2 1 13.8332 15 1 1 1 1 4.1425 16 1 1 0 1 3.0710 17 1 1 1 0 4.5185 18 1 1 0 0 6.4222 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3493 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.42 2 C002 has 36 12 12 11.54 3 C003 has 2628 876 876 0.00 4 C004 has 810 270 270 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 807 269 269 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1239 413 413 0.00 Total of12403 atoms and 4127 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 3493 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3493 Number of groups = 1157 Number of bonds = 3487 Number of angles = 1261 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1155 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 = 3493 Number of groups = 1157 Number of bonds = 3487 Number of angles = 1261 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1155 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 <- "35.606" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1152" Evaluating: 1152-13 Parameter: NUMWAT <- "1139" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1139" Comparing "1075" and "1139". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.606" Parameter: BOX -> "35.606" Parameter: BOX -> "35.606" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.60600 B = 35.60600 C = 35.60600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3669 2 1 -1 -2 -1 13.8301 3 1 -1 -1 -1 4.1423 4 1 -1 0 -1 3.0712 5 1 0 -1 -1 5.0814 6 1 0 0 -1 2.6408 7 1 -1 -1 0 4.5184 8 1 -1 0 0 6.4206 9 1 0 -1 0 2.6695 10 1 0 1 0 2.6695 11 1 0 0 1 2.6408 12 1 0 1 1 5.0814 13 1 2 1 1 10.3669 14 1 1 2 1 13.8301 15 1 1 1 1 4.1423 16 1 1 0 1 3.0712 17 1 1 1 0 4.5184 18 1 1 0 0 6.4206 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3493 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 29 OPERATED ON BY TRANSFORMATION C015 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.41 2 C002 has 36 12 12 11.54 3 C003 has 2631 877 877 0.00 4 C004 has 813 271 271 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1239 413 413 0.00 Total of12418 atoms and 4132 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> 3 atoms have been selected out of 3493 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 = 3490 Number of groups = 1156 Number of bonds = 3484 Number of angles = 1260 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1154 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 = 3490 Number of groups = 1156 Number of bonds = 3484 Number of angles = 1260 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1154 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 <- "35.604" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1151" Evaluating: 1151-13 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1138" Comparing "1075" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.604" Parameter: BOX -> "35.604" Parameter: BOX -> "35.604" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.60400 B = 35.60400 C = 35.60400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3643 2 1 -1 -2 -1 13.8269 3 1 -1 -1 -1 4.1421 4 1 -1 0 -1 3.0715 5 1 0 -1 -1 5.0818 6 1 0 0 -1 2.6396 7 1 -1 -1 0 4.5183 8 1 -1 0 0 6.4189 9 1 0 -1 0 2.6679 10 1 0 1 0 2.6679 11 1 0 0 1 2.6396 12 1 0 1 1 5.0818 13 1 2 1 1 10.3643 14 1 1 2 1 13.8269 15 1 1 1 1 4.1421 16 1 1 0 1 3.0715 17 1 1 1 0 4.5183 18 1 1 0 0 6.4189 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3490 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.41 2 C002 has 36 12 12 11.54 3 C003 has 2628 876 876 0.00 4 C004 has 810 270 270 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1239 413 413 0.00 Total of12403 atoms and 4127 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 3490 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3490 Number of groups = 1156 Number of bonds = 3484 Number of angles = 1260 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1154 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 = 3490 Number of groups = 1156 Number of bonds = 3484 Number of angles = 1260 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1154 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 <- "35.602" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1151" Evaluating: 1151-13 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1138" Comparing "1075" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.602" Parameter: BOX -> "35.602" Parameter: BOX -> "35.602" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.60200 B = 35.60200 C = 35.60200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3618 2 1 -1 -2 -1 13.8238 3 1 -1 -1 -1 4.1419 4 1 -1 0 -1 3.0717 5 1 0 -1 -1 5.0822 6 1 0 0 -1 2.6383 7 1 -1 -1 0 4.5182 8 1 -1 0 0 6.4173 9 1 0 -1 0 2.6663 10 1 0 1 0 2.6663 11 1 0 0 1 2.6383 12 1 0 1 1 5.0822 13 1 2 1 1 10.3618 14 1 1 2 1 13.8238 15 1 1 1 1 4.1419 16 1 1 0 1 3.0717 17 1 1 1 0 4.5182 18 1 1 0 0 6.4173 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3490 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.41 2 C002 has 36 12 12 11.53 3 C003 has 2631 877 877 0.00 4 C004 has 810 270 270 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1239 413 413 0.00 Total of12409 atoms and 4129 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> 0 atoms have been selected out of 3490 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3490 Number of groups = 1156 Number of bonds = 3484 Number of angles = 1260 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1154 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 = 3490 Number of groups = 1156 Number of bonds = 3484 Number of angles = 1260 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1154 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 <- "35.6" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1151" Evaluating: 1151-13 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1138" Comparing "1075" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.6" Parameter: BOX -> "35.6" Parameter: BOX -> "35.6" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.60000 B = 35.60000 C = 35.60000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3592 2 1 -1 -2 -1 13.8207 3 1 -1 -1 -1 4.1417 4 1 -1 0 -1 3.0719 5 1 0 -1 -1 5.0826 6 1 0 0 -1 2.6371 7 1 -1 -1 0 4.5181 8 1 -1 0 0 6.4157 9 1 0 -1 0 2.6648 10 1 0 1 0 2.6648 11 1 0 0 1 2.6371 12 1 0 1 1 5.0826 13 1 2 1 1 10.3592 14 1 1 2 1 13.8207 15 1 1 1 1 4.1417 16 1 1 0 1 3.0719 17 1 1 1 0 4.5181 18 1 1 0 0 6.4157 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3490 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.41 2 C002 has 36 12 12 11.53 3 C003 has 2631 877 877 0.00 4 C004 has 810 270 270 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1239 413 413 0.00 Total of12409 atoms and 4129 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> 0 atoms have been selected out of 3490 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3490 Number of groups = 1156 Number of bonds = 3484 Number of angles = 1260 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1154 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 = 3490 Number of groups = 1156 Number of bonds = 3484 Number of angles = 1260 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1154 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 <- "35.598" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1151" Evaluating: 1151-13 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1138" Comparing "1075" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.598" Parameter: BOX -> "35.598" Parameter: BOX -> "35.598" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.59800 B = 35.59800 C = 35.59800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3566 2 1 -1 -2 -1 13.8175 3 1 -1 -1 -1 4.1415 4 1 -1 0 -1 3.0721 5 1 0 -1 -1 5.0830 6 1 0 0 -1 2.6358 7 1 -1 -1 0 4.5179 8 1 -1 0 0 6.4141 9 1 0 -1 0 2.6632 10 1 0 1 0 2.6632 11 1 0 0 1 2.6358 12 1 0 1 1 5.0830 13 1 2 1 1 10.3566 14 1 1 2 1 13.8175 15 1 1 1 1 4.1415 16 1 1 0 1 3.0721 17 1 1 1 0 4.5179 18 1 1 0 0 6.4141 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3490 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.40 2 C002 has 36 12 12 11.53 3 C003 has 2631 877 877 0.00 4 C004 has 810 270 270 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1239 413 413 0.00 Total of12409 atoms and 4129 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> 0 atoms have been selected out of 3490 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3490 Number of groups = 1156 Number of bonds = 3484 Number of angles = 1260 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1154 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 = 3490 Number of groups = 1156 Number of bonds = 3484 Number of angles = 1260 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1154 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 <- "35.596" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1151" Evaluating: 1151-13 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1138" Comparing "1075" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.596" Parameter: BOX -> "35.596" Parameter: BOX -> "35.596" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.59600 B = 35.59600 C = 35.59600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3540 2 1 -1 -2 -1 13.8144 3 1 -1 -1 -1 4.1413 4 1 -1 0 -1 3.0724 5 1 0 -1 -1 5.0834 6 1 0 0 -1 2.6346 7 1 -1 -1 0 4.5178 8 1 -1 0 0 6.4125 9 1 0 -1 0 2.6616 10 1 0 1 0 2.6616 11 1 0 0 1 2.6346 12 1 0 1 1 5.0834 13 1 2 1 1 10.3540 14 1 1 2 1 13.8144 15 1 1 1 1 4.1413 16 1 1 0 1 3.0724 17 1 1 1 0 4.5178 18 1 1 0 0 6.4125 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3490 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.40 2 C002 has 36 12 12 11.52 3 C003 has 2631 877 877 0.00 4 C004 has 810 270 270 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1239 413 413 0.00 Total of12409 atoms and 4129 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> 0 atoms have been selected out of 3490 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3490 Number of groups = 1156 Number of bonds = 3484 Number of angles = 1260 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1154 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 = 3490 Number of groups = 1156 Number of bonds = 3484 Number of angles = 1260 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1154 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 <- "35.594" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1151" Evaluating: 1151-13 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1138" Comparing "1075" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.594" Parameter: BOX -> "35.594" Parameter: BOX -> "35.594" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.59400 B = 35.59400 C = 35.59400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3515 2 1 -1 -2 -1 13.8113 3 1 -1 -1 -1 4.1411 4 1 -1 0 -1 3.0726 5 1 0 -1 -1 5.0837 6 1 0 0 -1 2.6333 7 1 -1 -1 0 4.5177 8 1 -1 0 0 6.4108 9 1 0 -1 0 2.6600 10 1 0 1 0 2.6600 11 1 0 0 1 2.6333 12 1 0 1 1 5.0837 13 1 2 1 1 10.3515 14 1 1 2 1 13.8113 15 1 1 1 1 4.1411 16 1 1 0 1 3.0726 17 1 1 1 0 4.5177 18 1 1 0 0 6.4108 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3490 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.40 2 C002 has 36 12 12 11.52 3 C003 has 2631 877 877 0.00 4 C004 has 810 270 270 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1239 413 413 0.00 Total of12409 atoms and 4129 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> 0 atoms have been selected out of 3490 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3490 Number of groups = 1156 Number of bonds = 3484 Number of angles = 1260 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1154 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 = 3490 Number of groups = 1156 Number of bonds = 3484 Number of angles = 1260 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1154 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 <- "35.592" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1151" Evaluating: 1151-13 Parameter: NUMWAT <- "1138" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1138" Comparing "1075" and "1138". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.592" Parameter: BOX -> "35.592" Parameter: BOX -> "35.592" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.59200 B = 35.59200 C = 35.59200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3489 2 1 -1 -2 -1 13.8082 3 1 -1 -1 -1 4.1409 4 1 -1 0 -1 3.0728 5 1 0 -1 -1 5.0841 6 1 0 0 -1 2.6321 7 1 -1 -1 0 4.5176 8 1 -1 0 0 6.4092 9 1 0 -1 0 2.6585 10 1 0 1 0 2.6585 11 1 0 0 1 2.6321 12 1 0 1 1 5.0841 13 1 2 1 1 10.3489 14 1 1 2 1 13.8082 15 1 1 1 1 4.1409 16 1 1 0 1 3.0728 17 1 1 1 0 4.5176 18 1 1 0 0 6.4092 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3490 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 860 OPERATED ON BY TRANSFORMATION C004 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.39 2 C002 has 36 12 12 11.52 3 C003 has 2628 876 876 0.00 4 C004 has 819 273 273 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1146 382 382 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1242 414 414 0.00 Total of12418 atoms and 4132 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> 3 atoms have been selected out of 3490 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 = 3487 Number of groups = 1155 Number of bonds = 3481 Number of angles = 1259 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1153 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 = 3487 Number of groups = 1155 Number of bonds = 3481 Number of angles = 1259 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1153 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 <- "35.59" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1150" Evaluating: 1150-13 Parameter: NUMWAT <- "1137" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1137" Comparing "1075" and "1137". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.59" Parameter: BOX -> "35.59" Parameter: BOX -> "35.59" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.59000 B = 35.59000 C = 35.59000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3463 2 1 -1 -2 -1 13.8050 3 1 -1 -1 -1 4.1407 4 1 -1 0 -1 3.0731 5 1 0 -1 -1 5.0845 6 1 0 0 -1 2.6308 7 1 -1 -1 0 4.5175 8 1 -1 0 0 6.4076 9 1 0 -1 0 2.6569 10 1 0 1 0 2.6569 11 1 0 0 1 2.6308 12 1 0 1 1 5.0845 13 1 2 1 1 10.3463 14 1 1 2 1 13.8050 15 1 1 1 1 4.1407 16 1 1 0 1 3.0731 17 1 1 1 0 4.5175 18 1 1 0 0 6.4076 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3487 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 111 OPERATED ON BY TRANSFORMATION C015 RESIDUE 490 OPERATED ON BY TRANSFORMATION C009 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.39 2 C002 has 33 11 11 11.80 3 C003 has 2631 877 877 0.00 4 C004 has 813 271 271 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1152 384 384 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1233 411 411 0.00 9 C009 has 1239 413 413 0.00 Total of12415 atoms and 4131 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> 6 atoms have been selected out of 3487 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 = 3481 Number of groups = 1153 Number of bonds = 3475 Number of angles = 1257 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1151 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 = 3481 Number of groups = 1153 Number of bonds = 3475 Number of angles = 1257 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1151 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 <- "35.588" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1148" Evaluating: 1148-13 Parameter: NUMWAT <- "1135" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1135" Comparing "1075" and "1135". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.588" Parameter: BOX -> "35.588" Parameter: BOX -> "35.588" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.58800 B = 35.58800 C = 35.58800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3438 2 1 -1 -2 -1 13.8019 3 1 -1 -1 -1 4.1406 4 1 -1 0 -1 3.0733 5 1 0 -1 -1 5.0849 6 1 0 0 -1 2.6296 7 1 -1 -1 0 4.5174 8 1 -1 0 0 6.4060 9 1 0 -1 0 2.6553 10 1 0 1 0 2.6553 11 1 0 0 1 2.6296 12 1 0 1 1 5.0849 13 1 2 1 1 10.3438 14 1 1 2 1 13.8019 15 1 1 1 1 4.1406 16 1 1 0 1 3.0733 17 1 1 1 0 4.5174 18 1 1 0 0 6.4060 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3481 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.39 2 C002 has 33 11 11 11.79 3 C003 has 2625 875 875 0.00 4 C004 has 807 269 269 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1236 412 412 0.00 Total of12385 atoms and 4121 groups and 4116 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3481 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3481 Number of groups = 1153 Number of bonds = 3475 Number of angles = 1257 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1151 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 = 3481 Number of groups = 1153 Number of bonds = 3475 Number of angles = 1257 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1151 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 <- "35.586" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1148" Evaluating: 1148-13 Parameter: NUMWAT <- "1135" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1135" Comparing "1075" and "1135". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.586" Parameter: BOX -> "35.586" Parameter: BOX -> "35.586" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.58600 B = 35.58600 C = 35.58600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3412 2 1 -1 -2 -1 13.7988 3 1 -1 -1 -1 4.1404 4 1 -1 0 -1 3.0735 5 1 0 -1 -1 5.0853 6 1 0 0 -1 2.6283 7 1 -1 -1 0 4.5173 8 1 -1 0 0 6.4043 9 1 0 -1 0 2.6538 10 1 0 1 0 2.6538 11 1 0 0 1 2.6283 12 1 0 1 1 5.0853 13 1 2 1 1 10.3412 14 1 1 2 1 13.7988 15 1 1 1 1 4.1404 16 1 1 0 1 3.0735 17 1 1 1 0 4.5173 18 1 1 0 0 6.4043 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3481 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.38 2 C002 has 33 11 11 11.79 3 C003 has 2625 875 875 0.00 4 C004 has 807 269 269 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1236 412 412 0.00 Total of12385 atoms and 4121 groups and 4116 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3481 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3481 Number of groups = 1153 Number of bonds = 3475 Number of angles = 1257 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1151 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 = 3481 Number of groups = 1153 Number of bonds = 3475 Number of angles = 1257 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1151 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 <- "35.584" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1148" Evaluating: 1148-13 Parameter: NUMWAT <- "1135" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1135" Comparing "1075" and "1135". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.584" Parameter: BOX -> "35.584" Parameter: BOX -> "35.584" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.58400 B = 35.58400 C = 35.58400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3386 2 1 -1 -2 -1 13.7956 3 1 -1 -1 -1 4.1402 4 1 -1 0 -1 3.0738 5 1 0 -1 -1 5.0857 6 1 0 0 -1 2.6271 7 1 -1 -1 0 4.5172 8 1 -1 0 0 6.4027 9 1 0 -1 0 2.6522 10 1 0 1 0 2.6522 11 1 0 0 1 2.6271 12 1 0 1 1 5.0857 13 1 2 1 1 10.3386 14 1 1 2 1 13.7956 15 1 1 1 1 4.1402 16 1 1 0 1 3.0738 17 1 1 1 0 4.5172 18 1 1 0 0 6.4027 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3481 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.38 2 C002 has 33 11 11 11.79 3 C003 has 2625 875 875 0.00 4 C004 has 807 269 269 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1236 412 412 0.00 Total of12385 atoms and 4121 groups and 4116 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3481 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3481 Number of groups = 1153 Number of bonds = 3475 Number of angles = 1257 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1151 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 = 3481 Number of groups = 1153 Number of bonds = 3475 Number of angles = 1257 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1151 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 <- "35.582" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1148" Evaluating: 1148-13 Parameter: NUMWAT <- "1135" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1135" Comparing "1075" and "1135". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.582" Parameter: BOX -> "35.582" Parameter: BOX -> "35.582" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.58200 B = 35.58200 C = 35.58200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3360 2 1 -1 -2 -1 13.7925 3 1 -1 -1 -1 4.1400 4 1 -1 0 -1 3.0740 5 1 0 -1 -1 5.0861 6 1 0 0 -1 2.6259 7 1 -1 -1 0 4.5172 8 1 -1 0 0 6.4011 9 1 0 -1 0 2.6506 10 1 0 1 0 2.6506 11 1 0 0 1 2.6259 12 1 0 1 1 5.0861 13 1 2 1 1 10.3360 14 1 1 2 1 13.7925 15 1 1 1 1 4.1400 16 1 1 0 1 3.0740 17 1 1 1 0 4.5172 18 1 1 0 0 6.4011 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3481 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 165 55 55 6.38 2 C002 has 33 11 11 11.78 3 C003 has 2625 875 875 0.00 4 C004 has 807 269 269 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1236 412 412 0.00 Total of12385 atoms and 4121 groups and 4116 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3481 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3481 Number of groups = 1153 Number of bonds = 3475 Number of angles = 1257 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1151 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 = 3481 Number of groups = 1153 Number of bonds = 3475 Number of angles = 1257 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1151 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 <- "35.58" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1148" Evaluating: 1148-13 Parameter: NUMWAT <- "1135" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1135" Comparing "1075" and "1135". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.58" Parameter: BOX -> "35.58" Parameter: BOX -> "35.58" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.58000 B = 35.58000 C = 35.58000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3335 2 1 -1 -2 -1 13.7894 3 1 -1 -1 -1 4.1398 4 1 -1 0 -1 3.0742 5 1 0 -1 -1 5.0865 6 1 0 0 -1 2.6246 7 1 -1 -1 0 4.5171 8 1 -1 0 0 6.3995 9 1 0 -1 0 2.6491 10 1 0 1 0 2.6491 11 1 0 0 1 2.6246 12 1 0 1 1 5.0865 13 1 2 1 1 10.3335 14 1 1 2 1 13.7894 15 1 1 1 1 4.1398 16 1 1 0 1 3.0742 17 1 1 1 0 4.5171 18 1 1 0 0 6.3995 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3481 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.37 2 C002 has 33 11 11 11.78 3 C003 has 2625 875 875 0.00 4 C004 has 807 269 269 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1236 412 412 0.00 Total of12388 atoms and 4122 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 3481 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3481 Number of groups = 1153 Number of bonds = 3475 Number of angles = 1257 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1151 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 = 3481 Number of groups = 1153 Number of bonds = 3475 Number of angles = 1257 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1151 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 <- "35.578" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1148" Evaluating: 1148-13 Parameter: NUMWAT <- "1135" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1135" Comparing "1075" and "1135". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.578" Parameter: BOX -> "35.578" Parameter: BOX -> "35.578" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.57800 B = 35.57800 C = 35.57800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3309 2 1 -1 -2 -1 13.7863 3 1 -1 -1 -1 4.1396 4 1 -1 0 -1 3.0745 5 1 0 -1 -1 5.0869 6 1 0 0 -1 2.6234 7 1 -1 -1 0 4.5170 8 1 -1 0 0 6.3979 9 1 0 -1 0 2.6475 10 1 0 1 0 2.6475 11 1 0 0 1 2.6234 12 1 0 1 1 5.0869 13 1 2 1 1 10.3309 14 1 1 2 1 13.7863 15 1 1 1 1 4.1396 16 1 1 0 1 3.0745 17 1 1 1 0 4.5170 18 1 1 0 0 6.3979 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3481 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.37 2 C002 has 33 11 11 11.78 3 C003 has 2625 875 875 0.00 4 C004 has 807 269 269 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1236 412 412 0.00 Total of12388 atoms and 4122 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 3481 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3481 Number of groups = 1153 Number of bonds = 3475 Number of angles = 1257 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1151 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 = 3481 Number of groups = 1153 Number of bonds = 3475 Number of angles = 1257 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1151 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 <- "35.576" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1148" Evaluating: 1148-13 Parameter: NUMWAT <- "1135" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1135" Comparing "1075" and "1135". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.576" Parameter: BOX -> "35.576" Parameter: BOX -> "35.576" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.57600 B = 35.57600 C = 35.57600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3283 2 1 -1 -2 -1 13.7831 3 1 -1 -1 -1 4.1394 4 1 -1 0 -1 3.0747 5 1 0 -1 -1 5.0873 6 1 0 0 -1 2.6222 7 1 -1 -1 0 4.5169 8 1 -1 0 0 6.3962 9 1 0 -1 0 2.6459 10 1 0 1 0 2.6459 11 1 0 0 1 2.6222 12 1 0 1 1 5.0873 13 1 2 1 1 10.3283 14 1 1 2 1 13.7831 15 1 1 1 1 4.1394 16 1 1 0 1 3.0747 17 1 1 1 0 4.5169 18 1 1 0 0 6.3962 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3481 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.37 2 C002 has 33 11 11 11.78 3 C003 has 2625 875 875 0.00 4 C004 has 807 269 269 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1236 412 412 0.00 Total of12388 atoms and 4122 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 3481 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3481 Number of groups = 1153 Number of bonds = 3475 Number of angles = 1257 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1151 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 = 3481 Number of groups = 1153 Number of bonds = 3475 Number of angles = 1257 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1151 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 <- "35.574" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1148" Evaluating: 1148-13 Parameter: NUMWAT <- "1135" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1135" Comparing "1075" and "1135". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.574" Parameter: BOX -> "35.574" Parameter: BOX -> "35.574" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.57400 B = 35.57400 C = 35.57400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3258 2 1 -1 -2 -1 13.7800 3 1 -1 -1 -1 4.1392 4 1 -1 0 -1 3.0750 5 1 0 -1 -1 5.0877 6 1 0 0 -1 2.6209 7 1 -1 -1 0 4.5168 8 1 -1 0 0 6.3946 9 1 0 -1 0 2.6444 10 1 0 1 0 2.6444 11 1 0 0 1 2.6209 12 1 0 1 1 5.0877 13 1 2 1 1 10.3258 14 1 1 2 1 13.7800 15 1 1 1 1 4.1392 16 1 1 0 1 3.0750 17 1 1 1 0 4.5168 18 1 1 0 0 6.3946 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3481 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 564 OPERATED ON BY TRANSFORMATION C009 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.37 2 C002 has 30 10 10 11.77 3 C003 has 2625 875 875 0.00 4 C004 has 810 270 270 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1230 410 410 0.00 9 C009 has 1245 415 415 0.00 Total of12397 atoms and 4125 groups and 4120 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3481 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 = 3478 Number of groups = 1152 Number of bonds = 3472 Number of angles = 1256 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1150 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 = 3478 Number of groups = 1152 Number of bonds = 3472 Number of angles = 1256 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1150 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 <- "35.572" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1147" Evaluating: 1147-13 Parameter: NUMWAT <- "1134" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1134" Comparing "1075" and "1134". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.572" Parameter: BOX -> "35.572" Parameter: BOX -> "35.572" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.57200 B = 35.57200 C = 35.57200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3232 2 1 -1 -2 -1 13.7769 3 1 -1 -1 -1 4.1391 4 1 -1 0 -1 3.0752 5 1 0 -1 -1 5.0881 6 1 0 0 -1 2.6197 7 1 -1 -1 0 4.5167 8 1 -1 0 0 6.3930 9 1 0 -1 0 2.6428 10 1 0 1 0 2.6428 11 1 0 0 1 2.6197 12 1 0 1 1 5.0881 13 1 2 1 1 10.3232 14 1 1 2 1 13.7769 15 1 1 1 1 4.1391 16 1 1 0 1 3.0752 17 1 1 1 0 4.5167 18 1 1 0 0 6.3930 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3478 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.36 2 C002 has 30 10 10 11.77 3 C003 has 2625 875 875 0.00 4 C004 has 807 269 269 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1233 411 411 0.00 Total of12376 atoms and 4118 groups and 4113 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3478 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3478 Number of groups = 1152 Number of bonds = 3472 Number of angles = 1256 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1150 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 = 3478 Number of groups = 1152 Number of bonds = 3472 Number of angles = 1256 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1150 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 <- "35.57" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1147" Evaluating: 1147-13 Parameter: NUMWAT <- "1134" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1134" Comparing "1075" and "1134". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.57" Parameter: BOX -> "35.57" Parameter: BOX -> "35.57" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.57000 B = 35.57000 C = 35.57000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3206 2 1 -1 -2 -1 13.7737 3 1 -1 -1 -1 4.1389 4 1 -1 0 -1 3.0755 5 1 0 -1 -1 5.0885 6 1 0 0 -1 2.6184 7 1 -1 -1 0 4.5166 8 1 -1 0 0 6.3914 9 1 0 -1 0 2.6412 10 1 0 1 0 2.6412 11 1 0 0 1 2.6184 12 1 0 1 1 5.0885 13 1 2 1 1 10.3206 14 1 1 2 1 13.7737 15 1 1 1 1 4.1389 16 1 1 0 1 3.0755 17 1 1 1 0 4.5166 18 1 1 0 0 6.3914 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3478 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.36 2 C002 has 30 10 10 11.77 3 C003 has 2625 875 875 0.00 4 C004 has 807 269 269 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1233 411 411 0.00 Total of12376 atoms and 4118 groups and 4113 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3478 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3478 Number of groups = 1152 Number of bonds = 3472 Number of angles = 1256 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1150 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 = 3478 Number of groups = 1152 Number of bonds = 3472 Number of angles = 1256 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1150 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 <- "35.568" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1147" Evaluating: 1147-13 Parameter: NUMWAT <- "1134" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1134" Comparing "1075" and "1134". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.568" Parameter: BOX -> "35.568" Parameter: BOX -> "35.568" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.56800 B = 35.56800 C = 35.56800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3181 2 1 -1 -2 -1 13.7706 3 1 -1 -1 -1 4.1387 4 1 -1 0 -1 3.0757 5 1 0 -1 -1 5.0889 6 1 0 0 -1 2.6172 7 1 -1 -1 0 4.5165 8 1 -1 0 0 6.3898 9 1 0 -1 0 2.6397 10 1 0 1 0 2.6397 11 1 0 0 1 2.6172 12 1 0 1 1 5.0889 13 1 2 1 1 10.3181 14 1 1 2 1 13.7706 15 1 1 1 1 4.1387 16 1 1 0 1 3.0757 17 1 1 1 0 4.5165 18 1 1 0 0 6.3898 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3478 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.36 2 C002 has 30 10 10 11.76 3 C003 has 2628 876 876 0.00 4 C004 has 807 269 269 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1233 411 411 0.00 Total of12379 atoms and 4119 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 3478 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3478 Number of groups = 1152 Number of bonds = 3472 Number of angles = 1256 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1150 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 = 3478 Number of groups = 1152 Number of bonds = 3472 Number of angles = 1256 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1150 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 <- "35.566" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1147" Evaluating: 1147-13 Parameter: NUMWAT <- "1134" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1134" Comparing "1075" and "1134". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.566" Parameter: BOX -> "35.566" Parameter: BOX -> "35.566" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.56600 B = 35.56600 C = 35.56600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3155 2 1 -1 -2 -1 13.7675 3 1 -1 -1 -1 4.1385 4 1 -1 0 -1 3.0760 5 1 0 -1 -1 5.0893 6 1 0 0 -1 2.6160 7 1 -1 -1 0 4.5164 8 1 -1 0 0 6.3881 9 1 0 -1 0 2.6381 10 1 0 1 0 2.6381 11 1 0 0 1 2.6160 12 1 0 1 1 5.0893 13 1 2 1 1 10.3155 14 1 1 2 1 13.7675 15 1 1 1 1 4.1385 16 1 1 0 1 3.0760 17 1 1 1 0 4.5164 18 1 1 0 0 6.3881 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3478 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 C015 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 171 57 57 6.35 2 C002 has 30 10 10 11.76 3 C003 has 2631 877 877 0.00 4 C004 has 810 270 270 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1233 411 411 0.00 Total of12394 atoms and 4124 groups and 4119 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3478 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 = 3475 Number of groups = 1151 Number of bonds = 3469 Number of angles = 1255 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1149 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 = 3475 Number of groups = 1151 Number of bonds = 3469 Number of angles = 1255 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1149 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 <- "35.564" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1146" Evaluating: 1146-13 Parameter: NUMWAT <- "1133" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1133" Comparing "1075" and "1133". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.564" Parameter: BOX -> "35.564" Parameter: BOX -> "35.564" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.56400 B = 35.56400 C = 35.56400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3129 2 1 -1 -2 -1 13.7644 3 1 -1 -1 -1 4.1383 4 1 -1 0 -1 3.0762 5 1 0 -1 -1 5.0897 6 1 0 0 -1 2.6147 7 1 -1 -1 0 4.5163 8 1 -1 0 0 6.3865 9 1 0 -1 0 2.6366 10 1 0 1 0 2.6366 11 1 0 0 1 2.6147 12 1 0 1 1 5.0897 13 1 2 1 1 10.3129 14 1 1 2 1 13.7644 15 1 1 1 1 4.1383 16 1 1 0 1 3.0762 17 1 1 1 0 4.5163 18 1 1 0 0 6.3865 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3475 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.35 2 C002 has 30 10 10 11.76 3 C003 has 2628 876 876 0.00 4 C004 has 807 269 269 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1233 411 411 0.00 Total of12379 atoms and 4119 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 3475 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3475 Number of groups = 1151 Number of bonds = 3469 Number of angles = 1255 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1149 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 = 3475 Number of groups = 1151 Number of bonds = 3469 Number of angles = 1255 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1149 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 <- "35.562" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1146" Evaluating: 1146-13 Parameter: NUMWAT <- "1133" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1133" Comparing "1075" and "1133". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.562" Parameter: BOX -> "35.562" Parameter: BOX -> "35.562" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.56200 B = 35.56200 C = 35.56200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3104 2 1 -1 -2 -1 13.7612 3 1 -1 -1 -1 4.1382 4 1 -1 0 -1 3.0765 5 1 0 -1 -1 5.0901 6 1 0 0 -1 2.6135 7 1 -1 -1 0 4.5163 8 1 -1 0 0 6.3849 9 1 0 -1 0 2.6350 10 1 0 1 0 2.6350 11 1 0 0 1 2.6135 12 1 0 1 1 5.0901 13 1 2 1 1 10.3104 14 1 1 2 1 13.7612 15 1 1 1 1 4.1382 16 1 1 0 1 3.0765 17 1 1 1 0 4.5163 18 1 1 0 0 6.3849 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3475 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.35 2 C002 has 30 10 10 11.75 3 C003 has 2628 876 876 0.00 4 C004 has 807 269 269 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1233 411 411 0.00 Total of12379 atoms and 4119 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 3475 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3475 Number of groups = 1151 Number of bonds = 3469 Number of angles = 1255 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1149 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 = 3475 Number of groups = 1151 Number of bonds = 3469 Number of angles = 1255 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1149 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 <- "35.56" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1146" Evaluating: 1146-13 Parameter: NUMWAT <- "1133" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1133" Comparing "1075" and "1133". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.56" Parameter: BOX -> "35.56" Parameter: BOX -> "35.56" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.56000 B = 35.56000 C = 35.56000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3078 2 1 -1 -2 -1 13.7581 3 1 -1 -1 -1 4.1380 4 1 -1 0 -1 3.0768 5 1 0 -1 -1 5.0905 6 1 0 0 -1 2.6123 7 1 -1 -1 0 4.5162 8 1 -1 0 0 6.3833 9 1 0 -1 0 2.6334 10 1 0 1 0 2.6334 11 1 0 0 1 2.6123 12 1 0 1 1 5.0905 13 1 2 1 1 10.3078 14 1 1 2 1 13.7581 15 1 1 1 1 4.1380 16 1 1 0 1 3.0768 17 1 1 1 0 4.5162 18 1 1 0 0 6.3833 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3475 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.34 2 C002 has 30 10 10 11.75 3 C003 has 2631 877 877 0.00 4 C004 has 807 269 269 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1233 411 411 0.00 Total of12382 atoms and 4120 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 3475 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3475 Number of groups = 1151 Number of bonds = 3469 Number of angles = 1255 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1149 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 = 3475 Number of groups = 1151 Number of bonds = 3469 Number of angles = 1255 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1149 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 <- "35.558" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1146" Evaluating: 1146-13 Parameter: NUMWAT <- "1133" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1133" Comparing "1075" and "1133". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.558" Parameter: BOX -> "35.558" Parameter: BOX -> "35.558" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.55800 B = 35.55800 C = 35.55800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3052 2 1 -1 -2 -1 13.7550 3 1 -1 -1 -1 4.1378 4 1 -1 0 -1 3.0770 5 1 0 -1 -1 5.0909 6 1 0 0 -1 2.6111 7 1 -1 -1 0 4.5161 8 1 -1 0 0 6.3817 9 1 0 -1 0 2.6319 10 1 0 1 0 2.6319 11 1 0 0 1 2.6111 12 1 0 1 1 5.0909 13 1 2 1 1 10.3052 14 1 1 2 1 13.7550 15 1 1 1 1 4.1378 16 1 1 0 1 3.0770 17 1 1 1 0 4.5161 18 1 1 0 0 6.3817 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3475 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.34 2 C002 has 30 10 10 11.75 3 C003 has 2631 877 877 0.00 4 C004 has 807 269 269 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1152 384 384 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1236 412 412 0.00 Total of12388 atoms and 4122 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 3475 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3475 Number of groups = 1151 Number of bonds = 3469 Number of angles = 1255 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1149 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 = 3475 Number of groups = 1151 Number of bonds = 3469 Number of angles = 1255 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1149 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 <- "35.556" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1146" Evaluating: 1146-13 Parameter: NUMWAT <- "1133" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1133" Comparing "1075" and "1133". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.556" Parameter: BOX -> "35.556" Parameter: BOX -> "35.556" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.55600 B = 35.55600 C = 35.55600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3027 2 1 -1 -2 -1 13.7518 3 1 -1 -1 -1 4.1376 4 1 -1 0 -1 3.0773 5 1 0 -1 -1 5.0913 6 1 0 0 -1 2.6098 7 1 -1 -1 0 4.5160 8 1 -1 0 0 6.3801 9 1 0 -1 0 2.6303 10 1 0 1 0 2.6303 11 1 0 0 1 2.6098 12 1 0 1 1 5.0913 13 1 2 1 1 10.3027 14 1 1 2 1 13.7518 15 1 1 1 1 4.1376 16 1 1 0 1 3.0773 17 1 1 1 0 4.5160 18 1 1 0 0 6.3801 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3475 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 C003 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.34 2 C002 has 30 10 10 11.74 3 C003 has 2628 876 876 0.00 4 C004 has 807 269 269 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1173 391 391 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1233 411 411 0.00 Total of12397 atoms and 4125 groups and 4120 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3475 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 = 3472 Number of groups = 1150 Number of bonds = 3466 Number of angles = 1254 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1148 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 = 3472 Number of groups = 1150 Number of bonds = 3466 Number of angles = 1254 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1148 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 <- "35.554" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-13 Parameter: NUMWAT <- "1132" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1132" Comparing "1075" and "1132". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.554" Parameter: BOX -> "35.554" Parameter: BOX -> "35.554" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.55400 B = 35.55400 C = 35.55400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.3001 2 1 -1 -2 -1 13.7487 3 1 -1 -1 -1 4.1375 4 1 -1 0 -1 3.0775 5 1 0 -1 -1 5.0917 6 1 0 0 -1 2.6086 7 1 -1 -1 0 3.0804 8 1 -1 0 0 6.2108 9 1 0 -1 0 2.6288 10 1 0 1 0 2.6288 11 1 0 0 1 2.6086 12 1 0 1 1 5.0917 13 1 2 1 1 10.3001 14 1 1 2 1 13.7487 15 1 1 1 1 4.1375 16 1 1 0 1 3.0775 17 1 1 1 0 3.0804 18 1 1 0 0 6.2108 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3472 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.33 2 C002 has 30 10 10 11.74 3 C003 has 2628 876 876 0.00 4 C004 has 807 269 269 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1152 384 384 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1233 411 411 0.00 Total of12373 atoms and 4117 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 3472 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3472 Number of groups = 1150 Number of bonds = 3466 Number of angles = 1254 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1148 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 = 3472 Number of groups = 1150 Number of bonds = 3466 Number of angles = 1254 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1148 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 <- "35.552" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-13 Parameter: NUMWAT <- "1132" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1132" Comparing "1075" and "1132". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.552" Parameter: BOX -> "35.552" Parameter: BOX -> "35.552" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.55200 B = 35.55200 C = 35.55200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2975 2 1 -1 -2 -1 13.7456 3 1 -1 -1 -1 4.1373 4 1 -1 0 -1 3.0778 5 1 0 -1 -1 5.0921 6 1 0 0 -1 2.6074 7 1 -1 -1 0 3.0802 8 1 -1 0 0 6.2100 9 1 0 -1 0 2.6272 10 1 0 1 0 2.6272 11 1 0 0 1 2.6074 12 1 0 1 1 5.0921 13 1 2 1 1 10.2975 14 1 1 2 1 13.7456 15 1 1 1 1 4.1373 16 1 1 0 1 3.0778 17 1 1 1 0 3.0802 18 1 1 0 0 6.2100 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3472 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.33 2 C002 has 30 10 10 11.74 3 C003 has 2628 876 876 0.00 4 C004 has 807 269 269 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1152 384 384 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1233 411 411 0.00 Total of12376 atoms and 4118 groups and 4113 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3472 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3472 Number of groups = 1150 Number of bonds = 3466 Number of angles = 1254 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1148 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 = 3472 Number of groups = 1150 Number of bonds = 3466 Number of angles = 1254 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1148 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 <- "35.55" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-13 Parameter: NUMWAT <- "1132" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1132" Comparing "1075" and "1132". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.55" Parameter: BOX -> "35.55" Parameter: BOX -> "35.55" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.55000 B = 35.55000 C = 35.55000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2950 2 1 -1 -2 -1 13.7425 3 1 -1 -1 -1 4.1371 4 1 -1 0 -1 3.0781 5 1 0 -1 -1 5.0925 6 1 0 0 -1 2.6062 7 1 -1 -1 0 3.0799 8 1 -1 0 0 6.2092 9 1 0 -1 0 2.6256 10 1 0 1 0 2.6256 11 1 0 0 1 2.6062 12 1 0 1 1 5.0925 13 1 2 1 1 10.2950 14 1 1 2 1 13.7425 15 1 1 1 1 4.1371 16 1 1 0 1 3.0781 17 1 1 1 0 3.0799 18 1 1 0 0 6.2092 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3472 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.33 2 C002 has 30 10 10 11.74 3 C003 has 2628 876 876 0.00 4 C004 has 807 269 269 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1152 384 384 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1233 411 411 0.00 Total of12376 atoms and 4118 groups and 4113 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3472 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3472 Number of groups = 1150 Number of bonds = 3466 Number of angles = 1254 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1148 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 = 3472 Number of groups = 1150 Number of bonds = 3466 Number of angles = 1254 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1148 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 <- "35.548" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-13 Parameter: NUMWAT <- "1132" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1132" Comparing "1075" and "1132". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.548" Parameter: BOX -> "35.548" Parameter: BOX -> "35.548" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.54800 B = 35.54800 C = 35.54800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2924 2 1 -1 -2 -1 13.7393 3 1 -1 -1 -1 4.1370 4 1 -1 0 -1 3.0784 5 1 0 -1 -1 5.0929 6 1 0 0 -1 2.6049 7 1 -1 -1 0 3.0797 8 1 -1 0 0 6.2085 9 1 0 -1 0 2.6241 10 1 0 1 0 2.6241 11 1 0 0 1 2.6049 12 1 0 1 1 5.0929 13 1 2 1 1 10.2924 14 1 1 2 1 13.7393 15 1 1 1 1 4.1370 16 1 1 0 1 3.0784 17 1 1 1 0 3.0797 18 1 1 0 0 6.2085 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3472 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.33 2 C002 has 30 10 10 11.73 3 C003 has 2628 876 876 0.00 4 C004 has 807 269 269 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1152 384 384 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1233 411 411 0.00 Total of12379 atoms and 4119 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 3472 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3472 Number of groups = 1150 Number of bonds = 3466 Number of angles = 1254 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1148 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 = 3472 Number of groups = 1150 Number of bonds = 3466 Number of angles = 1254 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1148 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 <- "35.546" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1145" Evaluating: 1145-13 Parameter: NUMWAT <- "1132" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1132" Comparing "1075" and "1132". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.546" Parameter: BOX -> "35.546" Parameter: BOX -> "35.546" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.54600 B = 35.54600 C = 35.54600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2899 2 1 -1 -2 -1 13.7362 3 1 -1 -1 -1 4.1368 4 1 -1 0 -1 3.0786 5 1 0 -1 -1 5.0934 6 1 0 0 -1 2.6037 7 1 -1 -1 0 3.0794 8 1 -1 0 0 6.2077 9 1 0 -1 0 2.6225 10 1 0 1 0 2.6225 11 1 0 0 1 2.6037 12 1 0 1 1 5.0934 13 1 2 1 1 10.2899 14 1 1 2 1 13.7362 15 1 1 1 1 4.1368 16 1 1 0 1 3.0786 17 1 1 1 0 3.0794 18 1 1 0 0 6.2077 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3472 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 414 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.32 2 C002 has 30 10 10 11.73 3 C003 has 2631 877 877 0.00 4 C004 has 807 269 269 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1230 410 410 0.00 Total of12385 atoms and 4121 groups and 4116 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3472 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 = 3469 Number of groups = 1149 Number of bonds = 3463 Number of angles = 1253 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1147 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 = 3469 Number of groups = 1149 Number of bonds = 3463 Number of angles = 1253 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1147 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 <- "35.544" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1144" Evaluating: 1144-13 Parameter: NUMWAT <- "1131" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1131" Comparing "1075" and "1131". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.544" Parameter: BOX -> "35.544" Parameter: BOX -> "35.544" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.54400 B = 35.54400 C = 35.54400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2873 2 1 -1 -2 -1 13.7331 3 1 -1 -1 -1 4.1366 4 1 -1 0 -1 3.0789 5 1 0 -1 -1 5.0938 6 1 0 0 -1 2.6025 7 1 -1 -1 0 3.0792 8 1 -1 0 0 6.2069 9 1 0 -1 0 2.6210 10 1 0 1 0 2.6210 11 1 0 0 1 2.6025 12 1 0 1 1 5.0938 13 1 2 1 1 10.2873 14 1 1 2 1 13.7331 15 1 1 1 1 4.1366 16 1 1 0 1 3.0789 17 1 1 1 0 3.0792 18 1 1 0 0 6.2069 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3469 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.32 2 C002 has 30 10 10 11.73 3 C003 has 2628 876 876 0.00 4 C004 has 804 268 268 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1152 384 384 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1230 410 410 0.00 Total of12373 atoms and 4117 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 3469 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3469 Number of groups = 1149 Number of bonds = 3463 Number of angles = 1253 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1147 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 = 3469 Number of groups = 1149 Number of bonds = 3463 Number of angles = 1253 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1147 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 <- "35.542" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1144" Evaluating: 1144-13 Parameter: NUMWAT <- "1131" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1131" Comparing "1075" and "1131". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.542" Parameter: BOX -> "35.542" Parameter: BOX -> "35.542" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.54200 B = 35.54200 C = 35.54200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2847 2 1 -1 -2 -1 13.7300 3 1 -1 -1 -1 4.1364 4 1 -1 0 -1 3.0792 5 1 0 -1 -1 5.0942 6 1 0 0 -1 2.6013 7 1 -1 -1 0 3.0789 8 1 -1 0 0 6.2061 9 1 0 -1 0 2.6194 10 1 0 1 0 2.6194 11 1 0 0 1 2.6013 12 1 0 1 1 5.0942 13 1 2 1 1 10.2847 14 1 1 2 1 13.7300 15 1 1 1 1 4.1364 16 1 1 0 1 3.0792 17 1 1 1 0 3.0789 18 1 1 0 0 6.2061 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3469 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.32 2 C002 has 30 10 10 11.72 3 C003 has 2628 876 876 0.00 4 C004 has 804 268 268 0.00 5 C005 has 867 289 289 0.00 6 C006 has 1152 384 384 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1230 410 410 0.00 Total of12379 atoms and 4119 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 3469 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3469 Number of groups = 1149 Number of bonds = 3463 Number of angles = 1253 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1147 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 = 3469 Number of groups = 1149 Number of bonds = 3463 Number of angles = 1253 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1147 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 <- "35.54" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1144" Evaluating: 1144-13 Parameter: NUMWAT <- "1131" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1131" Comparing "1075" and "1131". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.54" Parameter: BOX -> "35.54" Parameter: BOX -> "35.54" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.54000 B = 35.54000 C = 35.54000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2822 2 1 -1 -2 -1 13.7268 3 1 -1 -1 -1 4.1363 4 1 -1 0 -1 3.0794 5 1 0 -1 -1 5.0946 6 1 0 0 -1 2.6000 7 1 -1 -1 0 3.0787 8 1 -1 0 0 6.2054 9 1 0 -1 0 2.6179 10 1 0 1 0 2.6179 11 1 0 0 1 2.6000 12 1 0 1 1 5.0946 13 1 2 1 1 10.2822 14 1 1 2 1 13.7268 15 1 1 1 1 4.1363 16 1 1 0 1 3.0794 17 1 1 1 0 3.0787 18 1 1 0 0 6.2054 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3469 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.31 2 C002 has 30 10 10 11.72 3 C003 has 2628 876 876 0.00 4 C004 has 804 268 268 0.00 5 C005 has 867 289 289 0.00 6 C006 has 1152 384 384 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1230 410 410 0.00 Total of12382 atoms and 4120 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 3469 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3469 Number of groups = 1149 Number of bonds = 3463 Number of angles = 1253 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1147 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 = 3469 Number of groups = 1149 Number of bonds = 3463 Number of angles = 1253 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1147 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 <- "35.538" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1144" Evaluating: 1144-13 Parameter: NUMWAT <- "1131" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1131" Comparing "1075" and "1131". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.538" Parameter: BOX -> "35.538" Parameter: BOX -> "35.538" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.53800 B = 35.53800 C = 35.53800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2796 2 1 -1 -2 -1 13.7237 3 1 -1 -1 -1 4.1361 4 1 -1 0 -1 3.0797 5 1 0 -1 -1 5.0950 6 1 0 0 -1 2.5988 7 1 -1 -1 0 3.0784 8 1 -1 0 0 6.2046 9 1 0 -1 0 2.6163 10 1 0 1 0 2.6163 11 1 0 0 1 2.5988 12 1 0 1 1 5.0950 13 1 2 1 1 10.2796 14 1 1 2 1 13.7237 15 1 1 1 1 4.1361 16 1 1 0 1 3.0797 17 1 1 1 0 3.0784 18 1 1 0 0 6.2046 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3469 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.31 2 C002 has 30 10 10 11.72 3 C003 has 2628 876 876 0.00 4 C004 has 804 268 268 0.00 5 C005 has 867 289 289 0.00 6 C006 has 1152 384 384 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1230 410 410 0.00 Total of12382 atoms and 4120 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 3469 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3469 Number of groups = 1149 Number of bonds = 3463 Number of angles = 1253 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1147 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 = 3469 Number of groups = 1149 Number of bonds = 3463 Number of angles = 1253 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1147 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 <- "35.536" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1144" Evaluating: 1144-13 Parameter: NUMWAT <- "1131" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1131" Comparing "1075" and "1131". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.536" Parameter: BOX -> "35.536" Parameter: BOX -> "35.536" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.53600 B = 35.53600 C = 35.53600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2771 2 1 -1 -2 -1 13.7206 3 1 -1 -1 -1 4.1360 4 1 -1 0 -1 3.0800 5 1 0 -1 -1 5.0954 6 1 0 0 -1 2.5976 7 1 -1 -1 0 3.0782 8 1 -1 0 0 6.2038 9 1 0 -1 0 2.6148 10 1 0 1 0 2.6148 11 1 0 0 1 2.5976 12 1 0 1 1 5.0954 13 1 2 1 1 10.2771 14 1 1 2 1 13.7206 15 1 1 1 1 4.1360 16 1 1 0 1 3.0800 17 1 1 1 0 3.0782 18 1 1 0 0 6.2038 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3469 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.31 2 C002 has 30 10 10 11.71 3 C003 has 2628 876 876 0.00 4 C004 has 804 268 268 0.00 5 C005 has 867 289 289 0.00 6 C006 has 1152 384 384 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1230 410 410 0.00 Total of12382 atoms and 4120 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 3469 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3469 Number of groups = 1149 Number of bonds = 3463 Number of angles = 1253 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1147 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 = 3469 Number of groups = 1149 Number of bonds = 3463 Number of angles = 1253 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1147 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 <- "35.534" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1144" Evaluating: 1144-13 Parameter: NUMWAT <- "1131" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1131" Comparing "1075" and "1131". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.534" Parameter: BOX -> "35.534" Parameter: BOX -> "35.534" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.53400 B = 35.53400 C = 35.53400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2745 2 1 -1 -2 -1 13.7174 3 1 -1 -1 -1 4.1358 4 1 -1 0 -1 3.0803 5 1 0 -1 -1 5.0959 6 1 0 0 -1 2.5964 7 1 -1 -1 0 3.0780 8 1 -1 0 0 6.2030 9 1 0 -1 0 2.6132 10 1 0 1 0 2.6132 11 1 0 0 1 2.5964 12 1 0 1 1 5.0959 13 1 2 1 1 10.2745 14 1 1 2 1 13.7174 15 1 1 1 1 4.1358 16 1 1 0 1 3.0803 17 1 1 1 0 3.0780 18 1 1 0 0 6.2030 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3469 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.30 2 C002 has 33 11 11 11.71 3 C003 has 2631 877 877 0.00 4 C004 has 804 268 268 0.00 5 C005 has 867 289 289 0.00 6 C006 has 1152 384 384 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1230 410 410 0.00 Total of12388 atoms and 4122 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 3469 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3469 Number of groups = 1149 Number of bonds = 3463 Number of angles = 1253 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1147 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 = 3469 Number of groups = 1149 Number of bonds = 3463 Number of angles = 1253 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1147 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 <- "35.532" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1144" Evaluating: 1144-13 Parameter: NUMWAT <- "1131" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1131" Comparing "1075" and "1131". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.532" Parameter: BOX -> "35.532" Parameter: BOX -> "35.532" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.53200 B = 35.53200 C = 35.53200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2719 2 1 -1 -2 -1 13.7143 3 1 -1 -1 -1 4.1356 4 1 -1 0 -1 3.0806 5 1 0 -1 -1 5.0963 6 1 0 0 -1 2.5952 7 1 -1 -1 0 3.0777 8 1 -1 0 0 6.2023 9 1 0 -1 0 2.6116 10 1 0 1 0 2.6116 11 1 0 0 1 2.5952 12 1 0 1 1 5.0963 13 1 2 1 1 10.2719 14 1 1 2 1 13.7143 15 1 1 1 1 4.1356 16 1 1 0 1 3.0806 17 1 1 1 0 3.0777 18 1 1 0 0 6.2023 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3469 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.30 2 C002 has 33 11 11 11.71 3 C003 has 2631 877 877 0.00 4 C004 has 804 268 268 0.00 5 C005 has 867 289 289 0.00 6 C006 has 1152 384 384 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1230 410 410 0.00 Total of12388 atoms and 4122 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 3469 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3469 Number of groups = 1149 Number of bonds = 3463 Number of angles = 1253 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1147 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 = 3469 Number of groups = 1149 Number of bonds = 3463 Number of angles = 1253 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1147 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 <- "35.53" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1144" Evaluating: 1144-13 Parameter: NUMWAT <- "1131" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1131" Comparing "1075" and "1131". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.53" Parameter: BOX -> "35.53" Parameter: BOX -> "35.53" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.53000 B = 35.53000 C = 35.53000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2694 2 1 -1 -2 -1 13.7112 3 1 -1 -1 -1 4.1355 4 1 -1 0 -1 3.0809 5 1 0 -1 -1 5.0967 6 1 0 0 -1 2.5940 7 1 -1 -1 0 3.0775 8 1 -1 0 0 6.2015 9 1 0 -1 0 2.6101 10 1 0 1 0 2.6101 11 1 0 0 1 2.5940 12 1 0 1 1 5.0967 13 1 2 1 1 10.2694 14 1 1 2 1 13.7112 15 1 1 1 1 4.1355 16 1 1 0 1 3.0809 17 1 1 1 0 3.0775 18 1 1 0 0 6.2015 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3469 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.30 2 C002 has 33 11 11 11.70 3 C003 has 2631 877 877 0.00 4 C004 has 804 268 268 0.00 5 C005 has 867 289 289 0.00 6 C006 has 1152 384 384 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1230 410 410 0.00 Total of12388 atoms and 4122 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 3469 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3469 Number of groups = 1149 Number of bonds = 3463 Number of angles = 1253 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1147 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 = 3469 Number of groups = 1149 Number of bonds = 3463 Number of angles = 1253 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1147 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 <- "35.528" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1144" Evaluating: 1144-13 Parameter: NUMWAT <- "1131" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1131" Comparing "1075" and "1131". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.528" Parameter: BOX -> "35.528" Parameter: BOX -> "35.528" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.52800 B = 35.52800 C = 35.52800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2668 2 1 -1 -2 -1 13.7081 3 1 -1 -1 -1 4.1353 4 1 -1 0 -1 3.0811 5 1 0 -1 -1 5.0971 6 1 0 0 -1 2.5928 7 1 -1 -1 0 3.0773 8 1 -1 0 0 6.2007 9 1 0 -1 0 2.6085 10 1 0 1 0 2.6085 11 1 0 0 1 2.5928 12 1 0 1 1 5.0971 13 1 2 1 1 10.2668 14 1 1 2 1 13.7081 15 1 1 1 1 4.1353 16 1 1 0 1 3.0811 17 1 1 1 0 3.0773 18 1 1 0 0 6.2007 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3469 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.29 2 C002 has 33 11 11 11.70 3 C003 has 2631 877 877 0.00 4 C004 has 804 268 268 0.00 5 C005 has 867 289 289 0.00 6 C006 has 1152 384 384 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1230 410 410 0.00 Total of12388 atoms and 4122 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 3469 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3469 Number of groups = 1149 Number of bonds = 3463 Number of angles = 1253 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1147 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 = 3469 Number of groups = 1149 Number of bonds = 3463 Number of angles = 1253 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1147 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 <- "35.526" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1144" Evaluating: 1144-13 Parameter: NUMWAT <- "1131" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1131" Comparing "1075" and "1131". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.526" Parameter: BOX -> "35.526" Parameter: BOX -> "35.526" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.52600 B = 35.52600 C = 35.52600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2643 2 1 -1 -2 -1 13.7049 3 1 -1 -1 -1 4.1351 4 1 -1 0 -1 3.0814 5 1 0 -1 -1 5.0975 6 1 0 0 -1 2.5915 7 1 -1 -1 0 3.0770 8 1 -1 0 0 6.2000 9 1 0 -1 0 2.6070 10 1 0 1 0 2.6070 11 1 0 0 1 2.5915 12 1 0 1 1 5.0975 13 1 2 1 1 10.2643 14 1 1 2 1 13.7049 15 1 1 1 1 4.1351 16 1 1 0 1 3.0814 17 1 1 1 0 3.0770 18 1 1 0 0 6.2000 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3469 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 381 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.29 2 C002 has 33 11 11 11.70 3 C003 has 2634 878 878 0.00 4 C004 has 804 268 268 0.00 5 C005 has 870 290 290 0.00 6 C006 has 1143 381 381 0.00 7 C007 has 807 269 269 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1227 409 409 0.00 Total of12379 atoms and 4119 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 3469 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 = 3466 Number of groups = 1148 Number of bonds = 3460 Number of angles = 1252 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1146 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 = 3466 Number of groups = 1148 Number of bonds = 3460 Number of angles = 1252 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1146 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 <- "35.524" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1143" Evaluating: 1143-13 Parameter: NUMWAT <- "1130" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1130" Comparing "1075" and "1130". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.524" Parameter: BOX -> "35.524" Parameter: BOX -> "35.524" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.52400 B = 35.52400 C = 35.52400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2617 2 1 -1 -2 -1 13.7018 3 1 -1 -1 -1 4.1350 4 1 -1 0 -1 3.0817 5 1 0 -1 -1 5.0980 6 1 0 0 -1 2.5903 7 1 -1 -1 0 3.0768 8 1 -1 0 0 6.1992 9 1 0 -1 0 2.6054 10 1 0 1 0 2.6054 11 1 0 0 1 2.5903 12 1 0 1 1 5.0980 13 1 2 1 1 10.2617 14 1 1 2 1 13.7018 15 1 1 1 1 4.1350 16 1 1 0 1 3.0817 17 1 1 1 0 3.0768 18 1 1 0 0 6.1992 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3466 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 927 OPERATED ON BY TRANSFORMATION C018 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 171 57 57 6.29 2 C002 has 33 11 11 11.70 3 C003 has 2631 877 877 0.00 4 C004 has 807 269 269 0.00 5 C005 has 864 288 288 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1224 408 408 0.00 Total of12373 atoms and 4117 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 3466 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 = 3463 Number of groups = 1147 Number of bonds = 3457 Number of angles = 1251 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1145 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 = 3463 Number of groups = 1147 Number of bonds = 3457 Number of angles = 1251 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1145 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 <- "35.522" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1142" Evaluating: 1142-13 Parameter: NUMWAT <- "1129" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1129" Comparing "1075" and "1129". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.522" Parameter: BOX -> "35.522" Parameter: BOX -> "35.522" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.52200 B = 35.52200 C = 35.52200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2591 2 1 -1 -2 -1 13.6987 3 1 -1 -1 -1 4.1348 4 1 -1 0 -1 3.0820 5 1 0 -1 -1 5.0984 6 1 0 0 -1 2.5891 7 1 -1 -1 0 3.0766 8 1 -1 0 0 6.1984 9 1 0 -1 0 2.6039 10 1 0 1 0 2.6039 11 1 0 0 1 2.5891 12 1 0 1 1 5.0984 13 1 2 1 1 10.2591 14 1 1 2 1 13.6987 15 1 1 1 1 4.1348 16 1 1 0 1 3.0820 17 1 1 1 0 3.0766 18 1 1 0 0 6.1984 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3463 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.29 2 C002 has 33 11 11 11.69 3 C003 has 2628 876 876 0.00 4 C004 has 807 269 269 0.00 5 C005 has 864 288 288 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 807 269 269 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1224 408 408 0.00 Total of12358 atoms and 4112 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 3463 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3463 Number of groups = 1147 Number of bonds = 3457 Number of angles = 1251 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1145 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 = 3463 Number of groups = 1147 Number of bonds = 3457 Number of angles = 1251 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1145 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 <- "35.52" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1142" Evaluating: 1142-13 Parameter: NUMWAT <- "1129" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1129" Comparing "1075" and "1129". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.52" Parameter: BOX -> "35.52" Parameter: BOX -> "35.52" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.52000 B = 35.52000 C = 35.52000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2566 2 1 -1 -2 -1 13.6956 3 1 -1 -1 -1 4.1347 4 1 -1 0 -1 3.0823 5 1 0 -1 -1 5.0988 6 1 0 0 -1 2.5879 7 1 -1 -1 0 3.0764 8 1 -1 0 0 6.1977 9 1 0 -1 0 2.6023 10 1 0 1 0 2.6023 11 1 0 0 1 2.5879 12 1 0 1 1 5.0988 13 1 2 1 1 10.2566 14 1 1 2 1 13.6956 15 1 1 1 1 4.1347 16 1 1 0 1 3.0823 17 1 1 1 0 3.0764 18 1 1 0 0 6.1977 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3463 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.28 2 C002 has 33 11 11 11.69 3 C003 has 2628 876 876 0.00 4 C004 has 807 269 269 0.00 5 C005 has 864 288 288 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 807 269 269 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1224 408 408 0.00 Total of12358 atoms and 4112 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 3463 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3463 Number of groups = 1147 Number of bonds = 3457 Number of angles = 1251 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1145 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 = 3463 Number of groups = 1147 Number of bonds = 3457 Number of angles = 1251 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1145 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 <- "35.518" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1142" Evaluating: 1142-13 Parameter: NUMWAT <- "1129" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1129" Comparing "1075" and "1129". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.518" Parameter: BOX -> "35.518" Parameter: BOX -> "35.518" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.51800 B = 35.51800 C = 35.51800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2540 2 1 -1 -2 -1 13.6924 3 1 -1 -1 -1 4.1345 4 1 -1 0 -1 3.0826 5 1 0 -1 -1 5.0992 6 1 0 0 -1 2.5867 7 1 -1 -1 0 3.0761 8 1 -1 0 0 6.1969 9 1 0 -1 0 2.6008 10 1 0 1 0 2.6008 11 1 0 0 1 2.5867 12 1 0 1 1 5.0992 13 1 2 1 1 10.2540 14 1 1 2 1 13.6924 15 1 1 1 1 4.1345 16 1 1 0 1 3.0826 17 1 1 1 0 3.0761 18 1 1 0 0 6.1969 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3463 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.28 2 C002 has 33 11 11 11.69 3 C003 has 2628 876 876 0.00 4 C004 has 807 269 269 0.00 5 C005 has 864 288 288 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 807 269 269 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1224 408 408 0.00 Total of12358 atoms and 4112 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 3463 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3463 Number of groups = 1147 Number of bonds = 3457 Number of angles = 1251 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1145 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 = 3463 Number of groups = 1147 Number of bonds = 3457 Number of angles = 1251 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1145 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 <- "35.516" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1142" Evaluating: 1142-13 Parameter: NUMWAT <- "1129" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1129" Comparing "1075" and "1129". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.516" Parameter: BOX -> "35.516" Parameter: BOX -> "35.516" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.51600 B = 35.51600 C = 35.51600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2515 2 1 -1 -2 -1 13.6893 3 1 -1 -1 -1 4.1344 4 1 -1 0 -1 3.0829 5 1 0 -1 -1 5.0997 6 1 0 0 -1 2.5855 7 1 -1 -1 0 3.0759 8 1 -1 0 0 6.1961 9 1 0 -1 0 2.5993 10 1 0 1 0 2.5993 11 1 0 0 1 2.5855 12 1 0 1 1 5.0997 13 1 2 1 1 10.2515 14 1 1 2 1 13.6893 15 1 1 1 1 4.1344 16 1 1 0 1 3.0829 17 1 1 1 0 3.0759 18 1 1 0 0 6.1961 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3463 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.28 2 C002 has 33 11 11 11.68 3 C003 has 2628 876 876 0.00 4 C004 has 807 269 269 0.00 5 C005 has 864 288 288 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 807 269 269 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1224 408 408 0.00 Total of12358 atoms and 4112 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 3463 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3463 Number of groups = 1147 Number of bonds = 3457 Number of angles = 1251 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1145 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 = 3463 Number of groups = 1147 Number of bonds = 3457 Number of angles = 1251 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1145 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 <- "35.514" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1142" Evaluating: 1142-13 Parameter: NUMWAT <- "1129" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1129" Comparing "1075" and "1129". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.514" Parameter: BOX -> "35.514" Parameter: BOX -> "35.514" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.51400 B = 35.51400 C = 35.51400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2489 2 1 -1 -2 -1 13.6862 3 1 -1 -1 -1 4.1342 4 1 -1 0 -1 3.0832 5 1 0 -1 -1 5.1001 6 1 0 0 -1 2.5843 7 1 -1 -1 0 3.0757 8 1 -1 0 0 6.1953 9 1 0 -1 0 2.5977 10 1 0 1 0 2.5977 11 1 0 0 1 2.5843 12 1 0 1 1 5.1001 13 1 2 1 1 10.2489 14 1 1 2 1 13.6862 15 1 1 1 1 4.1342 16 1 1 0 1 3.0832 17 1 1 1 0 3.0757 18 1 1 0 0 6.1953 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3463 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.27 2 C002 has 33 11 11 11.68 3 C003 has 2631 877 877 0.00 4 C004 has 807 269 269 0.00 5 C005 has 864 288 288 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 807 269 269 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1224 408 408 0.00 Total of12361 atoms and 4113 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 3463 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3463 Number of groups = 1147 Number of bonds = 3457 Number of angles = 1251 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1145 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 = 3463 Number of groups = 1147 Number of bonds = 3457 Number of angles = 1251 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1145 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 <- "35.512" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1142" Evaluating: 1142-13 Parameter: NUMWAT <- "1129" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1129" Comparing "1075" and "1129". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.512" Parameter: BOX -> "35.512" Parameter: BOX -> "35.512" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.51200 B = 35.51200 C = 35.51200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2464 2 1 -1 -2 -1 13.6831 3 1 -1 -1 -1 4.1340 4 1 -1 0 -1 3.0835 5 1 0 -1 -1 5.1005 6 1 0 0 -1 2.5831 7 1 -1 -1 0 3.0755 8 1 -1 0 0 6.1946 9 1 0 -1 0 2.5962 10 1 0 1 0 2.5962 11 1 0 0 1 2.5831 12 1 0 1 1 5.1005 13 1 2 1 1 10.2464 14 1 1 2 1 13.6831 15 1 1 1 1 4.1340 16 1 1 0 1 3.0835 17 1 1 1 0 3.0755 18 1 1 0 0 6.1946 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3463 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.27 2 C002 has 33 11 11 11.68 3 C003 has 2631 877 877 0.00 4 C004 has 807 269 269 0.00 5 C005 has 864 288 288 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 807 269 269 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1224 408 408 0.00 Total of12361 atoms and 4113 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 3463 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3463 Number of groups = 1147 Number of bonds = 3457 Number of angles = 1251 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1145 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 = 3463 Number of groups = 1147 Number of bonds = 3457 Number of angles = 1251 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1145 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 <- "35.51" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1142" Evaluating: 1142-13 Parameter: NUMWAT <- "1129" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1129" Comparing "1075" and "1129". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.51" Parameter: BOX -> "35.51" Parameter: BOX -> "35.51" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.51000 B = 35.51000 C = 35.51000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2438 2 1 -1 -2 -1 13.6799 3 1 -1 -1 -1 4.1339 4 1 -1 0 -1 3.0838 5 1 0 -1 -1 5.1010 6 1 0 0 -1 2.5819 7 1 -1 -1 0 3.0753 8 1 -1 0 0 6.1938 9 1 0 -1 0 2.5946 10 1 0 1 0 2.5946 11 1 0 0 1 2.5819 12 1 0 1 1 5.1010 13 1 2 1 1 10.2438 14 1 1 2 1 13.6799 15 1 1 1 1 4.1339 16 1 1 0 1 3.0838 17 1 1 1 0 3.0753 18 1 1 0 0 6.1938 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3463 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.27 2 C002 has 33 11 11 11.67 3 C003 has 2631 877 877 0.00 4 C004 has 807 269 269 0.00 5 C005 has 864 288 288 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 807 269 269 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1224 408 408 0.00 Total of12361 atoms and 4113 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 3463 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3463 Number of groups = 1147 Number of bonds = 3457 Number of angles = 1251 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1145 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 = 3463 Number of groups = 1147 Number of bonds = 3457 Number of angles = 1251 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1145 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 <- "35.508" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1142" Evaluating: 1142-13 Parameter: NUMWAT <- "1129" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1129" Comparing "1075" and "1129". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.508" Parameter: BOX -> "35.508" Parameter: BOX -> "35.508" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.50800 B = 35.50800 C = 35.50800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2412 2 1 -1 -2 -1 13.6768 3 1 -1 -1 -1 4.1337 4 1 -1 0 -1 3.0841 5 1 0 -1 -1 5.1014 6 1 0 0 -1 2.5807 7 1 -1 -1 0 3.0750 8 1 -1 0 0 6.1930 9 1 0 -1 0 2.5931 10 1 0 1 0 2.5931 11 1 0 0 1 2.5807 12 1 0 1 1 5.1014 13 1 2 1 1 10.2412 14 1 1 2 1 13.6768 15 1 1 1 1 4.1337 16 1 1 0 1 3.0841 17 1 1 1 0 3.0750 18 1 1 0 0 6.1930 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3463 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.26 2 C002 has 33 11 11 11.67 3 C003 has 2631 877 877 0.00 4 C004 has 807 269 269 0.00 5 C005 has 864 288 288 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 807 269 269 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1224 408 408 0.00 Total of12361 atoms and 4113 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 3463 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3463 Number of groups = 1147 Number of bonds = 3457 Number of angles = 1251 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1145 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 = 3463 Number of groups = 1147 Number of bonds = 3457 Number of angles = 1251 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1145 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 <- "35.506" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1142" Evaluating: 1142-13 Parameter: NUMWAT <- "1129" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1129" Comparing "1075" and "1129". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.506" Parameter: BOX -> "35.506" Parameter: BOX -> "35.506" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.50600 B = 35.50600 C = 35.50600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2387 2 1 -1 -2 -1 13.6737 3 1 -1 -1 -1 4.1336 4 1 -1 0 -1 3.0844 5 1 0 -1 -1 5.1018 6 1 0 0 -1 2.5795 7 1 -1 -1 0 3.0748 8 1 -1 0 0 6.1923 9 1 0 -1 0 2.5915 10 1 0 1 0 2.5915 11 1 0 0 1 2.5795 12 1 0 1 1 5.1018 13 1 2 1 1 10.2387 14 1 1 2 1 13.6737 15 1 1 1 1 4.1336 16 1 1 0 1 3.0844 17 1 1 1 0 3.0748 18 1 1 0 0 6.1923 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3463 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.26 2 C002 has 33 11 11 11.67 3 C003 has 2631 877 877 0.00 4 C004 has 807 269 269 0.00 5 C005 has 864 288 288 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1227 409 409 0.00 Total of12367 atoms and 4115 groups and 4110 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3463 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3463 Number of groups = 1147 Number of bonds = 3457 Number of angles = 1251 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1145 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 = 3463 Number of groups = 1147 Number of bonds = 3457 Number of angles = 1251 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1145 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 <- "35.504" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1142" Evaluating: 1142-13 Parameter: NUMWAT <- "1129" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1129" Comparing "1075" and "1129". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.504" Parameter: BOX -> "35.504" Parameter: BOX -> "35.504" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.50400 B = 35.50400 C = 35.50400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2361 2 1 -1 -2 -1 13.6705 3 1 -1 -1 -1 4.1334 4 1 -1 0 -1 3.0847 5 1 0 -1 -1 5.1023 6 1 0 0 -1 2.5783 7 1 -1 -1 0 3.0746 8 1 -1 0 0 6.1915 9 1 0 -1 0 2.5900 10 1 0 1 0 2.5900 11 1 0 0 1 2.5783 12 1 0 1 1 5.1023 13 1 2 1 1 10.2361 14 1 1 2 1 13.6705 15 1 1 1 1 4.1334 16 1 1 0 1 3.0847 17 1 1 1 0 3.0746 18 1 1 0 0 6.1915 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3463 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.26 2 C002 has 33 11 11 11.66 3 C003 has 2631 877 877 0.00 4 C004 has 807 269 269 0.00 5 C005 has 864 288 288 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1227 409 409 0.00 Total of12367 atoms and 4115 groups and 4110 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3463 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3463 Number of groups = 1147 Number of bonds = 3457 Number of angles = 1251 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1145 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 = 3463 Number of groups = 1147 Number of bonds = 3457 Number of angles = 1251 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1145 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 <- "35.502" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1142" Evaluating: 1142-13 Parameter: NUMWAT <- "1129" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1129" Comparing "1075" and "1129". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.502" Parameter: BOX -> "35.502" Parameter: BOX -> "35.502" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.50200 B = 35.50200 C = 35.50200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2336 2 1 -1 -2 -1 13.6674 3 1 -1 -1 -1 4.1333 4 1 -1 0 -1 3.0850 5 1 0 -1 -1 5.1027 6 1 0 0 -1 2.5771 7 1 -1 -1 0 3.0744 8 1 -1 0 0 6.1908 9 1 0 -1 0 2.5884 10 1 0 1 0 2.5884 11 1 0 0 1 2.5771 12 1 0 1 1 5.1027 13 1 2 1 1 10.2336 14 1 1 2 1 13.6674 15 1 1 1 1 4.1333 16 1 1 0 1 3.0850 17 1 1 1 0 3.0744 18 1 1 0 0 6.1908 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3463 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.25 2 C002 has 33 11 11 11.66 3 C003 has 2631 877 877 0.00 4 C004 has 807 269 269 0.00 5 C005 has 867 289 289 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1227 409 409 0.00 Total of12370 atoms and 4116 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 3463 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3463 Number of groups = 1147 Number of bonds = 3457 Number of angles = 1251 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1145 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 = 3463 Number of groups = 1147 Number of bonds = 3457 Number of angles = 1251 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1145 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 <- "35.5" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1142" Evaluating: 1142-13 Parameter: NUMWAT <- "1129" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1129" Comparing "1075" and "1129". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.5" Parameter: BOX -> "35.5" Parameter: BOX -> "35.5" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.50000 B = 35.50000 C = 35.50000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2310 2 1 -1 -2 -1 13.6643 3 1 -1 -1 -1 4.1331 4 1 -1 0 -1 3.0853 5 1 0 -1 -1 5.1031 6 1 0 0 -1 2.5759 7 1 -1 -1 0 3.0742 8 1 -1 0 0 6.1900 9 1 0 -1 0 2.5869 10 1 0 1 0 2.5869 11 1 0 0 1 2.5759 12 1 0 1 1 5.1031 13 1 2 1 1 10.2310 14 1 1 2 1 13.6643 15 1 1 1 1 4.1331 16 1 1 0 1 3.0853 17 1 1 1 0 3.0742 18 1 1 0 0 6.1900 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3463 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.25 2 C002 has 33 11 11 11.66 3 C003 has 2634 878 878 0.00 4 C004 has 807 269 269 0.00 5 C005 has 867 289 289 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1227 409 409 0.00 Total of12373 atoms and 4117 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 3463 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3463 Number of groups = 1147 Number of bonds = 3457 Number of angles = 1251 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1145 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 = 3463 Number of groups = 1147 Number of bonds = 3457 Number of angles = 1251 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1145 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 <- "35.498" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1142" Evaluating: 1142-13 Parameter: NUMWAT <- "1129" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1129" Comparing "1075" and "1129". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.498" Parameter: BOX -> "35.498" Parameter: BOX -> "35.498" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.49800 B = 35.49800 C = 35.49800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2285 2 1 -1 -2 -1 13.6612 3 1 -1 -1 -1 4.1330 4 1 -1 0 -1 3.0856 5 1 0 -1 -1 5.1036 6 1 0 0 -1 2.5747 7 1 -1 -1 0 3.0740 8 1 -1 0 0 6.1892 9 1 0 -1 0 2.5854 10 1 0 1 0 2.5854 11 1 0 0 1 2.5747 12 1 0 1 1 5.1036 13 1 2 1 1 10.2285 14 1 1 2 1 13.6612 15 1 1 1 1 4.1330 16 1 1 0 1 3.0856 17 1 1 1 0 3.0740 18 1 1 0 0 6.1892 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3463 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 389 OPERATED ON BY TRANSFORMATION C016 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 168 56 56 6.25 2 C002 has 33 11 11 11.66 3 C003 has 2637 879 879 0.00 4 C004 has 807 269 269 0.00 5 C005 has 867 289 289 0.00 6 C006 has 1143 381 381 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1224 408 408 0.00 Total of12382 atoms and 4120 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> 3 atoms have been selected out of 3463 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 = 1141 Number of atoms = 3460 Number of groups = 1146 Number of bonds = 3454 Number of angles = 1250 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1144 Number of HB donors = 2264 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1141 Number of atoms = 3460 Number of groups = 1146 Number of bonds = 3454 Number of angles = 1250 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1144 Number of HB donors = 2264 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.496" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1141" Evaluating: 1141-13 Parameter: NUMWAT <- "1128" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1128" Comparing "1075" and "1128". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.496" Parameter: BOX -> "35.496" Parameter: BOX -> "35.496" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.49600 B = 35.49600 C = 35.49600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2259 2 1 -1 -2 -1 13.6580 3 1 -1 -1 -1 4.1329 4 1 -1 0 -1 0.4492 5 1 0 -1 -1 5.1040 6 1 0 0 -1 2.5735 7 1 -1 -1 0 3.0738 8 1 -1 0 0 6.1885 9 1 0 -1 0 4.2779 10 1 0 1 0 4.2779 11 1 0 0 1 2.5735 12 1 0 1 1 5.1040 13 1 2 1 1 10.2259 14 1 1 2 1 13.6580 15 1 1 1 1 4.1329 16 1 1 0 1 0.4492 17 1 1 1 0 3.0738 18 1 1 0 0 6.1885 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3384 atoms have been selected out of 3460 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 300 OPERATED ON BY TRANSFORMATION C009 RESIDUE 761 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 171 57 57 6.25 2 C002 has 33 11 11 11.65 3 C003 has 2634 878 878 0.00 4 C004 has 804 268 268 0.00 5 C005 has 867 289 289 0.00 6 C006 has 1143 381 381 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1215 405 405 0.00 Total of12364 atoms and 4114 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> 6 atoms have been selected out of 3460 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 = 1139 Number of atoms = 3454 Number of groups = 1144 Number of bonds = 3448 Number of angles = 1248 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1142 Number of HB donors = 2260 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1139 Number of atoms = 3454 Number of groups = 1144 Number of bonds = 3448 Number of angles = 1248 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1142 Number of HB donors = 2260 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.494" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1139" Evaluating: 1139-13 Parameter: NUMWAT <- "1126" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1126" Comparing "1075" and "1126". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.494" Parameter: BOX -> "35.494" Parameter: BOX -> "35.494" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.49400 B = 35.49400 C = 35.49400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2234 2 1 -1 -2 -1 13.6549 3 1 -1 -1 -1 4.1327 4 1 -1 0 -1 0.4482 5 1 0 -1 -1 5.1044 6 1 0 0 -1 2.5723 7 1 -1 -1 0 3.0736 8 1 -1 0 0 6.1877 9 1 0 -1 0 4.2772 10 1 0 1 0 4.2772 11 1 0 0 1 2.5723 12 1 0 1 1 5.1044 13 1 2 1 1 10.2234 14 1 1 2 1 13.6549 15 1 1 1 1 4.1327 16 1 1 0 1 0.4482 17 1 1 1 0 3.0736 18 1 1 0 0 6.1877 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3378 atoms have been selected out of 3454 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 C012 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 174 58 58 6.24 2 C002 has 33 11 11 11.65 3 C003 has 2634 878 878 0.00 4 C004 has 801 267 267 0.00 5 C005 has 864 288 288 0.00 6 C006 has 1143 381 381 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1209 403 403 0.00 Total of12346 atoms and 4108 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> 3 atoms have been selected out of 3454 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 = 1138 Number of atoms = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 <- "35.492" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1138" Evaluating: 1138-13 Parameter: NUMWAT <- "1125" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1125" Comparing "1075" and "1125". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.492" Parameter: BOX -> "35.492" Parameter: BOX -> "35.492" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.49200 B = 35.49200 C = 35.49200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2208 2 1 -1 -2 -1 13.6518 3 1 -1 -1 -1 4.1326 4 1 -1 0 -1 0.4472 5 1 0 -1 -1 5.1049 6 1 0 0 -1 2.5711 7 1 -1 -1 0 3.0734 8 1 -1 0 0 6.1869 9 1 0 -1 0 4.2765 10 1 0 1 0 4.2765 11 1 0 0 1 2.5711 12 1 0 1 1 5.1049 13 1 2 1 1 10.2208 14 1 1 2 1 13.6518 15 1 1 1 1 4.1326 16 1 1 0 1 0.4472 17 1 1 1 0 3.0734 18 1 1 0 0 6.1869 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3451 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 174 58 58 6.24 2 C002 has 33 11 11 11.65 3 C003 has 2631 877 877 0.00 4 C004 has 801 267 267 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1143 381 381 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1206 402 402 0.00 Total of12334 atoms and 4104 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 3451 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 <- "35.49" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1138" Evaluating: 1138-13 Parameter: NUMWAT <- "1125" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1125" Comparing "1075" and "1125". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.49" Parameter: BOX -> "35.49" Parameter: BOX -> "35.49" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.49000 B = 35.49000 C = 35.49000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2183 2 1 -1 -2 -1 13.6487 3 1 -1 -1 -1 4.1324 4 1 -1 0 -1 0.4461 5 1 0 -1 -1 5.1053 6 1 0 0 -1 2.5699 7 1 -1 -1 0 3.0732 8 1 -1 0 0 6.1862 9 1 0 -1 0 4.2757 10 1 0 1 0 4.2757 11 1 0 0 1 2.5699 12 1 0 1 1 5.1053 13 1 2 1 1 10.2183 14 1 1 2 1 13.6487 15 1 1 1 1 4.1324 16 1 1 0 1 0.4461 17 1 1 1 0 3.0732 18 1 1 0 0 6.1862 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3451 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 174 58 58 6.24 2 C002 has 33 11 11 11.64 3 C003 has 2631 877 877 0.00 4 C004 has 801 267 267 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1143 381 381 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1206 402 402 0.00 Total of12334 atoms and 4104 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 3451 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 <- "35.488" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1138" Evaluating: 1138-13 Parameter: NUMWAT <- "1125" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1125" Comparing "1075" and "1125". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.488" Parameter: BOX -> "35.488" Parameter: BOX -> "35.488" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.48800 B = 35.48800 C = 35.48800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2157 2 1 -1 -2 -1 13.6455 3 1 -1 -1 -1 4.1323 4 1 -1 0 -1 0.4451 5 1 0 -1 -1 5.1058 6 1 0 0 -1 2.5687 7 1 -1 -1 0 3.0730 8 1 -1 0 0 6.1854 9 1 0 -1 0 4.2750 10 1 0 1 0 4.2750 11 1 0 0 1 2.5687 12 1 0 1 1 5.1058 13 1 2 1 1 10.2157 14 1 1 2 1 13.6455 15 1 1 1 1 4.1323 16 1 1 0 1 0.4451 17 1 1 1 0 3.0730 18 1 1 0 0 6.1854 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3451 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 174 58 58 6.23 2 C002 has 33 11 11 11.64 3 C003 has 2631 877 877 0.00 4 C004 has 801 267 267 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1143 381 381 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1206 402 402 0.00 Total of12334 atoms and 4104 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 3451 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 <- "35.486" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1138" Evaluating: 1138-13 Parameter: NUMWAT <- "1125" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1125" Comparing "1075" and "1125". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.486" Parameter: BOX -> "35.486" Parameter: BOX -> "35.486" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.48600 B = 35.48600 C = 35.48600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2132 2 1 -1 -2 -1 13.6424 3 1 -1 -1 -1 4.1321 4 1 -1 0 -1 0.4441 5 1 0 -1 -1 5.1062 6 1 0 0 -1 2.5675 7 1 -1 -1 0 3.0728 8 1 -1 0 0 6.1847 9 1 0 -1 0 4.2743 10 1 0 1 0 4.2743 11 1 0 0 1 2.5675 12 1 0 1 1 5.1062 13 1 2 1 1 10.2132 14 1 1 2 1 13.6424 15 1 1 1 1 4.1321 16 1 1 0 1 0.4441 17 1 1 1 0 3.0728 18 1 1 0 0 6.1847 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3451 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 174 58 58 6.23 2 C002 has 33 11 11 11.64 3 C003 has 2634 878 878 0.00 4 C004 has 801 267 267 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1146 382 382 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1206 402 402 0.00 Total of12340 atoms and 4106 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 3451 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 <- "35.484" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1138" Evaluating: 1138-13 Parameter: NUMWAT <- "1125" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1125" Comparing "1075" and "1125". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.484" Parameter: BOX -> "35.484" Parameter: BOX -> "35.484" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.48400 B = 35.48400 C = 35.48400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2106 2 1 -1 -2 -1 13.6393 3 1 -1 -1 -1 4.1320 4 1 -1 0 -1 0.4431 5 1 0 -1 -1 5.1067 6 1 0 0 -1 2.5663 7 1 -1 -1 0 3.0726 8 1 -1 0 0 6.1839 9 1 0 -1 0 4.2736 10 1 0 1 0 4.2736 11 1 0 0 1 2.5663 12 1 0 1 1 5.1067 13 1 2 1 1 10.2106 14 1 1 2 1 13.6393 15 1 1 1 1 4.1320 16 1 1 0 1 0.4431 17 1 1 1 0 3.0726 18 1 1 0 0 6.1839 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3451 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 174 58 58 6.23 2 C002 has 33 11 11 11.63 3 C003 has 2634 878 878 0.00 4 C004 has 801 267 267 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1146 382 382 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1209 403 403 0.00 Total of12343 atoms and 4107 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 3451 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 <- "35.482" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1138" Evaluating: 1138-13 Parameter: NUMWAT <- "1125" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1125" Comparing "1075" and "1125". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.482" Parameter: BOX -> "35.482" Parameter: BOX -> "35.482" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.48200 B = 35.48200 C = 35.48200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2081 2 1 -1 -2 -1 13.6362 3 1 -1 -1 -1 4.1319 4 1 -1 0 -1 0.4421 5 1 0 -1 -1 5.1071 6 1 0 0 -1 2.5651 7 1 -1 -1 0 3.0724 8 1 -1 0 0 6.1831 9 1 0 -1 0 4.2729 10 1 0 1 0 4.2729 11 1 0 0 1 2.5651 12 1 0 1 1 5.1071 13 1 2 1 1 10.2081 14 1 1 2 1 13.6362 15 1 1 1 1 4.1319 16 1 1 0 1 0.4421 17 1 1 1 0 3.0724 18 1 1 0 0 6.1831 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3451 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 174 58 58 6.22 2 C002 has 33 11 11 11.63 3 C003 has 2634 878 878 0.00 4 C004 has 801 267 267 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1146 382 382 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1209 403 403 0.00 Total of12343 atoms and 4107 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 3451 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 <- "35.48" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1138" Evaluating: 1138-13 Parameter: NUMWAT <- "1125" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1125" Comparing "1075" and "1125". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.48" Parameter: BOX -> "35.48" Parameter: BOX -> "35.48" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.48000 B = 35.48000 C = 35.48000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2055 2 1 -1 -2 -1 13.6330 3 1 -1 -1 -1 4.1317 4 1 -1 0 -1 0.4412 5 1 0 -1 -1 5.1075 6 1 0 0 -1 2.5639 7 1 -1 -1 0 3.0722 8 1 -1 0 0 6.1824 9 1 0 -1 0 4.2721 10 1 0 1 0 4.2721 11 1 0 0 1 2.5639 12 1 0 1 1 5.1075 13 1 2 1 1 10.2055 14 1 1 2 1 13.6330 15 1 1 1 1 4.1317 16 1 1 0 1 0.4412 17 1 1 1 0 3.0722 18 1 1 0 0 6.1824 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3451 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 174 58 58 6.22 2 C002 has 33 11 11 11.63 3 C003 has 2634 878 878 0.00 4 C004 has 801 267 267 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1146 382 382 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1209 403 403 0.00 Total of12343 atoms and 4107 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 3451 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 <- "35.478" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1138" Evaluating: 1138-13 Parameter: NUMWAT <- "1125" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1125" Comparing "1075" and "1125". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.478" Parameter: BOX -> "35.478" Parameter: BOX -> "35.478" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.47800 B = 35.47800 C = 35.47800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2030 2 1 -1 -2 -1 13.6299 3 1 -1 -1 -1 4.1316 4 1 -1 0 -1 0.4402 5 1 0 -1 -1 5.1080 6 1 0 0 -1 2.5627 7 1 -1 -1 0 3.0720 8 1 -1 0 0 6.1816 9 1 0 -1 0 4.2714 10 1 0 1 0 4.2714 11 1 0 0 1 2.5627 12 1 0 1 1 5.1080 13 1 2 1 1 10.2030 14 1 1 2 1 13.6299 15 1 1 1 1 4.1316 16 1 1 0 1 0.4402 17 1 1 1 0 3.0720 18 1 1 0 0 6.1816 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3451 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 174 58 58 6.22 2 C002 has 33 11 11 11.62 3 C003 has 2634 878 878 0.00 4 C004 has 801 267 267 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1209 403 403 0.00 Total of12346 atoms and 4108 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 3451 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 <- "35.476" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1138" Evaluating: 1138-13 Parameter: NUMWAT <- "1125" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1125" Comparing "1075" and "1125". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.476" Parameter: BOX -> "35.476" Parameter: BOX -> "35.476" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.47600 B = 35.47600 C = 35.47600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.2004 2 1 -1 -2 -1 13.6268 3 1 -1 -1 -1 4.1315 4 1 -1 0 -1 0.4392 5 1 0 -1 -1 5.1084 6 1 0 0 -1 2.5615 7 1 -1 -1 0 3.0718 8 1 -1 0 0 6.1809 9 1 0 -1 0 4.2707 10 1 0 1 0 4.2707 11 1 0 0 1 2.5615 12 1 0 1 1 5.1084 13 1 2 1 1 10.2004 14 1 1 2 1 13.6268 15 1 1 1 1 4.1315 16 1 1 0 1 0.4392 17 1 1 1 0 3.0718 18 1 1 0 0 6.1809 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3451 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 174 58 58 6.21 2 C002 has 33 11 11 11.62 3 C003 has 2634 878 878 0.00 4 C004 has 801 267 267 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1209 403 403 0.00 Total of12346 atoms and 4108 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 3451 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 <- "35.474" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1138" Evaluating: 1138-13 Parameter: NUMWAT <- "1125" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1125" Comparing "1075" and "1125". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.474" Parameter: BOX -> "35.474" Parameter: BOX -> "35.474" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.47400 B = 35.47400 C = 35.47400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1979 2 1 -1 -2 -1 13.6237 3 1 -1 -1 -1 4.1313 4 1 -1 0 -1 0.4383 5 1 0 -1 -1 5.1089 6 1 0 0 -1 2.5604 7 1 -1 -1 0 3.0716 8 1 -1 0 0 6.1801 9 1 0 -1 0 4.2700 10 1 0 1 0 4.2700 11 1 0 0 1 2.5604 12 1 0 1 1 5.1089 13 1 2 1 1 10.1979 14 1 1 2 1 13.6237 15 1 1 1 1 4.1313 16 1 1 0 1 0.4383 17 1 1 1 0 3.0716 18 1 1 0 0 6.1801 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3451 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 174 58 58 6.21 2 C002 has 33 11 11 11.62 3 C003 has 2634 878 878 0.00 4 C004 has 801 267 267 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1209 403 403 0.00 Total of12346 atoms and 4108 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 3451 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 <- "35.472" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1138" Evaluating: 1138-13 Parameter: NUMWAT <- "1125" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1125" Comparing "1075" and "1125". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.472" Parameter: BOX -> "35.472" Parameter: BOX -> "35.472" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.47200 B = 35.47200 C = 35.47200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1953 2 1 -1 -2 -1 13.6205 3 1 -1 -1 -1 4.1312 4 1 -1 0 -1 0.4374 5 1 0 -1 -1 5.1093 6 1 0 0 -1 2.5592 7 1 -1 -1 0 3.0715 8 1 -1 0 0 6.1794 9 1 0 -1 0 4.2693 10 1 0 1 0 4.2693 11 1 0 0 1 2.5592 12 1 0 1 1 5.1093 13 1 2 1 1 10.1953 14 1 1 2 1 13.6205 15 1 1 1 1 4.1312 16 1 1 0 1 0.4374 17 1 1 1 0 3.0715 18 1 1 0 0 6.1794 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3451 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 177 59 59 6.21 2 C002 has 33 11 11 11.62 3 C003 has 2637 879 879 0.00 4 C004 has 801 267 267 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1209 403 403 0.00 Total of12352 atoms and 4110 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 3451 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 <- "35.47" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1138" Evaluating: 1138-13 Parameter: NUMWAT <- "1125" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1125" Comparing "1075" and "1125". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.47" Parameter: BOX -> "35.47" Parameter: BOX -> "35.47" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.47000 B = 35.47000 C = 35.47000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1928 2 1 -1 -2 -1 13.6174 3 1 -1 -1 -1 4.1310 4 1 -1 0 -1 0.4364 5 1 0 -1 -1 5.1098 6 1 0 0 -1 2.5580 7 1 -1 -1 0 3.0713 8 1 -1 0 0 6.1786 9 1 0 -1 0 4.2686 10 1 0 1 0 4.2686 11 1 0 0 1 2.5580 12 1 0 1 1 5.1098 13 1 2 1 1 10.1928 14 1 1 2 1 13.6174 15 1 1 1 1 4.1310 16 1 1 0 1 0.4364 17 1 1 1 0 3.0713 18 1 1 0 0 6.1786 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3451 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 177 59 59 6.21 2 C002 has 33 11 11 11.61 3 C003 has 2637 879 879 0.00 4 C004 has 801 267 267 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1152 384 384 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1209 403 403 0.00 Total of12355 atoms and 4111 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 3451 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 <- "35.468" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1138" Evaluating: 1138-13 Parameter: NUMWAT <- "1125" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1125" Comparing "1075" and "1125". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.468" Parameter: BOX -> "35.468" Parameter: BOX -> "35.468" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.46800 B = 35.46800 C = 35.46800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1902 2 1 -1 -2 -1 13.6143 3 1 -1 -1 -1 4.1309 4 1 -1 0 -1 0.4355 5 1 0 -1 -1 5.1102 6 1 0 0 -1 2.5568 7 1 -1 -1 0 3.0711 8 1 -1 0 0 6.1778 9 1 0 -1 0 4.2679 10 1 0 1 0 4.2679 11 1 0 0 1 2.5568 12 1 0 1 1 5.1102 13 1 2 1 1 10.1902 14 1 1 2 1 13.6143 15 1 1 1 1 4.1309 16 1 1 0 1 0.4355 17 1 1 1 0 3.0711 18 1 1 0 0 6.1778 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3451 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 177 59 59 6.20 2 C002 has 33 11 11 11.61 3 C003 has 2637 879 879 0.00 4 C004 has 801 267 267 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1152 384 384 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1209 403 403 0.00 Total of12355 atoms and 4111 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 3451 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 = 3451 Number of groups = 1143 Number of bonds = 3445 Number of angles = 1247 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1141 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 <- "35.466" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1138" Evaluating: 1138-13 Parameter: NUMWAT <- "1125" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1125" Comparing "1075" and "1125". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.466" Parameter: BOX -> "35.466" Parameter: BOX -> "35.466" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.46600 B = 35.46600 C = 35.46600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1877 2 1 -1 -2 -1 13.6112 3 1 -1 -1 -1 4.1308 4 1 -1 0 -1 0.4346 5 1 0 -1 -1 5.1107 6 1 0 0 -1 2.5556 7 1 -1 -1 0 3.0709 8 1 -1 0 0 6.1771 9 1 0 -1 0 4.2671 10 1 0 1 0 4.2671 11 1 0 0 1 2.5556 12 1 0 1 1 5.1107 13 1 2 1 1 10.1877 14 1 1 2 1 13.6112 15 1 1 1 1 4.1308 16 1 1 0 1 0.4346 17 1 1 1 0 3.0709 18 1 1 0 0 6.1771 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3451 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 878 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 177 59 59 6.20 2 C002 has 33 11 11 11.61 3 C003 has 2634 878 878 0.00 4 C004 has 801 267 267 0.00 5 C005 has 870 290 290 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1206 402 402 0.00 Total of12361 atoms and 4113 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> 3 atoms have been selected out of 3451 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 = 3448 Number of groups = 1142 Number of bonds = 3442 Number of angles = 1246 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1140 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 = 3448 Number of groups = 1142 Number of bonds = 3442 Number of angles = 1246 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1140 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 <- "35.464" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1137" Evaluating: 1137-13 Parameter: NUMWAT <- "1124" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1124" Comparing "1075" and "1124". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.464" Parameter: BOX -> "35.464" Parameter: BOX -> "35.464" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.46400 B = 35.46400 C = 35.46400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1851 2 1 -1 -2 -1 13.6080 3 1 -1 -1 -1 4.1307 4 1 -1 0 -1 0.4337 5 1 0 -1 -1 3.3145 6 1 0 0 -1 2.5544 7 1 -1 -1 0 3.0707 8 1 -1 0 0 6.1763 9 1 0 -1 0 4.2664 10 1 0 1 0 4.2664 11 1 0 0 1 2.5544 12 1 0 1 1 3.3145 13 1 2 1 1 10.1851 14 1 1 2 1 13.6080 15 1 1 1 1 4.1307 16 1 1 0 1 0.4337 17 1 1 1 0 3.0707 18 1 1 0 0 6.1763 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3448 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 177 59 59 6.20 2 C002 has 33 11 11 11.60 3 C003 has 2634 878 878 0.00 4 C004 has 801 267 267 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1206 402 402 0.00 Total of12343 atoms and 4107 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 3448 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3448 Number of groups = 1142 Number of bonds = 3442 Number of angles = 1246 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1140 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 = 3448 Number of groups = 1142 Number of bonds = 3442 Number of angles = 1246 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1140 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 <- "35.462" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1137" Evaluating: 1137-13 Parameter: NUMWAT <- "1124" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1124" Comparing "1075" and "1124". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.462" Parameter: BOX -> "35.462" Parameter: BOX -> "35.462" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.46200 B = 35.46200 C = 35.46200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1826 2 1 -1 -2 -1 13.6049 3 1 -1 -1 -1 4.1305 4 1 -1 0 -1 0.4328 5 1 0 -1 -1 3.3148 6 1 0 0 -1 2.5533 7 1 -1 -1 0 3.0706 8 1 -1 0 0 6.1756 9 1 0 -1 0 4.2657 10 1 0 1 0 4.2657 11 1 0 0 1 2.5533 12 1 0 1 1 3.3148 13 1 2 1 1 10.1826 14 1 1 2 1 13.6049 15 1 1 1 1 4.1305 16 1 1 0 1 0.4328 17 1 1 1 0 3.0706 18 1 1 0 0 6.1756 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3448 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 177 59 59 6.19 2 C002 has 33 11 11 11.60 3 C003 has 2637 879 879 0.00 4 C004 has 804 268 268 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1206 402 402 0.00 Total of12349 atoms and 4109 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 3448 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3448 Number of groups = 1142 Number of bonds = 3442 Number of angles = 1246 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1140 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 = 3448 Number of groups = 1142 Number of bonds = 3442 Number of angles = 1246 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1140 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 <- "35.46" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1137" Evaluating: 1137-13 Parameter: NUMWAT <- "1124" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1124" Comparing "1075" and "1124". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.46" Parameter: BOX -> "35.46" Parameter: BOX -> "35.46" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.46000 B = 35.46000 C = 35.46000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1801 2 1 -1 -2 -1 13.6018 3 1 -1 -1 -1 4.1304 4 1 -1 0 -1 0.4319 5 1 0 -1 -1 3.3151 6 1 0 0 -1 2.5521 7 1 -1 -1 0 3.0704 8 1 -1 0 0 6.1748 9 1 0 -1 0 4.2650 10 1 0 1 0 4.2650 11 1 0 0 1 2.5521 12 1 0 1 1 3.3151 13 1 2 1 1 10.1801 14 1 1 2 1 13.6018 15 1 1 1 1 4.1304 16 1 1 0 1 0.4319 17 1 1 1 0 3.0704 18 1 1 0 0 6.1748 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3448 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 180 60 60 6.19 2 C002 has 33 11 11 11.60 3 C003 has 2637 879 879 0.00 4 C004 has 804 268 268 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1206 402 402 0.00 Total of12352 atoms and 4110 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 3448 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3448 Number of groups = 1142 Number of bonds = 3442 Number of angles = 1246 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1140 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 = 3448 Number of groups = 1142 Number of bonds = 3442 Number of angles = 1246 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1140 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 <- "35.458" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1137" Evaluating: 1137-13 Parameter: NUMWAT <- "1124" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1124" Comparing "1075" and "1124". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.458" Parameter: BOX -> "35.458" Parameter: BOX -> "35.458" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.45800 B = 35.45800 C = 35.45800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1775 2 1 -1 -2 -1 13.5987 3 1 -1 -1 -1 4.1303 4 1 -1 0 -1 0.4311 5 1 0 -1 -1 3.3154 6 1 0 0 -1 2.5509 7 1 -1 -1 0 3.0702 8 1 -1 0 0 6.1741 9 1 0 -1 0 4.2643 10 1 0 1 0 4.2643 11 1 0 0 1 2.5509 12 1 0 1 1 3.3154 13 1 2 1 1 10.1775 14 1 1 2 1 13.5987 15 1 1 1 1 4.1303 16 1 1 0 1 0.4311 17 1 1 1 0 3.0702 18 1 1 0 0 6.1741 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3448 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 180 60 60 6.19 2 C002 has 33 11 11 11.59 3 C003 has 2637 879 879 0.00 4 C004 has 804 268 268 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1209 403 403 0.00 Total of12355 atoms and 4111 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 3448 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3448 Number of groups = 1142 Number of bonds = 3442 Number of angles = 1246 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1140 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 = 3448 Number of groups = 1142 Number of bonds = 3442 Number of angles = 1246 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1140 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 <- "35.456" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1137" Evaluating: 1137-13 Parameter: NUMWAT <- "1124" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1124" Comparing "1075" and "1124". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.456" Parameter: BOX -> "35.456" Parameter: BOX -> "35.456" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.45600 B = 35.45600 C = 35.45600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1750 2 1 -1 -2 -1 13.5955 3 1 -1 -1 -1 4.1301 4 1 -1 0 -1 0.4302 5 1 0 -1 -1 3.3157 6 1 0 0 -1 2.5497 7 1 -1 -1 0 3.0700 8 1 -1 0 0 6.1733 9 1 0 -1 0 4.2636 10 1 0 1 0 4.2636 11 1 0 0 1 2.5497 12 1 0 1 1 3.3157 13 1 2 1 1 10.1750 14 1 1 2 1 13.5955 15 1 1 1 1 4.1301 16 1 1 0 1 0.4302 17 1 1 1 0 3.0700 18 1 1 0 0 6.1733 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3448 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 180 60 60 6.18 2 C002 has 33 11 11 11.59 3 C003 has 2637 879 879 0.00 4 C004 has 804 268 268 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1209 403 403 0.00 Total of12358 atoms and 4112 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 3448 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3448 Number of groups = 1142 Number of bonds = 3442 Number of angles = 1246 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1140 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 = 3448 Number of groups = 1142 Number of bonds = 3442 Number of angles = 1246 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1140 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 <- "35.454" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1137" Evaluating: 1137-13 Parameter: NUMWAT <- "1124" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1124" Comparing "1075" and "1124". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.454" Parameter: BOX -> "35.454" Parameter: BOX -> "35.454" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.45400 B = 35.45400 C = 35.45400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1724 2 1 -1 -2 -1 13.5924 3 1 -1 -1 -1 4.1300 4 1 -1 0 -1 0.4294 5 1 0 -1 -1 3.3159 6 1 0 0 -1 2.5485 7 1 -1 -1 0 3.0699 8 1 -1 0 0 6.1726 9 1 0 -1 0 4.2629 10 1 0 1 0 4.2629 11 1 0 0 1 2.5485 12 1 0 1 1 3.3159 13 1 2 1 1 10.1724 14 1 1 2 1 13.5924 15 1 1 1 1 4.1300 16 1 1 0 1 0.4294 17 1 1 1 0 3.0699 18 1 1 0 0 6.1726 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3448 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 180 60 60 6.18 2 C002 has 33 11 11 11.59 3 C003 has 2637 879 879 0.00 4 C004 has 804 268 268 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1209 403 403 0.00 Total of12358 atoms and 4112 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 3448 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3448 Number of groups = 1142 Number of bonds = 3442 Number of angles = 1246 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1140 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 = 3448 Number of groups = 1142 Number of bonds = 3442 Number of angles = 1246 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1140 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 <- "35.452" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1137" Evaluating: 1137-13 Parameter: NUMWAT <- "1124" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1124" Comparing "1075" and "1124". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.452" Parameter: BOX -> "35.452" Parameter: BOX -> "35.452" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.45200 B = 35.45200 C = 35.45200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1699 2 1 -1 -2 -1 13.5893 3 1 -1 -1 -1 4.1299 4 1 -1 0 -1 0.4286 5 1 0 -1 -1 3.3162 6 1 0 0 -1 2.5474 7 1 -1 -1 0 3.0697 8 1 -1 0 0 6.1718 9 1 0 -1 0 4.2622 10 1 0 1 0 4.2622 11 1 0 0 1 2.5474 12 1 0 1 1 3.3162 13 1 2 1 1 10.1699 14 1 1 2 1 13.5893 15 1 1 1 1 4.1299 16 1 1 0 1 0.4286 17 1 1 1 0 3.0697 18 1 1 0 0 6.1718 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3448 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 180 60 60 6.18 2 C002 has 33 11 11 11.58 3 C003 has 2637 879 879 0.00 4 C004 has 804 268 268 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1209 403 403 0.00 Total of12358 atoms and 4112 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 3448 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3448 Number of groups = 1142 Number of bonds = 3442 Number of angles = 1246 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1140 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 = 3448 Number of groups = 1142 Number of bonds = 3442 Number of angles = 1246 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1140 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 <- "35.45" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1137" Evaluating: 1137-13 Parameter: NUMWAT <- "1124" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1124" Comparing "1075" and "1124". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.45" Parameter: BOX -> "35.45" Parameter: BOX -> "35.45" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.45000 B = 35.45000 C = 35.45000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1673 2 1 -1 -2 -1 13.5862 3 1 -1 -1 -1 4.1298 4 1 -1 0 -1 0.4277 5 1 0 -1 -1 3.3165 6 1 0 0 -1 2.5462 7 1 -1 -1 0 3.0695 8 1 -1 0 0 6.1711 9 1 0 -1 0 4.2615 10 1 0 1 0 4.2615 11 1 0 0 1 2.5462 12 1 0 1 1 3.3165 13 1 2 1 1 10.1673 14 1 1 2 1 13.5862 15 1 1 1 1 4.1298 16 1 1 0 1 0.4277 17 1 1 1 0 3.0695 18 1 1 0 0 6.1711 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3448 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 180 60 60 6.17 2 C002 has 33 11 11 11.58 3 C003 has 2637 879 879 0.00 4 C004 has 804 268 268 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1209 403 403 0.00 Total of12358 atoms and 4112 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 3448 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3448 Number of groups = 1142 Number of bonds = 3442 Number of angles = 1246 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1140 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 = 3448 Number of groups = 1142 Number of bonds = 3442 Number of angles = 1246 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1140 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 <- "35.448" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1137" Evaluating: 1137-13 Parameter: NUMWAT <- "1124" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1124" Comparing "1075" and "1124". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.448" Parameter: BOX -> "35.448" Parameter: BOX -> "35.448" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.44800 B = 35.44800 C = 35.44800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1648 2 1 -1 -2 -1 13.5830 3 1 -1 -1 -1 4.1296 4 1 -1 0 -1 0.4269 5 1 0 -1 -1 3.3168 6 1 0 0 -1 2.5450 7 1 -1 -1 0 3.0694 8 1 -1 0 0 6.1703 9 1 0 -1 0 4.2608 10 1 0 1 0 4.2608 11 1 0 0 1 2.5450 12 1 0 1 1 3.3168 13 1 2 1 1 10.1648 14 1 1 2 1 13.5830 15 1 1 1 1 4.1296 16 1 1 0 1 0.4269 17 1 1 1 0 3.0694 18 1 1 0 0 6.1703 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3448 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 180 60 60 6.17 2 C002 has 33 11 11 11.58 3 C003 has 2637 879 879 0.00 4 C004 has 804 268 268 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1209 403 403 0.00 Total of12358 atoms and 4112 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 3448 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3448 Number of groups = 1142 Number of bonds = 3442 Number of angles = 1246 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1140 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 = 3448 Number of groups = 1142 Number of bonds = 3442 Number of angles = 1246 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1140 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 <- "35.446" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1137" Evaluating: 1137-13 Parameter: NUMWAT <- "1124" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1124" Comparing "1075" and "1124". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.446" Parameter: BOX -> "35.446" Parameter: BOX -> "35.446" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.44600 B = 35.44600 C = 35.44600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1623 2 1 -1 -2 -1 13.5799 3 1 -1 -1 -1 4.1295 4 1 -1 0 -1 0.4261 5 1 0 -1 -1 3.3171 6 1 0 0 -1 2.5438 7 1 -1 -1 0 3.0692 8 1 -1 0 0 6.1696 9 1 0 -1 0 4.2601 10 1 0 1 0 4.2601 11 1 0 0 1 2.5438 12 1 0 1 1 3.3171 13 1 2 1 1 10.1623 14 1 1 2 1 13.5799 15 1 1 1 1 4.1295 16 1 1 0 1 0.4261 17 1 1 1 0 3.0692 18 1 1 0 0 6.1696 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3448 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 180 60 60 6.17 2 C002 has 33 11 11 11.58 3 C003 has 2640 880 880 0.00 4 C004 has 804 268 268 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1209 403 403 0.00 Total of12361 atoms and 4113 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 3448 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3448 Number of groups = 1142 Number of bonds = 3442 Number of angles = 1246 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1140 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 = 3448 Number of groups = 1142 Number of bonds = 3442 Number of angles = 1246 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1140 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 <- "35.444" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1137" Evaluating: 1137-13 Parameter: NUMWAT <- "1124" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1124" Comparing "1075" and "1124". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.444" Parameter: BOX -> "35.444" Parameter: BOX -> "35.444" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.44400 B = 35.44400 C = 35.44400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1597 2 1 -1 -2 -1 13.5768 3 1 -1 -1 -1 4.1294 4 1 -1 0 -1 0.4253 5 1 0 -1 -1 3.3174 6 1 0 0 -1 2.5427 7 1 -1 -1 0 3.0679 8 1 -1 0 0 6.1688 9 1 0 -1 0 4.2594 10 1 0 1 0 4.2594 11 1 0 0 1 2.5427 12 1 0 1 1 3.3174 13 1 2 1 1 10.1597 14 1 1 2 1 13.5768 15 1 1 1 1 4.1294 16 1 1 0 1 0.4253 17 1 1 1 0 3.0679 18 1 1 0 0 6.1688 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3448 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 658 OPERATED ON BY TRANSFORMATION C017 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 180 60 60 6.17 2 C002 has 33 11 11 11.57 3 C003 has 2643 881 881 0.00 4 C004 has 804 268 268 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1212 404 404 0.00 Total of12370 atoms and 4116 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> 3 atoms have been selected out of 3448 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 = 3445 Number of groups = 1141 Number of bonds = 3439 Number of angles = 1245 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1139 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 = 3445 Number of groups = 1141 Number of bonds = 3439 Number of angles = 1245 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1139 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 <- "35.442" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1136" Evaluating: 1136-13 Parameter: NUMWAT <- "1123" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1123" Comparing "1075" and "1123". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.442" Parameter: BOX -> "35.442" Parameter: BOX -> "35.442" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.44200 B = 35.44200 C = 35.44200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1572 2 1 -1 -2 -1 13.5737 3 1 -1 -1 -1 4.1293 4 1 -1 0 -1 0.4246 5 1 0 -1 -1 3.3177 6 1 0 0 -1 2.5415 7 1 -1 -1 0 3.0665 8 1 -1 0 0 6.1681 9 1 0 -1 0 4.2587 10 1 0 1 0 4.2587 11 1 0 0 1 2.5415 12 1 0 1 1 3.3177 13 1 2 1 1 10.1572 14 1 1 2 1 13.5737 15 1 1 1 1 4.1293 16 1 1 0 1 0.4246 17 1 1 1 0 3.0665 18 1 1 0 0 6.1681 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3445 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 180 60 60 6.16 2 C002 has 33 11 11 11.57 3 C003 has 2640 880 880 0.00 4 C004 has 804 268 268 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1209 403 403 0.00 Total of12355 atoms and 4111 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 3445 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3445 Number of groups = 1141 Number of bonds = 3439 Number of angles = 1245 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1139 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 = 3445 Number of groups = 1141 Number of bonds = 3439 Number of angles = 1245 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1139 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 <- "35.44" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1136" Evaluating: 1136-13 Parameter: NUMWAT <- "1123" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1123" Comparing "1075" and "1123". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.44" Parameter: BOX -> "35.44" Parameter: BOX -> "35.44" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.44000 B = 35.44000 C = 35.44000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1546 2 1 -1 -2 -1 13.5705 3 1 -1 -1 -1 4.1292 4 1 -1 0 -1 0.4238 5 1 0 -1 -1 3.3180 6 1 0 0 -1 2.5403 7 1 -1 -1 0 3.0650 8 1 -1 0 0 6.1673 9 1 0 -1 0 4.2580 10 1 0 1 0 4.2580 11 1 0 0 1 2.5403 12 1 0 1 1 3.3180 13 1 2 1 1 10.1546 14 1 1 2 1 13.5705 15 1 1 1 1 4.1292 16 1 1 0 1 0.4238 17 1 1 1 0 3.0650 18 1 1 0 0 6.1673 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3445 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 180 60 60 6.16 2 C002 has 36 12 12 11.57 3 C003 has 2640 880 880 0.00 4 C004 has 804 268 268 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 810 270 270 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1209 403 403 0.00 Total of12358 atoms and 4112 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 3445 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3445 Number of groups = 1141 Number of bonds = 3439 Number of angles = 1245 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1139 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 = 3445 Number of groups = 1141 Number of bonds = 3439 Number of angles = 1245 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1139 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 <- "35.438" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1136" Evaluating: 1136-13 Parameter: NUMWAT <- "1123" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1123" Comparing "1075" and "1123". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.438" Parameter: BOX -> "35.438" Parameter: BOX -> "35.438" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.43800 B = 35.43800 C = 35.43800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1521 2 1 -1 -2 -1 13.5674 3 1 -1 -1 -1 4.1291 4 1 -1 0 -1 0.4230 5 1 0 -1 -1 3.3183 6 1 0 0 -1 2.5392 7 1 -1 -1 0 3.0636 8 1 -1 0 0 6.1666 9 1 0 -1 0 4.2573 10 1 0 1 0 4.2573 11 1 0 0 1 2.5392 12 1 0 1 1 3.3183 13 1 2 1 1 10.1521 14 1 1 2 1 13.5674 15 1 1 1 1 4.1291 16 1 1 0 1 0.4230 17 1 1 1 0 3.0636 18 1 1 0 0 6.1666 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3445 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 180 60 60 6.16 2 C002 has 36 12 12 11.56 3 C003 has 2640 880 880 0.00 4 C004 has 804 268 268 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1209 403 403 0.00 Total of12361 atoms and 4113 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 3445 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3445 Number of groups = 1141 Number of bonds = 3439 Number of angles = 1245 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1139 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 = 3445 Number of groups = 1141 Number of bonds = 3439 Number of angles = 1245 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1139 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 <- "35.436" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1136" Evaluating: 1136-13 Parameter: NUMWAT <- "1123" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1123" Comparing "1075" and "1123". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.436" Parameter: BOX -> "35.436" Parameter: BOX -> "35.436" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.43600 B = 35.43600 C = 35.43600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1495 2 1 -1 -2 -1 13.5643 3 1 -1 -1 -1 4.1289 4 1 -1 0 -1 0.4223 5 1 0 -1 -1 3.3186 6 1 0 0 -1 2.5380 7 1 -1 -1 0 3.0621 8 1 -1 0 0 6.1658 9 1 0 -1 0 4.2566 10 1 0 1 0 4.2566 11 1 0 0 1 2.5380 12 1 0 1 1 3.3186 13 1 2 1 1 10.1495 14 1 1 2 1 13.5643 15 1 1 1 1 4.1289 16 1 1 0 1 0.4223 17 1 1 1 0 3.0621 18 1 1 0 0 6.1658 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3445 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 180 60 60 6.15 2 C002 has 36 12 12 11.56 3 C003 has 2640 880 880 0.00 4 C004 has 804 268 268 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1212 404 404 0.00 Total of12364 atoms and 4114 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 3445 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3445 Number of groups = 1141 Number of bonds = 3439 Number of angles = 1245 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1139 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 = 3445 Number of groups = 1141 Number of bonds = 3439 Number of angles = 1245 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1139 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 <- "35.434" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1136" Evaluating: 1136-13 Parameter: NUMWAT <- "1123" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1123" Comparing "1075" and "1123". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.434" Parameter: BOX -> "35.434" Parameter: BOX -> "35.434" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.43400 B = 35.43400 C = 35.43400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1470 2 1 -1 -2 -1 13.5612 3 1 -1 -1 -1 4.1288 4 1 -1 0 -1 0.4216 5 1 0 -1 -1 3.3189 6 1 0 0 -1 2.5368 7 1 -1 -1 0 3.0606 8 1 -1 0 0 6.1651 9 1 0 -1 0 4.2559 10 1 0 1 0 4.2559 11 1 0 0 1 2.5368 12 1 0 1 1 3.3189 13 1 2 1 1 10.1470 14 1 1 2 1 13.5612 15 1 1 1 1 4.1288 16 1 1 0 1 0.4216 17 1 1 1 0 3.0606 18 1 1 0 0 6.1651 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3445 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 180 60 60 6.15 2 C002 has 36 12 12 11.56 3 C003 has 2640 880 880 0.00 4 C004 has 804 268 268 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1212 404 404 0.00 Total of12370 atoms and 4116 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 3445 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3445 Number of groups = 1141 Number of bonds = 3439 Number of angles = 1245 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1139 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 = 3445 Number of groups = 1141 Number of bonds = 3439 Number of angles = 1245 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1139 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 <- "35.432" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1136" Evaluating: 1136-13 Parameter: NUMWAT <- "1123" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1123" Comparing "1075" and "1123". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.432" Parameter: BOX -> "35.432" Parameter: BOX -> "35.432" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.43200 B = 35.43200 C = 35.43200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1445 2 1 -1 -2 -1 13.5580 3 1 -1 -1 -1 4.1287 4 1 -1 0 -1 0.4209 5 1 0 -1 -1 3.3192 6 1 0 0 -1 2.5357 7 1 -1 -1 0 3.0592 8 1 -1 0 0 6.1643 9 1 0 -1 0 4.2552 10 1 0 1 0 4.2552 11 1 0 0 1 2.5357 12 1 0 1 1 3.3192 13 1 2 1 1 10.1445 14 1 1 2 1 13.5580 15 1 1 1 1 4.1287 16 1 1 0 1 0.4209 17 1 1 1 0 3.0592 18 1 1 0 0 6.1643 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3445 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.15 2 C002 has 36 12 12 11.55 3 C003 has 2640 880 880 0.00 4 C004 has 804 268 268 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1212 404 404 0.00 Total of12373 atoms and 4117 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 3445 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3445 Number of groups = 1141 Number of bonds = 3439 Number of angles = 1245 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1139 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 = 3445 Number of groups = 1141 Number of bonds = 3439 Number of angles = 1245 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1139 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 <- "35.43" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1136" Evaluating: 1136-13 Parameter: NUMWAT <- "1123" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1123" Comparing "1075" and "1123". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.43" Parameter: BOX -> "35.43" Parameter: BOX -> "35.43" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.43000 B = 35.43000 C = 35.43000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1419 2 1 -1 -2 -1 13.5549 3 1 -1 -1 -1 4.1286 4 1 -1 0 -1 0.4201 5 1 0 -1 -1 3.3195 6 1 0 0 -1 2.5345 7 1 -1 -1 0 3.0577 8 1 -1 0 0 6.1636 9 1 0 -1 0 4.2545 10 1 0 1 0 4.2545 11 1 0 0 1 2.5345 12 1 0 1 1 3.3195 13 1 2 1 1 10.1419 14 1 1 2 1 13.5549 15 1 1 1 1 4.1286 16 1 1 0 1 0.4201 17 1 1 1 0 3.0577 18 1 1 0 0 6.1636 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3445 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 666 OPERATED ON BY TRANSFORMATION C006 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.14 2 C002 has 36 12 12 11.55 3 C003 has 2637 879 879 0.00 4 C004 has 807 269 269 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1158 386 386 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1215 405 405 0.00 Total of12388 atoms and 4122 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> 3 atoms have been selected out of 3445 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 = 3442 Number of groups = 1140 Number of bonds = 3436 Number of angles = 1244 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1138 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 = 3442 Number of groups = 1140 Number of bonds = 3436 Number of angles = 1244 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1138 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 <- "35.428" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1135" Evaluating: 1135-13 Parameter: NUMWAT <- "1122" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1122" Comparing "1075" and "1122". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.428" Parameter: BOX -> "35.428" Parameter: BOX -> "35.428" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.42800 B = 35.42800 C = 35.42800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1394 2 1 -1 -2 -1 13.5518 3 1 -1 -1 -1 4.1285 4 1 -1 0 -1 0.4194 5 1 0 -1 -1 3.3198 6 1 0 0 -1 2.5333 7 1 -1 -1 0 3.0563 8 1 -1 0 0 6.1629 9 1 0 -1 0 4.2538 10 1 0 1 0 4.2538 11 1 0 0 1 2.5333 12 1 0 1 1 3.3198 13 1 2 1 1 10.1394 14 1 1 2 1 13.5518 15 1 1 1 1 4.1285 16 1 1 0 1 0.4194 17 1 1 1 0 3.0563 18 1 1 0 0 6.1629 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3442 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.14 2 C002 has 36 12 12 11.55 3 C003 has 2640 880 880 0.00 4 C004 has 807 269 269 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1146 382 382 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1212 404 404 0.00 Total of12370 atoms and 4116 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 3442 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3442 Number of groups = 1140 Number of bonds = 3436 Number of angles = 1244 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1138 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 = 3442 Number of groups = 1140 Number of bonds = 3436 Number of angles = 1244 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1138 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 <- "35.426" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1135" Evaluating: 1135-13 Parameter: NUMWAT <- "1122" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1122" Comparing "1075" and "1122". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.426" Parameter: BOX -> "35.426" Parameter: BOX -> "35.426" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.42600 B = 35.42600 C = 35.42600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1369 2 1 -1 -2 -1 13.5487 3 1 -1 -1 -1 4.1284 4 1 -1 0 -1 0.4188 5 1 0 -1 -1 3.3201 6 1 0 0 -1 2.5322 7 1 -1 -1 0 3.0548 8 1 -1 0 0 6.1621 9 1 0 -1 0 4.2531 10 1 0 1 0 4.2531 11 1 0 0 1 2.5322 12 1 0 1 1 3.3201 13 1 2 1 1 10.1369 14 1 1 2 1 13.5487 15 1 1 1 1 4.1284 16 1 1 0 1 0.4188 17 1 1 1 0 3.0548 18 1 1 0 0 6.1621 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3442 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.14 2 C002 has 36 12 12 11.54 3 C003 has 2643 881 881 0.00 4 C004 has 810 270 270 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1146 382 382 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1212 404 404 0.00 Total of12376 atoms and 4118 groups and 4113 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3442 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3442 Number of groups = 1140 Number of bonds = 3436 Number of angles = 1244 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1138 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 = 3442 Number of groups = 1140 Number of bonds = 3436 Number of angles = 1244 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1138 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 <- "35.424" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1135" Evaluating: 1135-13 Parameter: NUMWAT <- "1122" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1122" Comparing "1075" and "1122". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.424" Parameter: BOX -> "35.424" Parameter: BOX -> "35.424" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.42400 B = 35.42400 C = 35.42400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1343 2 1 -1 -2 -1 13.5456 3 1 -1 -1 -1 4.1283 4 1 -1 0 -1 0.4181 5 1 0 -1 -1 3.3204 6 1 0 0 -1 2.5310 7 1 -1 -1 0 3.0534 8 1 -1 0 0 6.1614 9 1 0 -1 0 4.2524 10 1 0 1 0 4.2524 11 1 0 0 1 2.5310 12 1 0 1 1 3.3204 13 1 2 1 1 10.1343 14 1 1 2 1 13.5456 15 1 1 1 1 4.1283 16 1 1 0 1 0.4181 17 1 1 1 0 3.0534 18 1 1 0 0 6.1614 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3442 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.13 2 C002 has 36 12 12 11.54 3 C003 has 2643 881 881 0.00 4 C004 has 810 270 270 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1146 382 382 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1212 404 404 0.00 Total of12376 atoms and 4118 groups and 4113 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3442 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3442 Number of groups = 1140 Number of bonds = 3436 Number of angles = 1244 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1138 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 = 3442 Number of groups = 1140 Number of bonds = 3436 Number of angles = 1244 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1138 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 <- "35.422" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1135" Evaluating: 1135-13 Parameter: NUMWAT <- "1122" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1122" Comparing "1075" and "1122". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.422" Parameter: BOX -> "35.422" Parameter: BOX -> "35.422" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.42200 B = 35.42200 C = 35.42200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1318 2 1 -1 -2 -1 13.5424 3 1 -1 -1 -1 4.1281 4 1 -1 0 -1 0.4174 5 1 0 -1 -1 3.3207 6 1 0 0 -1 2.5298 7 1 -1 -1 0 3.0519 8 1 -1 0 0 6.1606 9 1 0 -1 0 4.2517 10 1 0 1 0 4.2517 11 1 0 0 1 2.5298 12 1 0 1 1 3.3207 13 1 2 1 1 10.1318 14 1 1 2 1 13.5424 15 1 1 1 1 4.1281 16 1 1 0 1 0.4174 17 1 1 1 0 3.0519 18 1 1 0 0 6.1606 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3442 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.13 2 C002 has 36 12 12 11.54 3 C003 has 2643 881 881 0.00 4 C004 has 810 270 270 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1146 382 382 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1212 404 404 0.00 Total of12376 atoms and 4118 groups and 4113 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3442 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3442 Number of groups = 1140 Number of bonds = 3436 Number of angles = 1244 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1138 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 = 3442 Number of groups = 1140 Number of bonds = 3436 Number of angles = 1244 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1138 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 <- "35.42" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1135" Evaluating: 1135-13 Parameter: NUMWAT <- "1122" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1122" Comparing "1075" and "1122". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.42" Parameter: BOX -> "35.42" Parameter: BOX -> "35.42" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.42000 B = 35.42000 C = 35.42000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1292 2 1 -1 -2 -1 13.5393 3 1 -1 -1 -1 4.1280 4 1 -1 0 -1 0.4168 5 1 0 -1 -1 3.3210 6 1 0 0 -1 2.5287 7 1 -1 -1 0 3.0505 8 1 -1 0 0 6.1599 9 1 0 -1 0 4.2510 10 1 0 1 0 4.2510 11 1 0 0 1 2.5287 12 1 0 1 1 3.3210 13 1 2 1 1 10.1292 14 1 1 2 1 13.5393 15 1 1 1 1 4.1280 16 1 1 0 1 0.4168 17 1 1 1 0 3.0505 18 1 1 0 0 6.1599 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3442 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.13 2 C002 has 36 12 12 11.54 3 C003 has 2643 881 881 0.00 4 C004 has 810 270 270 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1146 382 382 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1212 404 404 0.00 Total of12376 atoms and 4118 groups and 4113 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3442 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3442 Number of groups = 1140 Number of bonds = 3436 Number of angles = 1244 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1138 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 = 3442 Number of groups = 1140 Number of bonds = 3436 Number of angles = 1244 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1138 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 <- "35.418" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1135" Evaluating: 1135-13 Parameter: NUMWAT <- "1122" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1122" Comparing "1075" and "1122". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.418" Parameter: BOX -> "35.418" Parameter: BOX -> "35.418" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.41800 B = 35.41800 C = 35.41800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1267 2 1 -1 -2 -1 13.5362 3 1 -1 -1 -1 4.1279 4 1 -1 0 -1 0.4161 5 1 0 -1 -1 3.3213 6 1 0 0 -1 2.5275 7 1 -1 -1 0 3.0490 8 1 -1 0 0 6.1591 9 1 0 -1 0 4.2503 10 1 0 1 0 4.2503 11 1 0 0 1 2.5275 12 1 0 1 1 3.3213 13 1 2 1 1 10.1267 14 1 1 2 1 13.5362 15 1 1 1 1 4.1279 16 1 1 0 1 0.4161 17 1 1 1 0 3.0490 18 1 1 0 0 6.1591 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3442 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.13 2 C002 has 36 12 12 11.53 3 C003 has 2643 881 881 0.00 4 C004 has 810 270 270 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1146 382 382 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1212 404 404 0.00 Total of12376 atoms and 4118 groups and 4113 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3442 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3442 Number of groups = 1140 Number of bonds = 3436 Number of angles = 1244 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1138 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 = 3442 Number of groups = 1140 Number of bonds = 3436 Number of angles = 1244 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1138 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 <- "35.416" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1135" Evaluating: 1135-13 Parameter: NUMWAT <- "1122" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1122" Comparing "1075" and "1122". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.416" Parameter: BOX -> "35.416" Parameter: BOX -> "35.416" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.41600 B = 35.41600 C = 35.41600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1242 2 1 -1 -2 -1 13.5331 3 1 -1 -1 -1 4.1278 4 1 -1 0 -1 0.4155 5 1 0 -1 -1 3.3216 6 1 0 0 -1 2.5264 7 1 -1 -1 0 3.0476 8 1 -1 0 0 6.1584 9 1 0 -1 0 4.2496 10 1 0 1 0 4.2496 11 1 0 0 1 2.5264 12 1 0 1 1 3.3216 13 1 2 1 1 10.1242 14 1 1 2 1 13.5331 15 1 1 1 1 4.1278 16 1 1 0 1 0.4155 17 1 1 1 0 3.0476 18 1 1 0 0 6.1584 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3442 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.12 2 C002 has 36 12 12 11.53 3 C003 has 2643 881 881 0.00 4 C004 has 810 270 270 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1146 382 382 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1212 404 404 0.00 Total of12376 atoms and 4118 groups and 4113 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3442 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3442 Number of groups = 1140 Number of bonds = 3436 Number of angles = 1244 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1138 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 = 3442 Number of groups = 1140 Number of bonds = 3436 Number of angles = 1244 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1138 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 <- "35.414" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1135" Evaluating: 1135-13 Parameter: NUMWAT <- "1122" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1122" Comparing "1075" and "1122". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.414" Parameter: BOX -> "35.414" Parameter: BOX -> "35.414" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.41400 B = 35.41400 C = 35.41400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1216 2 1 -1 -2 -1 13.5299 3 1 -1 -1 -1 4.1277 4 1 -1 0 -1 0.4149 5 1 0 -1 -1 3.3219 6 1 0 0 -1 2.5252 7 1 -1 -1 0 3.0461 8 1 -1 0 0 6.1577 9 1 0 -1 0 4.2489 10 1 0 1 0 4.2489 11 1 0 0 1 2.5252 12 1 0 1 1 3.3219 13 1 2 1 1 10.1216 14 1 1 2 1 13.5299 15 1 1 1 1 4.1277 16 1 1 0 1 0.4149 17 1 1 1 0 3.0461 18 1 1 0 0 6.1577 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3442 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.12 2 C002 has 36 12 12 11.53 3 C003 has 2643 881 881 0.00 4 C004 has 813 271 271 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1146 382 382 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1212 404 404 0.00 Total of12379 atoms and 4119 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 3442 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3442 Number of groups = 1140 Number of bonds = 3436 Number of angles = 1244 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1138 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 = 3442 Number of groups = 1140 Number of bonds = 3436 Number of angles = 1244 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1138 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 <- "35.412" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1135" Evaluating: 1135-13 Parameter: NUMWAT <- "1122" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1122" Comparing "1075" and "1122". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.412" Parameter: BOX -> "35.412" Parameter: BOX -> "35.412" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.41200 B = 35.41200 C = 35.41200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1191 2 1 -1 -2 -1 13.5268 3 1 -1 -1 -1 4.1276 4 1 -1 0 -1 0.4143 5 1 0 -1 -1 3.3222 6 1 0 0 -1 2.5241 7 1 -1 -1 0 3.0447 8 1 -1 0 0 6.1569 9 1 0 -1 0 4.2482 10 1 0 1 0 4.2482 11 1 0 0 1 2.5241 12 1 0 1 1 3.3222 13 1 2 1 1 10.1191 14 1 1 2 1 13.5268 15 1 1 1 1 4.1276 16 1 1 0 1 0.4143 17 1 1 1 0 3.0447 18 1 1 0 0 6.1569 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3442 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.12 2 C002 has 36 12 12 11.52 3 C003 has 2643 881 881 0.00 4 C004 has 813 271 271 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1146 382 382 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1212 404 404 0.00 Total of12379 atoms and 4119 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 3442 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3442 Number of groups = 1140 Number of bonds = 3436 Number of angles = 1244 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1138 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 = 3442 Number of groups = 1140 Number of bonds = 3436 Number of angles = 1244 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1138 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 <- "35.41" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1135" Evaluating: 1135-13 Parameter: NUMWAT <- "1122" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1122" Comparing "1075" and "1122". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.41" Parameter: BOX -> "35.41" Parameter: BOX -> "35.41" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.41000 B = 35.41000 C = 35.41000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1166 2 1 -1 -2 -1 13.5237 3 1 -1 -1 -1 4.1275 4 1 -1 0 -1 0.4137 5 1 0 -1 -1 3.3226 6 1 0 0 -1 2.5229 7 1 -1 -1 0 3.0432 8 1 -1 0 0 6.1562 9 1 0 -1 0 4.2475 10 1 0 1 0 4.2475 11 1 0 0 1 2.5229 12 1 0 1 1 3.3226 13 1 2 1 1 10.1166 14 1 1 2 1 13.5237 15 1 1 1 1 4.1275 16 1 1 0 1 0.4137 17 1 1 1 0 3.0432 18 1 1 0 0 6.1562 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3442 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.11 2 C002 has 36 12 12 11.52 3 C003 has 2643 881 881 0.00 4 C004 has 813 271 271 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1146 382 382 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1212 404 404 0.00 Total of12379 atoms and 4119 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 3442 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3442 Number of groups = 1140 Number of bonds = 3436 Number of angles = 1244 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1138 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 = 3442 Number of groups = 1140 Number of bonds = 3436 Number of angles = 1244 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1138 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 <- "35.408" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1135" Evaluating: 1135-13 Parameter: NUMWAT <- "1122" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1122" Comparing "1075" and "1122". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.408" Parameter: BOX -> "35.408" Parameter: BOX -> "35.408" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.40800 B = 35.40800 C = 35.40800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1140 2 1 -1 -2 -1 13.5206 3 1 -1 -1 -1 4.1274 4 1 -1 0 -1 0.4131 5 1 0 -1 -1 3.3229 6 1 0 0 -1 2.5218 7 1 -1 -1 0 3.0418 8 1 -1 0 0 6.1555 9 1 0 -1 0 4.2468 10 1 0 1 0 4.2468 11 1 0 0 1 2.5218 12 1 0 1 1 3.3229 13 1 2 1 1 10.1140 14 1 1 2 1 13.5206 15 1 1 1 1 4.1274 16 1 1 0 1 0.4131 17 1 1 1 0 3.0418 18 1 1 0 0 6.1555 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3442 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.11 2 C002 has 36 12 12 11.52 3 C003 has 2643 881 881 0.00 4 C004 has 813 271 271 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1146 382 382 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1212 404 404 0.00 Total of12379 atoms and 4119 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 3442 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3442 Number of groups = 1140 Number of bonds = 3436 Number of angles = 1244 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1138 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 = 3442 Number of groups = 1140 Number of bonds = 3436 Number of angles = 1244 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1138 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 <- "35.406" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1135" Evaluating: 1135-13 Parameter: NUMWAT <- "1122" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1122" Comparing "1075" and "1122". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.406" Parameter: BOX -> "35.406" Parameter: BOX -> "35.406" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.40600 B = 35.40600 C = 35.40600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1115 2 1 -1 -2 -1 13.5174 3 1 -1 -1 -1 4.1273 4 1 -1 0 -1 0.4126 5 1 0 -1 -1 3.3232 6 1 0 0 -1 2.5206 7 1 -1 -1 0 3.0403 8 1 -1 0 0 6.1547 9 1 0 -1 0 4.2461 10 1 0 1 0 4.2461 11 1 0 0 1 2.5206 12 1 0 1 1 3.3232 13 1 2 1 1 10.1115 14 1 1 2 1 13.5174 15 1 1 1 1 4.1273 16 1 1 0 1 0.4126 17 1 1 1 0 3.0403 18 1 1 0 0 6.1547 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3442 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 904 OPERATED ON BY TRANSFORMATION C018 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 6.11 2 C002 has 36 12 12 11.51 3 C003 has 2643 881 881 0.00 4 C004 has 813 271 271 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1146 382 382 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1227 409 409 0.00 9 C009 has 1209 403 403 0.00 Total of12379 atoms and 4119 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 3442 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 = 3439 Number of groups = 1139 Number of bonds = 3433 Number of angles = 1243 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1137 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 = 3439 Number of groups = 1139 Number of bonds = 3433 Number of angles = 1243 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1137 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 <- "35.404" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1134" Evaluating: 1134-13 Parameter: NUMWAT <- "1121" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1121" Comparing "1075" and "1121". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.404" Parameter: BOX -> "35.404" Parameter: BOX -> "35.404" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.40400 B = 35.40400 C = 35.40400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1090 2 1 -1 -2 -1 13.5143 3 1 -1 -1 -1 4.1272 4 1 -1 0 -1 0.4120 5 1 0 -1 -1 3.3235 6 1 0 0 -1 2.5195 7 1 -1 -1 0 3.0389 8 1 -1 0 0 6.1540 9 1 0 -1 0 4.2455 10 1 0 1 0 4.2455 11 1 0 0 1 2.5195 12 1 0 1 1 3.3235 13 1 2 1 1 10.1090 14 1 1 2 1 13.5143 15 1 1 1 1 4.1272 16 1 1 0 1 0.4120 17 1 1 1 0 3.0389 18 1 1 0 0 6.1540 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3439 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.10 2 C002 has 36 12 12 11.51 3 C003 has 2640 880 880 0.00 4 C004 has 813 271 271 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1146 382 382 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1209 403 403 0.00 Total of12364 atoms and 4114 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 3439 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3439 Number of groups = 1139 Number of bonds = 3433 Number of angles = 1243 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1137 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 = 3439 Number of groups = 1139 Number of bonds = 3433 Number of angles = 1243 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1137 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 <- "35.402" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1134" Evaluating: 1134-13 Parameter: NUMWAT <- "1121" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1121" Comparing "1075" and "1121". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.402" Parameter: BOX -> "35.402" Parameter: BOX -> "35.402" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.40200 B = 35.40200 C = 35.40200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1064 2 1 -1 -2 -1 13.5112 3 1 -1 -1 -1 4.1271 4 1 -1 0 -1 0.4115 5 1 0 -1 -1 3.3238 6 1 0 0 -1 2.5183 7 1 -1 -1 0 3.0374 8 1 -1 0 0 6.1532 9 1 0 -1 0 4.2448 10 1 0 1 0 4.2448 11 1 0 0 1 2.5183 12 1 0 1 1 3.3238 13 1 2 1 1 10.1064 14 1 1 2 1 13.5112 15 1 1 1 1 4.1271 16 1 1 0 1 0.4115 17 1 1 1 0 3.0374 18 1 1 0 0 6.1532 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3439 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.10 2 C002 has 36 12 12 11.51 3 C003 has 2640 880 880 0.00 4 C004 has 813 271 271 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1209 403 403 0.00 Total of12367 atoms and 4115 groups and 4110 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3439 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3439 Number of groups = 1139 Number of bonds = 3433 Number of angles = 1243 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1137 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 = 3439 Number of groups = 1139 Number of bonds = 3433 Number of angles = 1243 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1137 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 <- "35.4" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1134" Evaluating: 1134-13 Parameter: NUMWAT <- "1121" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1121" Comparing "1075" and "1121". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.4" Parameter: BOX -> "35.4" Parameter: BOX -> "35.4" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.40000 B = 35.40000 C = 35.40000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1039 2 1 -1 -2 -1 13.5081 3 1 -1 -1 -1 4.1270 4 1 -1 0 -1 0.4109 5 1 0 -1 -1 3.3242 6 1 0 0 -1 2.5172 7 1 -1 -1 0 3.0360 8 1 -1 0 0 6.1525 9 1 0 -1 0 4.2441 10 1 0 1 0 4.2441 11 1 0 0 1 2.5172 12 1 0 1 1 3.3242 13 1 2 1 1 10.1039 14 1 1 2 1 13.5081 15 1 1 1 1 4.1270 16 1 1 0 1 0.4109 17 1 1 1 0 3.0360 18 1 1 0 0 6.1525 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3439 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.10 2 C002 has 36 12 12 11.50 3 C003 has 2640 880 880 0.00 4 C004 has 813 271 271 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1209 403 403 0.00 Total of12367 atoms and 4115 groups and 4110 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3439 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3439 Number of groups = 1139 Number of bonds = 3433 Number of angles = 1243 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1137 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 = 3439 Number of groups = 1139 Number of bonds = 3433 Number of angles = 1243 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1137 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 <- "35.398" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1134" Evaluating: 1134-13 Parameter: NUMWAT <- "1121" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1121" Comparing "1075" and "1121". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.398" Parameter: BOX -> "35.398" Parameter: BOX -> "35.398" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.39800 B = 35.39800 C = 35.39800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.1014 2 1 -1 -2 -1 13.5050 3 1 -1 -1 -1 4.1269 4 1 -1 0 -1 0.4104 5 1 0 -1 -1 3.3245 6 1 0 0 -1 2.5160 7 1 -1 -1 0 3.0346 8 1 -1 0 0 6.1518 9 1 0 -1 0 4.2434 10 1 0 1 0 4.2434 11 1 0 0 1 2.5160 12 1 0 1 1 3.3245 13 1 2 1 1 10.1014 14 1 1 2 1 13.5050 15 1 1 1 1 4.1269 16 1 1 0 1 0.4104 17 1 1 1 0 3.0346 18 1 1 0 0 6.1518 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3439 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.09 2 C002 has 36 12 12 11.50 3 C003 has 2640 880 880 0.00 4 C004 has 813 271 271 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1152 384 384 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1209 403 403 0.00 Total of12370 atoms and 4116 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 3439 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3439 Number of groups = 1139 Number of bonds = 3433 Number of angles = 1243 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1137 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 = 3439 Number of groups = 1139 Number of bonds = 3433 Number of angles = 1243 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1137 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 <- "35.396" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1134" Evaluating: 1134-13 Parameter: NUMWAT <- "1121" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1121" Comparing "1075" and "1121". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.396" Parameter: BOX -> "35.396" Parameter: BOX -> "35.396" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.39600 B = 35.39600 C = 35.39600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0988 2 1 -1 -2 -1 13.5018 3 1 -1 -1 -1 4.1268 4 1 -1 0 -1 0.4099 5 1 0 -1 -1 3.3248 6 1 0 0 -1 2.5149 7 1 -1 -1 0 3.0331 8 1 -1 0 0 6.1510 9 1 0 -1 0 4.2427 10 1 0 1 0 4.2427 11 1 0 0 1 2.5149 12 1 0 1 1 3.3248 13 1 2 1 1 10.0988 14 1 1 2 1 13.5018 15 1 1 1 1 4.1268 16 1 1 0 1 0.4099 17 1 1 1 0 3.0331 18 1 1 0 0 6.1510 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3439 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 532 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.09 2 C002 has 36 12 12 11.50 3 C003 has 2646 882 882 0.00 4 C004 has 813 271 271 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1143 381 381 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1224 408 408 0.00 9 C009 has 1206 402 402 0.00 Total of12364 atoms and 4114 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 3439 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 = 1133 Number of atoms = 3436 Number of groups = 1138 Number of bonds = 3430 Number of angles = 1242 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1136 Number of HB donors = 2248 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1133 Number of atoms = 3436 Number of groups = 1138 Number of bonds = 3430 Number of angles = 1242 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1136 Number of HB donors = 2248 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.394" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1133" Evaluating: 1133-13 Parameter: NUMWAT <- "1120" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1120" Comparing "1075" and "1120". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.394" Parameter: BOX -> "35.394" Parameter: BOX -> "35.394" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.39400 B = 35.39400 C = 35.39400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0963 2 1 -1 -2 -1 13.4987 3 1 -1 -1 -1 4.1267 4 1 -1 0 -1 0.4094 5 1 0 -1 -1 3.3252 6 1 0 0 -1 2.5137 7 1 -1 -1 0 3.0317 8 1 -1 0 0 6.1503 9 1 0 -1 0 4.2420 10 1 0 1 0 4.2420 11 1 0 0 1 2.5137 12 1 0 1 1 3.3252 13 1 2 1 1 10.0963 14 1 1 2 1 13.4987 15 1 1 1 1 4.1267 16 1 1 0 1 0.4094 17 1 1 1 0 3.0317 18 1 1 0 0 6.1503 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3360 atoms have been selected out of 3436 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 C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.09 2 C002 has 39 13 13 11.50 3 C003 has 2643 881 881 0.00 4 C004 has 810 270 270 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1209 403 403 0.00 Total of12355 atoms and 4111 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> 3 atoms have been selected out of 3436 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 = 1132 Number of atoms = 3433 Number of groups = 1137 Number of bonds = 3427 Number of angles = 1241 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1135 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 = 3433 Number of groups = 1137 Number of bonds = 3427 Number of angles = 1241 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1135 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 <- "35.392" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1132" Evaluating: 1132-13 Parameter: NUMWAT <- "1119" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1119" Comparing "1075" and "1119". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.392" Parameter: BOX -> "35.392" Parameter: BOX -> "35.392" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.39200 B = 35.39200 C = 35.39200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0938 2 1 -1 -2 -1 13.4956 3 1 -1 -1 -1 4.1266 4 1 -1 0 -1 0.4089 5 1 0 -1 -1 3.3255 6 1 0 0 -1 2.5126 7 1 -1 -1 0 3.0302 8 1 -1 0 0 6.1496 9 1 0 -1 0 4.2414 10 1 0 1 0 4.2414 11 1 0 0 1 2.5126 12 1 0 1 1 3.3255 13 1 2 1 1 10.0938 14 1 1 2 1 13.4956 15 1 1 1 1 4.1266 16 1 1 0 1 0.4089 17 1 1 1 0 3.0302 18 1 1 0 0 6.1496 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3433 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.09 2 C002 has 36 12 12 11.49 3 C003 has 2640 880 880 0.00 4 C004 has 810 270 270 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1209 403 403 0.00 Total of12340 atoms and 4106 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 3433 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3433 Number of groups = 1137 Number of bonds = 3427 Number of angles = 1241 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1135 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 = 3433 Number of groups = 1137 Number of bonds = 3427 Number of angles = 1241 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1135 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 <- "35.39" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1132" Evaluating: 1132-13 Parameter: NUMWAT <- "1119" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1119" Comparing "1075" and "1119". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.39" Parameter: BOX -> "35.39" Parameter: BOX -> "35.39" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.39000 B = 35.39000 C = 35.39000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0912 2 1 -1 -2 -1 13.4925 3 1 -1 -1 -1 4.1265 4 1 -1 0 -1 0.4085 5 1 0 -1 -1 3.3258 6 1 0 0 -1 2.5114 7 1 -1 -1 0 3.0288 8 1 -1 0 0 6.1488 9 1 0 -1 0 4.2407 10 1 0 1 0 4.2407 11 1 0 0 1 2.5114 12 1 0 1 1 3.3258 13 1 2 1 1 10.0912 14 1 1 2 1 13.4925 15 1 1 1 1 4.1265 16 1 1 0 1 0.4085 17 1 1 1 0 3.0288 18 1 1 0 0 6.1488 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3433 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.08 2 C002 has 36 12 12 11.49 3 C003 has 2640 880 880 0.00 4 C004 has 810 270 270 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1209 403 403 0.00 Total of12340 atoms and 4106 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 3433 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3433 Number of groups = 1137 Number of bonds = 3427 Number of angles = 1241 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1135 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 = 3433 Number of groups = 1137 Number of bonds = 3427 Number of angles = 1241 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1135 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 <- "35.388" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1132" Evaluating: 1132-13 Parameter: NUMWAT <- "1119" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1119" Comparing "1075" and "1119". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.388" Parameter: BOX -> "35.388" Parameter: BOX -> "35.388" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.38800 B = 35.38800 C = 35.38800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0887 2 1 -1 -2 -1 13.4893 3 1 -1 -1 -1 4.1264 4 1 -1 0 -1 0.4080 5 1 0 -1 -1 3.3262 6 1 0 0 -1 2.5103 7 1 -1 -1 0 3.0274 8 1 -1 0 0 6.1481 9 1 0 -1 0 4.2400 10 1 0 1 0 4.2400 11 1 0 0 1 2.5103 12 1 0 1 1 3.3262 13 1 2 1 1 10.0887 14 1 1 2 1 13.4893 15 1 1 1 1 4.1264 16 1 1 0 1 0.4080 17 1 1 1 0 3.0274 18 1 1 0 0 6.1481 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3433 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.08 2 C002 has 36 12 12 11.49 3 C003 has 2640 880 880 0.00 4 C004 has 810 270 270 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1209 403 403 0.00 Total of12340 atoms and 4106 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 3433 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3433 Number of groups = 1137 Number of bonds = 3427 Number of angles = 1241 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1135 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 = 3433 Number of groups = 1137 Number of bonds = 3427 Number of angles = 1241 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1135 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 <- "35.386" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1132" Evaluating: 1132-13 Parameter: NUMWAT <- "1119" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1119" Comparing "1075" and "1119". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.386" Parameter: BOX -> "35.386" Parameter: BOX -> "35.386" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.38600 B = 35.38600 C = 35.38600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0862 2 1 -1 -2 -1 13.4862 3 1 -1 -1 -1 4.1263 4 1 -1 0 -1 0.4076 5 1 0 -1 -1 3.3265 6 1 0 0 -1 2.5091 7 1 -1 -1 0 3.0259 8 1 -1 0 0 6.1474 9 1 0 -1 0 4.2393 10 1 0 1 0 4.2393 11 1 0 0 1 2.5091 12 1 0 1 1 3.3265 13 1 2 1 1 10.0862 14 1 1 2 1 13.4862 15 1 1 1 1 4.1263 16 1 1 0 1 0.4076 17 1 1 1 0 3.0259 18 1 1 0 0 6.1474 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3433 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.08 2 C002 has 36 12 12 11.48 3 C003 has 2640 880 880 0.00 4 C004 has 810 270 270 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1209 403 403 0.00 Total of12340 atoms and 4106 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 3433 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3433 Number of groups = 1137 Number of bonds = 3427 Number of angles = 1241 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1135 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 = 3433 Number of groups = 1137 Number of bonds = 3427 Number of angles = 1241 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1135 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 <- "35.384" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1132" Evaluating: 1132-13 Parameter: NUMWAT <- "1119" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1119" Comparing "1075" and "1119". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.384" Parameter: BOX -> "35.384" Parameter: BOX -> "35.384" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.38400 B = 35.38400 C = 35.38400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0837 2 1 -1 -2 -1 13.4831 3 1 -1 -1 -1 4.1262 4 1 -1 0 -1 0.4071 5 1 0 -1 -1 3.3268 6 1 0 0 -1 2.5080 7 1 -1 -1 0 3.0245 8 1 -1 0 0 6.1466 9 1 0 -1 0 4.2386 10 1 0 1 0 4.2386 11 1 0 0 1 2.5080 12 1 0 1 1 3.3268 13 1 2 1 1 10.0837 14 1 1 2 1 13.4831 15 1 1 1 1 4.1262 16 1 1 0 1 0.4071 17 1 1 1 0 3.0245 18 1 1 0 0 6.1466 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3433 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.07 2 C002 has 36 12 12 11.48 3 C003 has 2640 880 880 0.00 4 C004 has 810 270 270 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1209 403 403 0.00 Total of12340 atoms and 4106 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 3433 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3433 Number of groups = 1137 Number of bonds = 3427 Number of angles = 1241 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1135 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 = 3433 Number of groups = 1137 Number of bonds = 3427 Number of angles = 1241 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1135 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 <- "35.382" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1132" Evaluating: 1132-13 Parameter: NUMWAT <- "1119" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1119" Comparing "1075" and "1119". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.382" Parameter: BOX -> "35.382" Parameter: BOX -> "35.382" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.38200 B = 35.38200 C = 35.38200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0811 2 1 -1 -2 -1 13.4800 3 1 -1 -1 -1 4.1261 4 1 -1 0 -1 0.4067 5 1 0 -1 -1 3.3272 6 1 0 0 -1 2.5069 7 1 -1 -1 0 3.0231 8 1 -1 0 0 6.1459 9 1 0 -1 0 4.2380 10 1 0 1 0 4.2380 11 1 0 0 1 2.5069 12 1 0 1 1 3.3272 13 1 2 1 1 10.0811 14 1 1 2 1 13.4800 15 1 1 1 1 4.1261 16 1 1 0 1 0.4067 17 1 1 1 0 3.0231 18 1 1 0 0 6.1459 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3433 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.07 2 C002 has 36 12 12 11.48 3 C003 has 2640 880 880 0.00 4 C004 has 810 270 270 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1212 404 404 0.00 Total of12349 atoms and 4109 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 3433 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3433 Number of groups = 1137 Number of bonds = 3427 Number of angles = 1241 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1135 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 = 3433 Number of groups = 1137 Number of bonds = 3427 Number of angles = 1241 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1135 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 <- "35.38" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1132" Evaluating: 1132-13 Parameter: NUMWAT <- "1119" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1119" Comparing "1075" and "1119". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.38" Parameter: BOX -> "35.38" Parameter: BOX -> "35.38" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.38000 B = 35.38000 C = 35.38000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0786 2 1 -1 -2 -1 13.4769 3 1 -1 -1 -1 4.1261 4 1 -1 0 -1 0.4063 5 1 0 -1 -1 3.3275 6 1 0 0 -1 2.5057 7 1 -1 -1 0 3.0217 8 1 -1 0 0 6.1452 9 1 0 -1 0 4.2373 10 1 0 1 0 4.2373 11 1 0 0 1 2.5057 12 1 0 1 1 3.3275 13 1 2 1 1 10.0786 14 1 1 2 1 13.4769 15 1 1 1 1 4.1261 16 1 1 0 1 0.4063 17 1 1 1 0 3.0217 18 1 1 0 0 6.1452 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3433 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.07 2 C002 has 36 12 12 11.47 3 C003 has 2640 880 880 0.00 4 C004 has 810 270 270 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1212 404 404 0.00 Total of12349 atoms and 4109 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 3433 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3433 Number of groups = 1137 Number of bonds = 3427 Number of angles = 1241 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1135 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 = 3433 Number of groups = 1137 Number of bonds = 3427 Number of angles = 1241 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1135 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 <- "35.378" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1132" Evaluating: 1132-13 Parameter: NUMWAT <- "1119" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1119" Comparing "1075" and "1119". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.378" Parameter: BOX -> "35.378" Parameter: BOX -> "35.378" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.37800 B = 35.37800 C = 35.37800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0761 2 1 -1 -2 -1 13.4737 3 1 -1 -1 -1 4.1260 4 1 -1 0 -1 0.4059 5 1 0 -1 -1 3.3279 6 1 0 0 -1 2.5046 7 1 -1 -1 0 3.0202 8 1 -1 0 0 6.1444 9 1 0 -1 0 4.2366 10 1 0 1 0 4.2366 11 1 0 0 1 2.5046 12 1 0 1 1 3.3279 13 1 2 1 1 10.0761 14 1 1 2 1 13.4737 15 1 1 1 1 4.1260 16 1 1 0 1 0.4059 17 1 1 1 0 3.0202 18 1 1 0 0 6.1444 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3433 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.06 2 C002 has 36 12 12 11.47 3 C003 has 2640 880 880 0.00 4 C004 has 810 270 270 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1212 404 404 0.00 Total of12349 atoms and 4109 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 3433 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3433 Number of groups = 1137 Number of bonds = 3427 Number of angles = 1241 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1135 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 = 3433 Number of groups = 1137 Number of bonds = 3427 Number of angles = 1241 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1135 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 <- "35.376" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1132" Evaluating: 1132-13 Parameter: NUMWAT <- "1119" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1119" Comparing "1075" and "1119". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.376" Parameter: BOX -> "35.376" Parameter: BOX -> "35.376" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.37600 B = 35.37600 C = 35.37600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0735 2 1 -1 -2 -1 13.4706 3 1 -1 -1 -1 4.1259 4 1 -1 0 -1 0.4055 5 1 0 -1 -1 3.3282 6 1 0 0 -1 2.5035 7 1 -1 -1 0 3.0188 8 1 -1 0 0 6.1437 9 1 0 -1 0 4.2359 10 1 0 1 0 4.2359 11 1 0 0 1 2.5035 12 1 0 1 1 3.3282 13 1 2 1 1 10.0735 14 1 1 2 1 13.4706 15 1 1 1 1 4.1259 16 1 1 0 1 0.4055 17 1 1 1 0 3.0188 18 1 1 0 0 6.1437 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3433 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.06 2 C002 has 36 12 12 11.47 3 C003 has 2640 880 880 0.00 4 C004 has 813 271 271 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1212 404 404 0.00 Total of12352 atoms and 4110 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 3433 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3433 Number of groups = 1137 Number of bonds = 3427 Number of angles = 1241 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1135 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 = 3433 Number of groups = 1137 Number of bonds = 3427 Number of angles = 1241 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1135 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 <- "35.374" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1132" Evaluating: 1132-13 Parameter: NUMWAT <- "1119" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1119" Comparing "1075" and "1119". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.374" Parameter: BOX -> "35.374" Parameter: BOX -> "35.374" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.37400 B = 35.37400 C = 35.37400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0710 2 1 -1 -2 -1 13.4675 3 1 -1 -1 -1 4.1258 4 1 -1 0 -1 0.4052 5 1 0 -1 -1 3.3285 6 1 0 0 -1 2.5023 7 1 -1 -1 0 3.0174 8 1 -1 0 0 6.1430 9 1 0 -1 0 4.2353 10 1 0 1 0 4.2353 11 1 0 0 1 2.5023 12 1 0 1 1 3.3285 13 1 2 1 1 10.0710 14 1 1 2 1 13.4675 15 1 1 1 1 4.1258 16 1 1 0 1 0.4052 17 1 1 1 0 3.0174 18 1 1 0 0 6.1430 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3433 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.06 2 C002 has 36 12 12 11.46 3 C003 has 2640 880 880 0.00 4 C004 has 813 271 271 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1215 405 405 0.00 Total of12355 atoms and 4111 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 3433 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3433 Number of groups = 1137 Number of bonds = 3427 Number of angles = 1241 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1135 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 = 3433 Number of groups = 1137 Number of bonds = 3427 Number of angles = 1241 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1135 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 <- "35.372" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1132" Evaluating: 1132-13 Parameter: NUMWAT <- "1119" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1119" Comparing "1075" and "1119". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.372" Parameter: BOX -> "35.372" Parameter: BOX -> "35.372" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.37200 B = 35.37200 C = 35.37200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0685 2 1 -1 -2 -1 13.4644 3 1 -1 -1 -1 4.1257 4 1 -1 0 -1 0.4048 5 1 0 -1 -1 3.3289 6 1 0 0 -1 2.5012 7 1 -1 -1 0 3.0159 8 1 -1 0 0 6.1423 9 1 0 -1 0 4.2346 10 1 0 1 0 4.2346 11 1 0 0 1 2.5012 12 1 0 1 1 3.3289 13 1 2 1 1 10.0685 14 1 1 2 1 13.4644 15 1 1 1 1 4.1257 16 1 1 0 1 0.4048 17 1 1 1 0 3.0159 18 1 1 0 0 6.1423 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3433 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.05 2 C002 has 36 12 12 11.46 3 C003 has 2640 880 880 0.00 4 C004 has 813 271 271 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1221 407 407 0.00 9 C009 has 1215 405 405 0.00 Total of12355 atoms and 4111 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 3433 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3433 Number of groups = 1137 Number of bonds = 3427 Number of angles = 1241 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1135 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 = 3433 Number of groups = 1137 Number of bonds = 3427 Number of angles = 1241 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1135 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 <- "35.37" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1132" Evaluating: 1132-13 Parameter: NUMWAT <- "1119" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1119" Comparing "1075" and "1119". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.37" Parameter: BOX -> "35.37" Parameter: BOX -> "35.37" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.37000 B = 35.37000 C = 35.37000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0660 2 1 -1 -2 -1 13.4612 3 1 -1 -1 -1 4.1256 4 1 -1 0 -1 0.4045 5 1 0 -1 -1 3.3292 6 1 0 0 -1 2.5001 7 1 -1 -1 0 3.0145 8 1 -1 0 0 6.1415 9 1 0 -1 0 4.2339 10 1 0 1 0 4.2339 11 1 0 0 1 2.5001 12 1 0 1 1 3.3292 13 1 2 1 1 10.0660 14 1 1 2 1 13.4612 15 1 1 1 1 4.1256 16 1 1 0 1 0.4045 17 1 1 1 0 3.0145 18 1 1 0 0 6.1415 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3433 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 513 OPERATED ON BY TRANSFORMATION C007 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.05 2 C002 has 36 12 12 11.46 3 C003 has 2640 880 880 0.00 4 C004 has 813 271 271 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1143 381 381 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1218 406 406 0.00 9 C009 has 1212 404 404 0.00 Total of12358 atoms and 4112 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> 3 atoms have been selected out of 3433 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 = 1131 Number of atoms = 3430 Number of groups = 1136 Number of bonds = 3424 Number of angles = 1240 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1134 Number of HB donors = 2244 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1131 Number of atoms = 3430 Number of groups = 1136 Number of bonds = 3424 Number of angles = 1240 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1134 Number of HB donors = 2244 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.368" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1131" Evaluating: 1131-13 Parameter: NUMWAT <- "1118" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1118" Comparing "1075" and "1118". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.368" Parameter: BOX -> "35.368" Parameter: BOX -> "35.368" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.36800 B = 35.36800 C = 35.36800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0634 2 1 -1 -2 -1 13.4581 3 1 -1 -1 -1 4.1255 4 1 -1 0 -1 0.4042 5 1 0 -1 -1 3.3296 6 1 0 0 -1 2.4989 7 1 -1 -1 0 3.0131 8 1 -1 0 0 6.1408 9 1 0 -1 0 4.2332 10 1 0 1 0 4.2332 11 1 0 0 1 2.4989 12 1 0 1 1 3.3296 13 1 2 1 1 10.0634 14 1 1 2 1 13.4581 15 1 1 1 1 4.1255 16 1 1 0 1 0.4042 17 1 1 1 0 3.0131 18 1 1 0 0 6.1408 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3354 atoms have been selected out of 3430 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.05 2 C002 has 36 12 12 11.46 3 C003 has 2640 880 880 0.00 4 C004 has 813 271 271 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1218 406 406 0.00 9 C009 has 1212 404 404 0.00 Total of12346 atoms and 4108 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 3430 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1131 Number of atoms = 3430 Number of groups = 1136 Number of bonds = 3424 Number of angles = 1240 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1134 Number of HB donors = 2244 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1131 Number of atoms = 3430 Number of groups = 1136 Number of bonds = 3424 Number of angles = 1240 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1134 Number of HB donors = 2244 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.366" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1131" Evaluating: 1131-13 Parameter: NUMWAT <- "1118" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1118" Comparing "1075" and "1118". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.366" Parameter: BOX -> "35.366" Parameter: BOX -> "35.366" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.36600 B = 35.36600 C = 35.36600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0609 2 1 -1 -2 -1 13.4550 3 1 -1 -1 -1 4.1255 4 1 -1 0 -1 0.4038 5 1 0 -1 -1 3.3299 6 1 0 0 -1 2.4978 7 1 -1 -1 0 3.0117 8 1 -1 0 0 6.1401 9 1 0 -1 0 4.2326 10 1 0 1 0 4.2326 11 1 0 0 1 2.4978 12 1 0 1 1 3.3299 13 1 2 1 1 10.0609 14 1 1 2 1 13.4550 15 1 1 1 1 4.1255 16 1 1 0 1 0.4038 17 1 1 1 0 3.0117 18 1 1 0 0 6.1401 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3354 atoms have been selected out of 3430 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 1087 OPERATED ON BY TRANSFORMATION C003 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.05 2 C002 has 36 12 12 11.45 3 C003 has 2637 879 879 0.00 4 C004 has 813 271 271 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 813 271 271 0.00 8 C008 has 1218 406 406 0.00 9 C009 has 1209 403 403 0.00 Total of12334 atoms and 4104 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> 3 atoms have been selected out of 3430 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 = 1130 Number of atoms = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 <- "35.364" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1130" Evaluating: 1130-13 Parameter: NUMWAT <- "1117" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1117" Comparing "1075" and "1117". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.364" Parameter: BOX -> "35.364" Parameter: BOX -> "35.364" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.36400 B = 35.36400 C = 35.36400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0584 2 1 -1 -2 -1 13.4519 3 1 -1 -1 -1 4.1254 4 1 -1 0 -1 0.4035 5 1 0 -1 -1 3.3303 6 1 0 0 -1 2.4967 7 1 -1 -1 0 3.0103 8 1 -1 0 0 6.1394 9 1 0 -1 0 4.2319 10 1 0 1 0 4.2319 11 1 0 0 1 2.4967 12 1 0 1 1 3.3303 13 1 2 1 1 10.0584 14 1 1 2 1 13.4519 15 1 1 1 1 4.1254 16 1 1 0 1 0.4035 17 1 1 1 0 3.0103 18 1 1 0 0 6.1394 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3427 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.04 2 C002 has 36 12 12 11.45 3 C003 has 2640 880 880 0.00 4 C004 has 813 271 271 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1218 406 406 0.00 9 C009 has 1209 403 403 0.00 Total of12337 atoms and 4105 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 3427 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 <- "35.362" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1130" Evaluating: 1130-13 Parameter: NUMWAT <- "1117" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1117" Comparing "1075" and "1117". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.362" Parameter: BOX -> "35.362" Parameter: BOX -> "35.362" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.36200 B = 35.36200 C = 35.36200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0559 2 1 -1 -2 -1 13.4488 3 1 -1 -1 -1 4.1253 4 1 -1 0 -1 0.4032 5 1 0 -1 -1 3.3307 6 1 0 0 -1 2.4955 7 1 -1 -1 0 3.0088 8 1 -1 0 0 6.1386 9 1 0 -1 0 4.2312 10 1 0 1 0 4.2312 11 1 0 0 1 2.4955 12 1 0 1 1 3.3307 13 1 2 1 1 10.0559 14 1 1 2 1 13.4488 15 1 1 1 1 4.1253 16 1 1 0 1 0.4032 17 1 1 1 0 3.0088 18 1 1 0 0 6.1386 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3427 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.04 2 C002 has 36 12 12 11.45 3 C003 has 2640 880 880 0.00 4 C004 has 813 271 271 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1218 406 406 0.00 9 C009 has 1209 403 403 0.00 Total of12337 atoms and 4105 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 3427 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 <- "35.36" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1130" Evaluating: 1130-13 Parameter: NUMWAT <- "1117" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1117" Comparing "1075" and "1117". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.36" Parameter: BOX -> "35.36" Parameter: BOX -> "35.36" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.36000 B = 35.36000 C = 35.36000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0533 2 1 -1 -2 -1 13.4456 3 1 -1 -1 -1 4.1252 4 1 -1 0 -1 0.4030 5 1 0 -1 -1 3.3310 6 1 0 0 -1 2.4944 7 1 -1 -1 0 3.0074 8 1 -1 0 0 6.1379 9 1 0 -1 0 4.2306 10 1 0 1 0 4.2306 11 1 0 0 1 2.4944 12 1 0 1 1 3.3310 13 1 2 1 1 10.0533 14 1 1 2 1 13.4456 15 1 1 1 1 4.1252 16 1 1 0 1 0.4030 17 1 1 1 0 3.0074 18 1 1 0 0 6.1379 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3427 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.04 2 C002 has 36 12 12 11.44 3 C003 has 2640 880 880 0.00 4 C004 has 813 271 271 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1218 406 406 0.00 9 C009 has 1209 403 403 0.00 Total of12337 atoms and 4105 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 3427 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 <- "35.358" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1130" Evaluating: 1130-13 Parameter: NUMWAT <- "1117" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1117" Comparing "1075" and "1117". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.358" Parameter: BOX -> "35.358" Parameter: BOX -> "35.358" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.35800 B = 35.35800 C = 35.35800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0508 2 1 -1 -2 -1 13.4425 3 1 -1 -1 -1 4.1251 4 1 -1 0 -1 0.4027 5 1 0 -1 -1 3.3314 6 1 0 0 -1 2.4933 7 1 -1 -1 0 3.0060 8 1 -1 0 0 6.1372 9 1 0 -1 0 4.2299 10 1 0 1 0 4.2299 11 1 0 0 1 2.4933 12 1 0 1 1 3.3314 13 1 2 1 1 10.0508 14 1 1 2 1 13.4425 15 1 1 1 1 4.1251 16 1 1 0 1 0.4027 17 1 1 1 0 3.0060 18 1 1 0 0 6.1372 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3427 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.03 2 C002 has 36 12 12 11.44 3 C003 has 2640 880 880 0.00 4 C004 has 816 272 272 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1218 406 406 0.00 9 C009 has 1209 403 403 0.00 Total of12340 atoms and 4106 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 3427 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 <- "35.356" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1130" Evaluating: 1130-13 Parameter: NUMWAT <- "1117" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1117" Comparing "1075" and "1117". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.356" Parameter: BOX -> "35.356" Parameter: BOX -> "35.356" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.35600 B = 35.35600 C = 35.35600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0483 2 1 -1 -2 -1 13.4394 3 1 -1 -1 -1 4.1251 4 1 -1 0 -1 0.4025 5 1 0 -1 -1 3.3317 6 1 0 0 -1 2.4922 7 1 -1 -1 0 3.0046 8 1 -1 0 0 6.1365 9 1 0 -1 0 4.2292 10 1 0 1 0 4.2292 11 1 0 0 1 2.4922 12 1 0 1 1 3.3317 13 1 2 1 1 10.0483 14 1 1 2 1 13.4394 15 1 1 1 1 4.1251 16 1 1 0 1 0.4025 17 1 1 1 0 3.0046 18 1 1 0 0 6.1365 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3427 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.03 2 C002 has 36 12 12 11.44 3 C003 has 2640 880 880 0.00 4 C004 has 816 272 272 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1218 406 406 0.00 9 C009 has 1209 403 403 0.00 Total of12340 atoms and 4106 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 3427 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 <- "35.354" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1130" Evaluating: 1130-13 Parameter: NUMWAT <- "1117" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1117" Comparing "1075" and "1117". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.354" Parameter: BOX -> "35.354" Parameter: BOX -> "35.354" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.35400 B = 35.35400 C = 35.35400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0458 2 1 -1 -2 -1 13.4363 3 1 -1 -1 -1 4.1250 4 1 -1 0 -1 0.4022 5 1 0 -1 -1 3.3321 6 1 0 0 -1 2.4910 7 1 -1 -1 0 3.0032 8 1 -1 0 0 6.1357 9 1 0 -1 0 4.2286 10 1 0 1 0 4.2286 11 1 0 0 1 2.4910 12 1 0 1 1 3.3321 13 1 2 1 1 10.0458 14 1 1 2 1 13.4363 15 1 1 1 1 4.1250 16 1 1 0 1 0.4022 17 1 1 1 0 3.0032 18 1 1 0 0 6.1357 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3427 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.03 2 C002 has 36 12 12 11.43 3 C003 has 2640 880 880 0.00 4 C004 has 816 272 272 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1218 406 406 0.00 9 C009 has 1209 403 403 0.00 Total of12340 atoms and 4106 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 3427 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 <- "35.352" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1130" Evaluating: 1130-13 Parameter: NUMWAT <- "1117" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1117" Comparing "1075" and "1117". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.352" Parameter: BOX -> "35.352" Parameter: BOX -> "35.352" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.35200 B = 35.35200 C = 35.35200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0432 2 1 -1 -2 -1 13.4332 3 1 -1 -1 -1 4.1249 4 1 -1 0 -1 0.4020 5 1 0 -1 -1 3.3325 6 1 0 0 -1 2.4899 7 1 -1 -1 0 3.0018 8 1 -1 0 0 6.1350 9 1 0 -1 0 4.2279 10 1 0 1 0 4.2279 11 1 0 0 1 2.4899 12 1 0 1 1 3.3325 13 1 2 1 1 10.0432 14 1 1 2 1 13.4332 15 1 1 1 1 4.1249 16 1 1 0 1 0.4020 17 1 1 1 0 3.0018 18 1 1 0 0 6.1350 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3427 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.02 2 C002 has 36 12 12 11.43 3 C003 has 2640 880 880 0.00 4 C004 has 816 272 272 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1218 406 406 0.00 9 C009 has 1209 403 403 0.00 Total of12340 atoms and 4106 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 3427 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 <- "35.35" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1130" Evaluating: 1130-13 Parameter: NUMWAT <- "1117" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1117" Comparing "1075" and "1117". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.35" Parameter: BOX -> "35.35" Parameter: BOX -> "35.35" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.35000 B = 35.35000 C = 35.35000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0407 2 1 -1 -2 -1 13.4300 3 1 -1 -1 -1 4.1248 4 1 -1 0 -1 0.4018 5 1 0 -1 -1 3.3328 6 1 0 0 -1 2.4888 7 1 -1 -1 0 3.0003 8 1 -1 0 0 6.1343 9 1 0 -1 0 4.2272 10 1 0 1 0 4.2272 11 1 0 0 1 2.4888 12 1 0 1 1 3.3328 13 1 2 1 1 10.0407 14 1 1 2 1 13.4300 15 1 1 1 1 4.1248 16 1 1 0 1 0.4018 17 1 1 1 0 3.0003 18 1 1 0 0 6.1343 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3427 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.02 2 C002 has 36 12 12 11.43 3 C003 has 2640 880 880 0.00 4 C004 has 816 272 272 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1218 406 406 0.00 9 C009 has 1209 403 403 0.00 Total of12340 atoms and 4106 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 3427 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 <- "35.348" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1130" Evaluating: 1130-13 Parameter: NUMWAT <- "1117" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1117" Comparing "1075" and "1117". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.348" Parameter: BOX -> "35.348" Parameter: BOX -> "35.348" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.34800 B = 35.34800 C = 35.34800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0382 2 1 -1 -2 -1 13.4269 3 1 -1 -1 -1 4.1248 4 1 -1 0 -1 0.4016 5 1 0 -1 -1 3.3332 6 1 0 0 -1 2.4877 7 1 -1 -1 0 2.9989 8 1 -1 0 0 6.1336 9 1 0 -1 0 4.2266 10 1 0 1 0 4.2266 11 1 0 0 1 2.4877 12 1 0 1 1 3.3332 13 1 2 1 1 10.0382 14 1 1 2 1 13.4269 15 1 1 1 1 4.1248 16 1 1 0 1 0.4016 17 1 1 1 0 2.9989 18 1 1 0 0 6.1336 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3427 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.02 2 C002 has 36 12 12 11.42 3 C003 has 2640 880 880 0.00 4 C004 has 819 273 273 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1218 406 406 0.00 9 C009 has 1209 403 403 0.00 Total of12343 atoms and 4107 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 3427 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 <- "35.346" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1130" Evaluating: 1130-13 Parameter: NUMWAT <- "1117" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1117" Comparing "1075" and "1117". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.346" Parameter: BOX -> "35.346" Parameter: BOX -> "35.346" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.34600 B = 35.34600 C = 35.34600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0357 2 1 -1 -2 -1 13.4238 3 1 -1 -1 -1 4.1247 4 1 -1 0 -1 0.4014 5 1 0 -1 -1 3.3336 6 1 0 0 -1 2.4865 7 1 -1 -1 0 2.9975 8 1 -1 0 0 6.1328 9 1 0 -1 0 4.2259 10 1 0 1 0 4.2259 11 1 0 0 1 2.4865 12 1 0 1 1 3.3336 13 1 2 1 1 10.0357 14 1 1 2 1 13.4238 15 1 1 1 1 4.1247 16 1 1 0 1 0.4014 17 1 1 1 0 2.9975 18 1 1 0 0 6.1328 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3427 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.01 2 C002 has 36 12 12 11.42 3 C003 has 2640 880 880 0.00 4 C004 has 819 273 273 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 816 272 272 0.00 8 C008 has 1218 406 406 0.00 9 C009 has 1209 403 403 0.00 Total of12343 atoms and 4107 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 3427 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 <- "35.344" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1130" Evaluating: 1130-13 Parameter: NUMWAT <- "1117" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1117" Comparing "1075" and "1117". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.344" Parameter: BOX -> "35.344" Parameter: BOX -> "35.344" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.34400 B = 35.34400 C = 35.34400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0332 2 1 -1 -2 -1 13.4207 3 1 -1 -1 -1 4.1246 4 1 -1 0 -1 0.4012 5 1 0 -1 -1 3.3339 6 1 0 0 -1 2.4854 7 1 -1 -1 0 2.9961 8 1 -1 0 0 6.1321 9 1 0 -1 0 4.2252 10 1 0 1 0 4.2252 11 1 0 0 1 2.4854 12 1 0 1 1 3.3339 13 1 2 1 1 10.0332 14 1 1 2 1 13.4207 15 1 1 1 1 4.1246 16 1 1 0 1 0.4012 17 1 1 1 0 2.9961 18 1 1 0 0 6.1321 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3427 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.01 2 C002 has 36 12 12 11.42 3 C003 has 2640 880 880 0.00 4 C004 has 819 273 273 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1218 406 406 0.00 9 C009 has 1209 403 403 0.00 Total of12349 atoms and 4109 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 3427 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 <- "35.342" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1130" Evaluating: 1130-13 Parameter: NUMWAT <- "1117" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1117" Comparing "1075" and "1117". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.342" Parameter: BOX -> "35.342" Parameter: BOX -> "35.342" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.34200 B = 35.34200 C = 35.34200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0306 2 1 -1 -2 -1 13.4176 3 1 -1 -1 -1 4.1245 4 1 -1 0 -1 0.4011 5 1 0 -1 -1 3.3343 6 1 0 0 -1 2.4843 7 1 -1 -1 0 2.9947 8 1 -1 0 0 6.1314 9 1 0 -1 0 4.2246 10 1 0 1 0 4.2246 11 1 0 0 1 2.4843 12 1 0 1 1 3.3343 13 1 2 1 1 10.0306 14 1 1 2 1 13.4176 15 1 1 1 1 4.1245 16 1 1 0 1 0.4011 17 1 1 1 0 2.9947 18 1 1 0 0 6.1314 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3427 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.01 2 C002 has 36 12 12 11.42 3 C003 has 2640 880 880 0.00 4 C004 has 819 273 273 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1218 406 406 0.00 9 C009 has 1209 403 403 0.00 Total of12349 atoms and 4109 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 3427 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 <- "35.34" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1130" Evaluating: 1130-13 Parameter: NUMWAT <- "1117" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1117" Comparing "1075" and "1117". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.34" Parameter: BOX -> "35.34" Parameter: BOX -> "35.34" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.34000 B = 35.34000 C = 35.34000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0281 2 1 -1 -2 -1 13.4144 3 1 -1 -1 -1 4.1245 4 1 -1 0 -1 0.4009 5 1 0 -1 -1 3.3347 6 1 0 0 -1 2.4832 7 1 -1 -1 0 2.9933 8 1 -1 0 0 6.1307 9 1 0 -1 0 4.2239 10 1 0 1 0 4.2239 11 1 0 0 1 2.4832 12 1 0 1 1 3.3347 13 1 2 1 1 10.0281 14 1 1 2 1 13.4144 15 1 1 1 1 4.1245 16 1 1 0 1 0.4009 17 1 1 1 0 2.9933 18 1 1 0 0 6.1307 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3427 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.01 2 C002 has 36 12 12 11.41 3 C003 has 2640 880 880 0.00 4 C004 has 819 273 273 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1218 406 406 0.00 9 C009 has 1209 403 403 0.00 Total of12349 atoms and 4109 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 3427 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 <- "35.338" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1130" Evaluating: 1130-13 Parameter: NUMWAT <- "1117" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1117" Comparing "1075" and "1117". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.338" Parameter: BOX -> "35.338" Parameter: BOX -> "35.338" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.33800 B = 35.33800 C = 35.33800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0256 2 1 -1 -2 -1 13.4113 3 1 -1 -1 -1 4.1244 4 1 -1 0 -1 0.4008 5 1 0 -1 -1 3.3350 6 1 0 0 -1 2.4821 7 1 -1 -1 0 2.9919 8 1 -1 0 0 6.1300 9 1 0 -1 0 4.2233 10 1 0 1 0 4.2233 11 1 0 0 1 2.4821 12 1 0 1 1 3.3350 13 1 2 1 1 10.0256 14 1 1 2 1 13.4113 15 1 1 1 1 4.1244 16 1 1 0 1 0.4008 17 1 1 1 0 2.9919 18 1 1 0 0 6.1300 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3427 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.00 2 C002 has 36 12 12 11.41 3 C003 has 2640 880 880 0.00 4 C004 has 822 274 274 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1218 406 406 0.00 9 C009 has 1209 403 403 0.00 Total of12352 atoms and 4110 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 3427 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 <- "35.336" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1130" Evaluating: 1130-13 Parameter: NUMWAT <- "1117" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1117" Comparing "1075" and "1117". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.336" Parameter: BOX -> "35.336" Parameter: BOX -> "35.336" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.33600 B = 35.33600 C = 35.33600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0231 2 1 -1 -2 -1 13.4082 3 1 -1 -1 -1 4.1243 4 1 -1 0 -1 0.4007 5 1 0 -1 -1 3.3354 6 1 0 0 -1 2.4810 7 1 -1 -1 0 2.9905 8 1 -1 0 0 6.1292 9 1 0 -1 0 4.2226 10 1 0 1 0 4.2226 11 1 0 0 1 2.4810 12 1 0 1 1 3.3354 13 1 2 1 1 10.0231 14 1 1 2 1 13.4082 15 1 1 1 1 4.1243 16 1 1 0 1 0.4007 17 1 1 1 0 2.9905 18 1 1 0 0 6.1292 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3427 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 183 61 61 6.00 2 C002 has 36 12 12 11.41 3 C003 has 2640 880 880 0.00 4 C004 has 822 274 274 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1218 406 406 0.00 9 C009 has 1209 403 403 0.00 Total of12352 atoms and 4110 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 3427 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 <- "35.334" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1130" Evaluating: 1130-13 Parameter: NUMWAT <- "1117" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1117" Comparing "1075" and "1117". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.334" Parameter: BOX -> "35.334" Parameter: BOX -> "35.334" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.33400 B = 35.33400 C = 35.33400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0206 2 1 -1 -2 -1 13.4051 3 1 -1 -1 -1 4.1243 4 1 -1 0 -1 0.4006 5 1 0 -1 -1 3.3358 6 1 0 0 -1 2.4799 7 1 -1 -1 0 2.9891 8 1 -1 0 0 6.1285 9 1 0 -1 0 4.2219 10 1 0 1 0 4.2219 11 1 0 0 1 2.4799 12 1 0 1 1 3.3358 13 1 2 1 1 10.0206 14 1 1 2 1 13.4051 15 1 1 1 1 4.1243 16 1 1 0 1 0.4006 17 1 1 1 0 2.9891 18 1 1 0 0 6.1285 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3427 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 6.00 2 C002 has 36 12 12 11.40 3 C003 has 2640 880 880 0.00 4 C004 has 822 274 274 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1143 381 381 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1218 406 406 0.00 9 C009 has 1209 403 403 0.00 Total of12358 atoms and 4112 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 3427 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 = 3427 Number of groups = 1135 Number of bonds = 3421 Number of angles = 1239 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1133 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 <- "35.332" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1130" Evaluating: 1130-13 Parameter: NUMWAT <- "1117" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1117" Comparing "1075" and "1117". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.332" Parameter: BOX -> "35.332" Parameter: BOX -> "35.332" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.33200 B = 35.33200 C = 35.33200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0180 2 1 -1 -2 -1 13.4019 3 1 -1 -1 -1 4.1242 4 1 -1 0 -1 0.4005 5 1 0 -1 -1 3.3362 6 1 0 0 -1 2.4787 7 1 -1 -1 0 2.9877 8 1 -1 0 0 6.1278 9 1 0 -1 0 4.2213 10 1 0 1 0 4.2213 11 1 0 0 1 2.4787 12 1 0 1 1 3.3362 13 1 2 1 1 10.0180 14 1 1 2 1 13.4019 15 1 1 1 1 4.1242 16 1 1 0 1 0.4005 17 1 1 1 0 2.9877 18 1 1 0 0 6.1278 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3427 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 455 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.99 2 C002 has 36 12 12 11.40 3 C003 has 2643 881 881 0.00 4 C004 has 825 275 275 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1134 378 378 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1215 405 405 0.00 9 C009 has 1209 403 403 0.00 Total of12349 atoms and 4109 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> 3 atoms have been selected out of 3427 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 = 3424 Number of groups = 1134 Number of bonds = 3418 Number of angles = 1238 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1132 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 = 3424 Number of groups = 1134 Number of bonds = 3418 Number of angles = 1238 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1132 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 <- "35.33" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1129" Evaluating: 1129-13 Parameter: NUMWAT <- "1116" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1116" Comparing "1075" and "1116". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.33" Parameter: BOX -> "35.33" Parameter: BOX -> "35.33" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.33000 B = 35.33000 C = 35.33000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0155 2 1 -1 -2 -1 13.3988 3 1 -1 -1 -1 4.1241 4 1 -1 0 -1 0.4004 5 1 0 -1 -1 3.3366 6 1 0 0 -1 2.4776 7 1 -1 -1 0 2.9863 8 1 -1 0 0 6.1271 9 1 0 -1 0 4.2206 10 1 0 1 0 4.2206 11 1 0 0 1 2.4776 12 1 0 1 1 3.3366 13 1 2 1 1 10.0155 14 1 1 2 1 13.3988 15 1 1 1 1 4.1241 16 1 1 0 1 0.4004 17 1 1 1 0 2.9863 18 1 1 0 0 6.1271 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3424 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.99 2 C002 has 36 12 12 11.40 3 C003 has 2640 880 880 0.00 4 C004 has 822 274 274 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1131 377 377 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1215 405 405 0.00 9 C009 has 1209 403 403 0.00 Total of12337 atoms and 4105 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 3424 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3424 Number of groups = 1134 Number of bonds = 3418 Number of angles = 1238 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1132 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 = 3424 Number of groups = 1134 Number of bonds = 3418 Number of angles = 1238 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1132 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 <- "35.328" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1129" Evaluating: 1129-13 Parameter: NUMWAT <- "1116" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1116" Comparing "1075" and "1116". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.328" Parameter: BOX -> "35.328" Parameter: BOX -> "35.328" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.32800 B = 35.32800 C = 35.32800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0130 2 1 -1 -2 -1 13.3957 3 1 -1 -1 -1 4.1241 4 1 -1 0 -1 0.4003 5 1 0 -1 -1 3.3369 6 1 0 0 -1 2.4765 7 1 -1 -1 0 2.9849 8 1 -1 0 0 6.1264 9 1 0 -1 0 4.2200 10 1 0 1 0 4.2200 11 1 0 0 1 2.4765 12 1 0 1 1 3.3369 13 1 2 1 1 10.0130 14 1 1 2 1 13.3957 15 1 1 1 1 4.1241 16 1 1 0 1 0.4003 17 1 1 1 0 2.9849 18 1 1 0 0 6.1264 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3424 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.99 2 C002 has 36 12 12 11.39 3 C003 has 2640 880 880 0.00 4 C004 has 822 274 274 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1131 377 377 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1215 405 405 0.00 9 C009 has 1209 403 403 0.00 Total of12340 atoms and 4106 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 3424 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3424 Number of groups = 1134 Number of bonds = 3418 Number of angles = 1238 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1132 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 = 3424 Number of groups = 1134 Number of bonds = 3418 Number of angles = 1238 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1132 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 <- "35.326" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1129" Evaluating: 1129-13 Parameter: NUMWAT <- "1116" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1116" Comparing "1075" and "1116". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.326" Parameter: BOX -> "35.326" Parameter: BOX -> "35.326" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.32600 B = 35.32600 C = 35.32600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0105 2 1 -1 -2 -1 13.3926 3 1 -1 -1 -1 4.1240 4 1 -1 0 -1 0.4003 5 1 0 -1 -1 3.3373 6 1 0 0 -1 2.4754 7 1 -1 -1 0 2.9835 8 1 -1 0 0 6.1257 9 1 0 -1 0 4.2193 10 1 0 1 0 4.2193 11 1 0 0 1 2.4754 12 1 0 1 1 3.3373 13 1 2 1 1 10.0105 14 1 1 2 1 13.3926 15 1 1 1 1 4.1240 16 1 1 0 1 0.4003 17 1 1 1 0 2.9835 18 1 1 0 0 6.1257 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3424 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.98 2 C002 has 36 12 12 11.39 3 C003 has 2640 880 880 0.00 4 C004 has 822 274 274 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1131 377 377 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1215 405 405 0.00 9 C009 has 1209 403 403 0.00 Total of12340 atoms and 4106 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 3424 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3424 Number of groups = 1134 Number of bonds = 3418 Number of angles = 1238 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1132 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 = 3424 Number of groups = 1134 Number of bonds = 3418 Number of angles = 1238 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1132 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 <- "35.324" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1129" Evaluating: 1129-13 Parameter: NUMWAT <- "1116" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1116" Comparing "1075" and "1116". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.324" Parameter: BOX -> "35.324" Parameter: BOX -> "35.324" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.32400 B = 35.32400 C = 35.32400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0080 2 1 -1 -2 -1 13.3895 3 1 -1 -1 -1 4.1239 4 1 -1 0 -1 0.4003 5 1 0 -1 -1 3.3377 6 1 0 0 -1 2.4743 7 1 -1 -1 0 2.9821 8 1 -1 0 0 6.1250 9 1 0 -1 0 4.2187 10 1 0 1 0 4.2187 11 1 0 0 1 2.4743 12 1 0 1 1 3.3377 13 1 2 1 1 10.0080 14 1 1 2 1 13.3895 15 1 1 1 1 4.1239 16 1 1 0 1 0.4003 17 1 1 1 0 2.9821 18 1 1 0 0 6.1250 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3424 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.98 2 C002 has 36 12 12 11.39 3 C003 has 2640 880 880 0.00 4 C004 has 822 274 274 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1131 377 377 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1215 405 405 0.00 9 C009 has 1209 403 403 0.00 Total of12340 atoms and 4106 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 3424 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3424 Number of groups = 1134 Number of bonds = 3418 Number of angles = 1238 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1132 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 = 3424 Number of groups = 1134 Number of bonds = 3418 Number of angles = 1238 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1132 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 <- "35.322" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1129" Evaluating: 1129-13 Parameter: NUMWAT <- "1116" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1116" Comparing "1075" and "1116". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.322" Parameter: BOX -> "35.322" Parameter: BOX -> "35.322" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.32200 B = 35.32200 C = 35.32200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0055 2 1 -1 -2 -1 13.3863 3 1 -1 -1 -1 4.1239 4 1 -1 0 -1 0.4002 5 1 0 -1 -1 3.3381 6 1 0 0 -1 2.4732 7 1 -1 -1 0 2.9807 8 1 -1 0 0 6.1242 9 1 0 -1 0 4.2180 10 1 0 1 0 4.2180 11 1 0 0 1 2.4732 12 1 0 1 1 3.3381 13 1 2 1 1 10.0055 14 1 1 2 1 13.3863 15 1 1 1 1 4.1239 16 1 1 0 1 0.4002 17 1 1 1 0 2.9807 18 1 1 0 0 6.1242 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3424 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.98 2 C002 has 36 12 12 11.38 3 C003 has 2640 880 880 0.00 4 C004 has 822 274 274 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1131 377 377 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1215 405 405 0.00 9 C009 has 1209 403 403 0.00 Total of12340 atoms and 4106 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 3424 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3424 Number of groups = 1134 Number of bonds = 3418 Number of angles = 1238 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1132 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 = 3424 Number of groups = 1134 Number of bonds = 3418 Number of angles = 1238 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1132 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 <- "35.32" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1129" Evaluating: 1129-13 Parameter: NUMWAT <- "1116" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1116" Comparing "1075" and "1116". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.32" Parameter: BOX -> "35.32" Parameter: BOX -> "35.32" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.32000 B = 35.32000 C = 35.32000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0029 2 1 -1 -2 -1 13.3832 3 1 -1 -1 -1 4.1238 4 1 -1 0 -1 0.4002 5 1 0 -1 -1 3.3385 6 1 0 0 -1 2.4721 7 1 -1 -1 0 2.9793 8 1 -1 0 0 6.1235 9 1 0 -1 0 4.2174 10 1 0 1 0 4.2174 11 1 0 0 1 2.4721 12 1 0 1 1 3.3385 13 1 2 1 1 10.0029 14 1 1 2 1 13.3832 15 1 1 1 1 4.1238 16 1 1 0 1 0.4002 17 1 1 1 0 2.9793 18 1 1 0 0 6.1235 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3424 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 75 OPERATED ON BY TRANSFORMATION C015 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.97 2 C002 has 36 12 12 11.38 3 C003 has 2643 881 881 0.00 4 C004 has 825 275 275 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1134 378 378 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1218 406 406 0.00 9 C009 has 1206 402 402 0.00 Total of12349 atoms and 4109 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> 3 atoms have been selected out of 3424 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 = 3421 Number of groups = 1133 Number of bonds = 3415 Number of angles = 1237 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1131 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 = 3421 Number of groups = 1133 Number of bonds = 3415 Number of angles = 1237 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1131 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 <- "35.318" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1128" Evaluating: 1128-13 Parameter: NUMWAT <- "1115" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1115" Comparing "1075" and "1115". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.318" Parameter: BOX -> "35.318" Parameter: BOX -> "35.318" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.31800 B = 35.31800 C = 35.31800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 10.0004 2 1 -1 -2 -1 13.3801 3 1 -1 -1 -1 2.4182 4 1 -1 0 -1 0.4002 5 1 0 -1 -1 3.3389 6 1 0 0 -1 2.4710 7 1 -1 -1 0 2.9779 8 1 -1 0 0 6.1228 9 1 0 -1 0 2.7693 10 1 0 1 0 2.7693 11 1 0 0 1 2.4710 12 1 0 1 1 3.3389 13 1 2 1 1 10.0004 14 1 1 2 1 13.3801 15 1 1 1 1 2.4182 16 1 1 0 1 0.4002 17 1 1 1 0 2.9779 18 1 1 0 0 6.1228 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3421 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.97 2 C002 has 36 12 12 11.38 3 C003 has 2640 880 880 0.00 4 C004 has 822 274 274 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1131 377 377 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1215 405 405 0.00 9 C009 has 1206 402 402 0.00 Total of12334 atoms and 4104 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 3421 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3421 Number of groups = 1133 Number of bonds = 3415 Number of angles = 1237 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1131 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 = 3421 Number of groups = 1133 Number of bonds = 3415 Number of angles = 1237 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1131 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 <- "35.316" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1128" Evaluating: 1128-13 Parameter: NUMWAT <- "1115" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1115" Comparing "1075" and "1115". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.316" Parameter: BOX -> "35.316" Parameter: BOX -> "35.316" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.31600 B = 35.31600 C = 35.31600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9979 2 1 -1 -2 -1 13.3770 3 1 -1 -1 -1 2.4162 4 1 -1 0 -1 0.4002 5 1 0 -1 -1 3.3393 6 1 0 0 -1 2.4699 7 1 -1 -1 0 2.9765 8 1 -1 0 0 6.1221 9 1 0 -1 0 2.7684 10 1 0 1 0 2.7684 11 1 0 0 1 2.4699 12 1 0 1 1 3.3393 13 1 2 1 1 9.9979 14 1 1 2 1 13.3770 15 1 1 1 1 2.4162 16 1 1 0 1 0.4002 17 1 1 1 0 2.9765 18 1 1 0 0 6.1221 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3421 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 309 OPERATED ON BY TRANSFORMATION C009 RESIDUE 793 OPERATED ON BY TRANSFORMATION C004 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.97 2 C002 has 36 12 12 11.38 3 C003 has 2634 878 878 0.00 4 C004 has 825 275 275 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1128 376 376 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1206 402 402 0.00 Total of12325 atoms and 4101 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> 6 atoms have been selected out of 3421 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 = 3415 Number of groups = 1131 Number of bonds = 3409 Number of angles = 1235 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1129 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 = 3415 Number of groups = 1131 Number of bonds = 3409 Number of angles = 1235 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1129 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 <- "35.314" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1126" Evaluating: 1126-13 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1113" Comparing "1075" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.314" Parameter: BOX -> "35.314" Parameter: BOX -> "35.314" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.31400 B = 35.31400 C = 35.31400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9954 2 1 -1 -2 -1 13.3739 3 1 -1 -1 -1 2.4142 4 1 -1 0 -1 0.4003 5 1 0 -1 -1 3.3397 6 1 0 0 -1 2.4688 7 1 -1 -1 0 2.9751 8 1 -1 0 0 6.1214 9 1 0 -1 0 2.7674 10 1 0 1 0 2.7674 11 1 0 0 1 2.4688 12 1 0 1 1 3.3397 13 1 2 1 1 9.9954 14 1 1 2 1 13.3739 15 1 1 1 1 2.4142 16 1 1 0 1 0.4003 17 1 1 1 0 2.9751 18 1 1 0 0 6.1214 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3415 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.97 2 C002 has 36 12 12 11.37 3 C003 has 2634 878 878 0.00 4 C004 has 819 273 273 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1128 376 376 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1203 401 401 0.00 Total of12310 atoms and 4096 groups and 4091 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3415 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3415 Number of groups = 1131 Number of bonds = 3409 Number of angles = 1235 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1129 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 = 3415 Number of groups = 1131 Number of bonds = 3409 Number of angles = 1235 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1129 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 <- "35.312" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1126" Evaluating: 1126-13 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1113" Comparing "1075" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.312" Parameter: BOX -> "35.312" Parameter: BOX -> "35.312" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.31200 B = 35.31200 C = 35.31200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9929 2 1 -1 -2 -1 13.3707 3 1 -1 -1 -1 2.4122 4 1 -1 0 -1 0.4003 5 1 0 -1 -1 3.3400 6 1 0 0 -1 2.4677 7 1 -1 -1 0 2.9737 8 1 -1 0 0 6.1207 9 1 0 -1 0 2.7665 10 1 0 1 0 2.7665 11 1 0 0 1 2.4677 12 1 0 1 1 3.3400 13 1 2 1 1 9.9929 14 1 1 2 1 13.3707 15 1 1 1 1 2.4122 16 1 1 0 1 0.4003 17 1 1 1 0 2.9737 18 1 1 0 0 6.1207 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3415 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.96 2 C002 has 36 12 12 11.37 3 C003 has 2634 878 878 0.00 4 C004 has 819 273 273 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1128 376 376 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1203 401 401 0.00 Total of12310 atoms and 4096 groups and 4091 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3415 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3415 Number of groups = 1131 Number of bonds = 3409 Number of angles = 1235 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1129 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 = 3415 Number of groups = 1131 Number of bonds = 3409 Number of angles = 1235 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1129 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 <- "35.31" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1126" Evaluating: 1126-13 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1113" Comparing "1075" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.31" Parameter: BOX -> "35.31" Parameter: BOX -> "35.31" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.31000 B = 35.31000 C = 35.31000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9904 2 1 -1 -2 -1 13.3676 3 1 -1 -1 -1 2.4103 4 1 -1 0 -1 0.4004 5 1 0 -1 -1 3.3404 6 1 0 0 -1 2.4666 7 1 -1 -1 0 2.9723 8 1 -1 0 0 6.1200 9 1 0 -1 0 2.7655 10 1 0 1 0 2.7655 11 1 0 0 1 2.4666 12 1 0 1 1 3.3404 13 1 2 1 1 9.9904 14 1 1 2 1 13.3676 15 1 1 1 1 2.4103 16 1 1 0 1 0.4004 17 1 1 1 0 2.9723 18 1 1 0 0 6.1200 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3415 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.96 2 C002 has 36 12 12 11.37 3 C003 has 2634 878 878 0.00 4 C004 has 819 273 273 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1128 376 376 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1203 401 401 0.00 Total of12310 atoms and 4096 groups and 4091 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3415 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3415 Number of groups = 1131 Number of bonds = 3409 Number of angles = 1235 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1129 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 = 3415 Number of groups = 1131 Number of bonds = 3409 Number of angles = 1235 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1129 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 <- "35.308" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1126" Evaluating: 1126-13 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1113" Comparing "1075" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.308" Parameter: BOX -> "35.308" Parameter: BOX -> "35.308" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.30800 B = 35.30800 C = 35.30800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9879 2 1 -1 -2 -1 13.3645 3 1 -1 -1 -1 2.4083 4 1 -1 0 -1 0.4004 5 1 0 -1 -1 3.3408 6 1 0 0 -1 2.4655 7 1 -1 -1 0 2.9709 8 1 -1 0 0 6.1193 9 1 0 -1 0 2.7646 10 1 0 1 0 2.7646 11 1 0 0 1 2.4655 12 1 0 1 1 3.3408 13 1 2 1 1 9.9879 14 1 1 2 1 13.3645 15 1 1 1 1 2.4083 16 1 1 0 1 0.4004 17 1 1 1 0 2.9709 18 1 1 0 0 6.1193 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3415 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.96 2 C002 has 36 12 12 11.36 3 C003 has 2634 878 878 0.00 4 C004 has 819 273 273 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1128 376 376 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1203 401 401 0.00 Total of12310 atoms and 4096 groups and 4091 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3415 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3415 Number of groups = 1131 Number of bonds = 3409 Number of angles = 1235 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1129 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 = 3415 Number of groups = 1131 Number of bonds = 3409 Number of angles = 1235 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1129 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 <- "35.306" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1126" Evaluating: 1126-13 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1113" Comparing "1075" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.306" Parameter: BOX -> "35.306" Parameter: BOX -> "35.306" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.30600 B = 35.30600 C = 35.30600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9853 2 1 -1 -2 -1 13.3614 3 1 -1 -1 -1 2.4063 4 1 -1 0 -1 0.4005 5 1 0 -1 -1 3.3412 6 1 0 0 -1 2.4644 7 1 -1 -1 0 2.9695 8 1 -1 0 0 6.1185 9 1 0 -1 0 2.7637 10 1 0 1 0 2.7637 11 1 0 0 1 2.4644 12 1 0 1 1 3.3412 13 1 2 1 1 9.9853 14 1 1 2 1 13.3614 15 1 1 1 1 2.4063 16 1 1 0 1 0.4005 17 1 1 1 0 2.9695 18 1 1 0 0 6.1185 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3415 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.95 2 C002 has 36 12 12 11.36 3 C003 has 2634 878 878 0.00 4 C004 has 819 273 273 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1128 376 376 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1203 401 401 0.00 Total of12310 atoms and 4096 groups and 4091 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3415 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3415 Number of groups = 1131 Number of bonds = 3409 Number of angles = 1235 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1129 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 = 3415 Number of groups = 1131 Number of bonds = 3409 Number of angles = 1235 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1129 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 <- "35.304" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1126" Evaluating: 1126-13 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1113" Comparing "1075" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.304" Parameter: BOX -> "35.304" Parameter: BOX -> "35.304" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.30400 B = 35.30400 C = 35.30400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9828 2 1 -1 -2 -1 13.3583 3 1 -1 -1 -1 2.4043 4 1 -1 0 -1 0.4006 5 1 0 -1 -1 3.3416 6 1 0 0 -1 2.4633 7 1 -1 -1 0 2.9682 8 1 -1 0 0 6.1178 9 1 0 -1 0 2.7627 10 1 0 1 0 2.7627 11 1 0 0 1 2.4633 12 1 0 1 1 3.3416 13 1 2 1 1 9.9828 14 1 1 2 1 13.3583 15 1 1 1 1 2.4043 16 1 1 0 1 0.4006 17 1 1 1 0 2.9682 18 1 1 0 0 6.1178 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3415 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.95 2 C002 has 36 12 12 11.36 3 C003 has 2637 879 879 0.00 4 C004 has 819 273 273 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1128 376 376 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1206 402 402 0.00 Total of12316 atoms and 4098 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 3415 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3415 Number of groups = 1131 Number of bonds = 3409 Number of angles = 1235 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1129 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 = 3415 Number of groups = 1131 Number of bonds = 3409 Number of angles = 1235 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1129 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 <- "35.302" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1126" Evaluating: 1126-13 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1113" Comparing "1075" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.302" Parameter: BOX -> "35.302" Parameter: BOX -> "35.302" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.30200 B = 35.30200 C = 35.30200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9803 2 1 -1 -2 -1 13.3552 3 1 -1 -1 -1 2.4023 4 1 -1 0 -1 0.4007 5 1 0 -1 -1 3.3420 6 1 0 0 -1 2.4622 7 1 -1 -1 0 2.9668 8 1 -1 0 0 6.1171 9 1 0 -1 0 2.7618 10 1 0 1 0 2.7618 11 1 0 0 1 2.4622 12 1 0 1 1 3.3420 13 1 2 1 1 9.9803 14 1 1 2 1 13.3552 15 1 1 1 1 2.4023 16 1 1 0 1 0.4007 17 1 1 1 0 2.9668 18 1 1 0 0 6.1171 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3415 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.95 2 C002 has 36 12 12 11.35 3 C003 has 2640 880 880 0.00 4 C004 has 819 273 273 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1128 376 376 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1206 402 402 0.00 Total of12319 atoms and 4099 groups and 4094 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3415 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3415 Number of groups = 1131 Number of bonds = 3409 Number of angles = 1235 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1129 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 = 3415 Number of groups = 1131 Number of bonds = 3409 Number of angles = 1235 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1129 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 <- "35.3" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1126" Evaluating: 1126-13 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1113" Comparing "1075" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.3" Parameter: BOX -> "35.3" Parameter: BOX -> "35.3" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.30000 B = 35.30000 C = 35.30000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9778 2 1 -1 -2 -1 13.3520 3 1 -1 -1 -1 2.4003 4 1 -1 0 -1 0.4008 5 1 0 -1 -1 3.3424 6 1 0 0 -1 2.4611 7 1 -1 -1 0 2.9654 8 1 -1 0 0 6.1164 9 1 0 -1 0 2.7608 10 1 0 1 0 2.7608 11 1 0 0 1 2.4611 12 1 0 1 1 3.3424 13 1 2 1 1 9.9778 14 1 1 2 1 13.3520 15 1 1 1 1 2.4003 16 1 1 0 1 0.4008 17 1 1 1 0 2.9654 18 1 1 0 0 6.1164 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3415 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.94 2 C002 has 36 12 12 11.35 3 C003 has 2640 880 880 0.00 4 C004 has 819 273 273 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1128 376 376 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1206 402 402 0.00 Total of12319 atoms and 4099 groups and 4094 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3415 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3415 Number of groups = 1131 Number of bonds = 3409 Number of angles = 1235 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1129 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 = 3415 Number of groups = 1131 Number of bonds = 3409 Number of angles = 1235 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1129 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 <- "35.298" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1126" Evaluating: 1126-13 Parameter: NUMWAT <- "1113" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1113" Comparing "1075" and "1113". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.298" Parameter: BOX -> "35.298" Parameter: BOX -> "35.298" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.29800 B = 35.29800 C = 35.29800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9753 2 1 -1 -2 -1 13.3489 3 1 -1 -1 -1 2.3983 4 1 -1 0 -1 0.4010 5 1 0 -1 -1 3.3428 6 1 0 0 -1 2.4600 7 1 -1 -1 0 2.9640 8 1 -1 0 0 6.1157 9 1 0 -1 0 2.7599 10 1 0 1 0 2.7599 11 1 0 0 1 2.4600 12 1 0 1 1 3.3428 13 1 2 1 1 9.9753 14 1 1 2 1 13.3489 15 1 1 1 1 2.3983 16 1 1 0 1 0.4010 17 1 1 1 0 2.9640 18 1 1 0 0 6.1157 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3415 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 377 OPERATED ON BY TRANSFORMATION C018 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 189 63 63 5.94 2 C002 has 36 12 12 11.35 3 C003 has 2640 880 880 0.00 4 C004 has 819 273 273 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1131 377 377 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1215 405 405 0.00 9 C009 has 1203 401 401 0.00 Total of12325 atoms and 4101 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> 3 atoms have been selected out of 3415 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 = 3412 Number of groups = 1130 Number of bonds = 3406 Number of angles = 1234 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1128 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 = 3412 Number of groups = 1130 Number of bonds = 3406 Number of angles = 1234 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1128 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 <- "35.296" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1125" Evaluating: 1125-13 Parameter: NUMWAT <- "1112" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1112" Comparing "1075" and "1112". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.296" Parameter: BOX -> "35.296" Parameter: BOX -> "35.296" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.29600 B = 35.29600 C = 35.29600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9728 2 1 -1 -2 -1 13.3458 3 1 -1 -1 -1 2.3964 4 1 -1 0 -1 0.4011 5 1 0 -1 -1 3.3433 6 1 0 0 -1 2.4589 7 1 -1 -1 0 2.9626 8 1 -1 0 0 6.1150 9 1 0 -1 0 2.7590 10 1 0 1 0 2.7590 11 1 0 0 1 2.4589 12 1 0 1 1 3.3433 13 1 2 1 1 9.9728 14 1 1 2 1 13.3458 15 1 1 1 1 2.3964 16 1 1 0 1 0.4011 17 1 1 1 0 2.9626 18 1 1 0 0 6.1150 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3412 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.94 2 C002 has 36 12 12 11.34 3 C003 has 2637 879 879 0.00 4 C004 has 819 273 273 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1131 377 377 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1203 401 401 0.00 Total of12310 atoms and 4096 groups and 4091 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3412 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3412 Number of groups = 1130 Number of bonds = 3406 Number of angles = 1234 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1128 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 = 3412 Number of groups = 1130 Number of bonds = 3406 Number of angles = 1234 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1128 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 <- "35.294" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1125" Evaluating: 1125-13 Parameter: NUMWAT <- "1112" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1112" Comparing "1075" and "1112". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.294" Parameter: BOX -> "35.294" Parameter: BOX -> "35.294" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.29400 B = 35.29400 C = 35.29400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9703 2 1 -1 -2 -1 13.3427 3 1 -1 -1 -1 2.3944 4 1 -1 0 -1 0.4013 5 1 0 -1 -1 3.3437 6 1 0 0 -1 2.4578 7 1 -1 -1 0 2.9612 8 1 -1 0 0 6.1143 9 1 0 -1 0 2.7580 10 1 0 1 0 2.7580 11 1 0 0 1 2.4578 12 1 0 1 1 3.3437 13 1 2 1 1 9.9703 14 1 1 2 1 13.3427 15 1 1 1 1 2.3944 16 1 1 0 1 0.4013 17 1 1 1 0 2.9612 18 1 1 0 0 6.1143 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3412 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.93 2 C002 has 36 12 12 11.34 3 C003 has 2637 879 879 0.00 4 C004 has 819 273 273 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1131 377 377 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1203 401 401 0.00 Total of12310 atoms and 4096 groups and 4091 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3412 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3412 Number of groups = 1130 Number of bonds = 3406 Number of angles = 1234 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1128 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 = 3412 Number of groups = 1130 Number of bonds = 3406 Number of angles = 1234 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1128 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 <- "35.292" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1125" Evaluating: 1125-13 Parameter: NUMWAT <- "1112" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1112" Comparing "1075" and "1112". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.292" Parameter: BOX -> "35.292" Parameter: BOX -> "35.292" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.29200 B = 35.29200 C = 35.29200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9678 2 1 -1 -2 -1 13.3396 3 1 -1 -1 -1 2.3924 4 1 -1 0 -1 0.4015 5 1 0 -1 -1 3.3441 6 1 0 0 -1 2.4567 7 1 -1 -1 0 2.9599 8 1 -1 0 0 6.1136 9 1 0 -1 0 2.7571 10 1 0 1 0 2.7571 11 1 0 0 1 2.4567 12 1 0 1 1 3.3441 13 1 2 1 1 9.9678 14 1 1 2 1 13.3396 15 1 1 1 1 2.3924 16 1 1 0 1 0.4015 17 1 1 1 0 2.9599 18 1 1 0 0 6.1136 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3412 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.93 2 C002 has 36 12 12 11.34 3 C003 has 2637 879 879 0.00 4 C004 has 819 273 273 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1131 377 377 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1203 401 401 0.00 Total of12310 atoms and 4096 groups and 4091 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3412 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3412 Number of groups = 1130 Number of bonds = 3406 Number of angles = 1234 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1128 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 = 3412 Number of groups = 1130 Number of bonds = 3406 Number of angles = 1234 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1128 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 <- "35.29" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1125" Evaluating: 1125-13 Parameter: NUMWAT <- "1112" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1112" Comparing "1075" and "1112". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.29" Parameter: BOX -> "35.29" Parameter: BOX -> "35.29" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.29000 B = 35.29000 C = 35.29000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9653 2 1 -1 -2 -1 13.3364 3 1 -1 -1 -1 2.3904 4 1 -1 0 -1 0.4016 5 1 0 -1 -1 3.3445 6 1 0 0 -1 2.4557 7 1 -1 -1 0 2.9585 8 1 -1 0 0 6.1129 9 1 0 -1 0 2.7562 10 1 0 1 0 2.7562 11 1 0 0 1 2.4557 12 1 0 1 1 3.3445 13 1 2 1 1 9.9653 14 1 1 2 1 13.3364 15 1 1 1 1 2.3904 16 1 1 0 1 0.4016 17 1 1 1 0 2.9585 18 1 1 0 0 6.1129 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3412 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.93 2 C002 has 36 12 12 11.34 3 C003 has 2637 879 879 0.00 4 C004 has 819 273 273 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1134 378 378 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1203 401 401 0.00 Total of12313 atoms and 4097 groups and 4092 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3412 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3412 Number of groups = 1130 Number of bonds = 3406 Number of angles = 1234 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1128 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 = 3412 Number of groups = 1130 Number of bonds = 3406 Number of angles = 1234 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1128 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 <- "35.288" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1125" Evaluating: 1125-13 Parameter: NUMWAT <- "1112" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1112" Comparing "1075" and "1112". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.288" Parameter: BOX -> "35.288" Parameter: BOX -> "35.288" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.28800 B = 35.28800 C = 35.28800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9628 2 1 -1 -2 -1 13.3333 3 1 -1 -1 -1 2.3884 4 1 -1 0 -1 0.4018 5 1 0 -1 -1 3.3449 6 1 0 0 -1 2.4546 7 1 -1 -1 0 2.9571 8 1 -1 0 0 6.1122 9 1 0 -1 0 2.7552 10 1 0 1 0 2.7552 11 1 0 0 1 2.4546 12 1 0 1 1 3.3449 13 1 2 1 1 9.9628 14 1 1 2 1 13.3333 15 1 1 1 1 2.3884 16 1 1 0 1 0.4018 17 1 1 1 0 2.9571 18 1 1 0 0 6.1122 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3412 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.93 2 C002 has 36 12 12 11.33 3 C003 has 2637 879 879 0.00 4 C004 has 819 273 273 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1134 378 378 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1203 401 401 0.00 Total of12313 atoms and 4097 groups and 4092 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3412 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3412 Number of groups = 1130 Number of bonds = 3406 Number of angles = 1234 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1128 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 = 3412 Number of groups = 1130 Number of bonds = 3406 Number of angles = 1234 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1128 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 <- "35.286" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1125" Evaluating: 1125-13 Parameter: NUMWAT <- "1112" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1112" Comparing "1075" and "1112". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.286" Parameter: BOX -> "35.286" Parameter: BOX -> "35.286" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.28600 B = 35.28600 C = 35.28600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9602 2 1 -1 -2 -1 13.3302 3 1 -1 -1 -1 2.3864 4 1 -1 0 -1 0.4021 5 1 0 -1 -1 3.3453 6 1 0 0 -1 2.4535 7 1 -1 -1 0 2.9557 8 1 -1 0 0 6.1115 9 1 0 -1 0 2.7543 10 1 0 1 0 2.7543 11 1 0 0 1 2.4535 12 1 0 1 1 3.3453 13 1 2 1 1 9.9602 14 1 1 2 1 13.3302 15 1 1 1 1 2.3864 16 1 1 0 1 0.4021 17 1 1 1 0 2.9557 18 1 1 0 0 6.1115 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3412 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.92 2 C002 has 36 12 12 11.33 3 C003 has 2637 879 879 0.00 4 C004 has 819 273 273 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1134 378 378 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1203 401 401 0.00 Total of12313 atoms and 4097 groups and 4092 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3412 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3412 Number of groups = 1130 Number of bonds = 3406 Number of angles = 1234 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1128 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 = 3412 Number of groups = 1130 Number of bonds = 3406 Number of angles = 1234 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1128 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 <- "35.284" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1125" Evaluating: 1125-13 Parameter: NUMWAT <- "1112" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1112" Comparing "1075" and "1112". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.284" Parameter: BOX -> "35.284" Parameter: BOX -> "35.284" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.28400 B = 35.28400 C = 35.28400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9577 2 1 -1 -2 -1 13.3271 3 1 -1 -1 -1 2.3844 4 1 -1 0 -1 0.4023 5 1 0 -1 -1 3.3457 6 1 0 0 -1 2.4524 7 1 -1 -1 0 2.9543 8 1 -1 0 0 6.1108 9 1 0 -1 0 2.7534 10 1 0 1 0 2.7534 11 1 0 0 1 2.4524 12 1 0 1 1 3.3457 13 1 2 1 1 9.9577 14 1 1 2 1 13.3271 15 1 1 1 1 2.3844 16 1 1 0 1 0.4023 17 1 1 1 0 2.9543 18 1 1 0 0 6.1108 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3412 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.92 2 C002 has 36 12 12 11.33 3 C003 has 2637 879 879 0.00 4 C004 has 819 273 273 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1134 378 378 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1203 401 401 0.00 Total of12313 atoms and 4097 groups and 4092 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3412 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3412 Number of groups = 1130 Number of bonds = 3406 Number of angles = 1234 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1128 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 = 3412 Number of groups = 1130 Number of bonds = 3406 Number of angles = 1234 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1128 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 <- "35.282" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1125" Evaluating: 1125-13 Parameter: NUMWAT <- "1112" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1112" Comparing "1075" and "1112". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.282" Parameter: BOX -> "35.282" Parameter: BOX -> "35.282" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.28200 B = 35.28200 C = 35.28200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9552 2 1 -1 -2 -1 13.3240 3 1 -1 -1 -1 2.3825 4 1 -1 0 -1 0.4025 5 1 0 -1 -1 3.3461 6 1 0 0 -1 2.4513 7 1 -1 -1 0 2.9530 8 1 -1 0 0 6.1101 9 1 0 -1 0 2.7525 10 1 0 1 0 2.7525 11 1 0 0 1 2.4513 12 1 0 1 1 3.3461 13 1 2 1 1 9.9552 14 1 1 2 1 13.3240 15 1 1 1 1 2.3825 16 1 1 0 1 0.4025 17 1 1 1 0 2.9530 18 1 1 0 0 6.1101 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3412 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.92 2 C002 has 36 12 12 11.32 3 C003 has 2637 879 879 0.00 4 C004 has 822 274 274 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1134 378 378 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1215 405 405 0.00 9 C009 has 1203 401 401 0.00 Total of12319 atoms and 4099 groups and 4094 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3412 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3412 Number of groups = 1130 Number of bonds = 3406 Number of angles = 1234 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1128 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 = 3412 Number of groups = 1130 Number of bonds = 3406 Number of angles = 1234 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1128 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 <- "35.28" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1125" Evaluating: 1125-13 Parameter: NUMWAT <- "1112" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1112" Comparing "1075" and "1112". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.28" Parameter: BOX -> "35.28" Parameter: BOX -> "35.28" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.28000 B = 35.28000 C = 35.28000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9527 2 1 -1 -2 -1 13.3208 3 1 -1 -1 -1 2.3805 4 1 -1 0 -1 0.4028 5 1 0 -1 -1 3.3466 6 1 0 0 -1 2.4502 7 1 -1 -1 0 2.9516 8 1 -1 0 0 6.1094 9 1 0 -1 0 2.7515 10 1 0 1 0 2.7515 11 1 0 0 1 2.4502 12 1 0 1 1 3.3466 13 1 2 1 1 9.9527 14 1 1 2 1 13.3208 15 1 1 1 1 2.3805 16 1 1 0 1 0.4028 17 1 1 1 0 2.9516 18 1 1 0 0 6.1094 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3412 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.91 2 C002 has 36 12 12 11.32 3 C003 has 2640 880 880 0.00 4 C004 has 822 274 274 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1134 378 378 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1215 405 405 0.00 9 C009 has 1203 401 401 0.00 Total of12322 atoms and 4100 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 3412 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3412 Number of groups = 1130 Number of bonds = 3406 Number of angles = 1234 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1128 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 = 3412 Number of groups = 1130 Number of bonds = 3406 Number of angles = 1234 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1128 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 <- "35.278" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1125" Evaluating: 1125-13 Parameter: NUMWAT <- "1112" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1112" Comparing "1075" and "1112". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.278" Parameter: BOX -> "35.278" Parameter: BOX -> "35.278" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.27800 B = 35.27800 C = 35.27800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9502 2 1 -1 -2 -1 13.3177 3 1 -1 -1 -1 2.3785 4 1 -1 0 -1 0.4030 5 1 0 -1 -1 3.3470 6 1 0 0 -1 2.4492 7 1 -1 -1 0 2.9502 8 1 -1 0 0 6.1087 9 1 0 -1 0 2.7506 10 1 0 1 0 2.7506 11 1 0 0 1 2.4492 12 1 0 1 1 3.3470 13 1 2 1 1 9.9502 14 1 1 2 1 13.3177 15 1 1 1 1 2.3785 16 1 1 0 1 0.4030 17 1 1 1 0 2.9502 18 1 1 0 0 6.1087 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3412 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.91 2 C002 has 36 12 12 11.32 3 C003 has 2640 880 880 0.00 4 C004 has 822 274 274 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1134 378 378 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1215 405 405 0.00 9 C009 has 1206 402 402 0.00 Total of12325 atoms and 4101 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 3412 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3412 Number of groups = 1130 Number of bonds = 3406 Number of angles = 1234 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1128 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 = 3412 Number of groups = 1130 Number of bonds = 3406 Number of angles = 1234 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1128 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 <- "35.276" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1125" Evaluating: 1125-13 Parameter: NUMWAT <- "1112" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1112" Comparing "1075" and "1112". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.276" Parameter: BOX -> "35.276" Parameter: BOX -> "35.276" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.27600 B = 35.27600 C = 35.27600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9477 2 1 -1 -2 -1 13.3146 3 1 -1 -1 -1 2.3765 4 1 -1 0 -1 0.4033 5 1 0 -1 -1 3.3474 6 1 0 0 -1 2.4481 7 1 -1 -1 0 2.9489 8 1 -1 0 0 6.1080 9 1 0 -1 0 2.7497 10 1 0 1 0 2.7497 11 1 0 0 1 2.4481 12 1 0 1 1 3.3474 13 1 2 1 1 9.9477 14 1 1 2 1 13.3146 15 1 1 1 1 2.3765 16 1 1 0 1 0.4033 17 1 1 1 0 2.9489 18 1 1 0 0 6.1080 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3412 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.91 2 C002 has 36 12 12 11.31 3 C003 has 2640 880 880 0.00 4 C004 has 822 274 274 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1134 378 378 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1215 405 405 0.00 9 C009 has 1206 402 402 0.00 Total of12325 atoms and 4101 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 3412 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3412 Number of groups = 1130 Number of bonds = 3406 Number of angles = 1234 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1128 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 = 3412 Number of groups = 1130 Number of bonds = 3406 Number of angles = 1234 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1128 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 <- "35.274" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1125" Evaluating: 1125-13 Parameter: NUMWAT <- "1112" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1112" Comparing "1075" and "1112". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.274" Parameter: BOX -> "35.274" Parameter: BOX -> "35.274" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.27400 B = 35.27400 C = 35.27400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9452 2 1 -1 -2 -1 13.3115 3 1 -1 -1 -1 2.3745 4 1 -1 0 -1 0.4036 5 1 0 -1 -1 3.3478 6 1 0 0 -1 2.4470 7 1 -1 -1 0 2.9475 8 1 -1 0 0 6.1073 9 1 0 -1 0 2.7488 10 1 0 1 0 2.7488 11 1 0 0 1 2.4470 12 1 0 1 1 3.3478 13 1 2 1 1 9.9452 14 1 1 2 1 13.3115 15 1 1 1 1 2.3745 16 1 1 0 1 0.4036 17 1 1 1 0 2.9475 18 1 1 0 0 6.1073 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3412 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 373 OPERATED ON BY TRANSFORMATION C018 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 189 63 63 5.90 2 C002 has 36 12 12 11.31 3 C003 has 2640 880 880 0.00 4 C004 has 822 274 274 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1134 378 378 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1203 401 401 0.00 Total of12322 atoms and 4100 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 3412 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 = 3409 Number of groups = 1129 Number of bonds = 3403 Number of angles = 1233 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1127 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 = 3409 Number of groups = 1129 Number of bonds = 3403 Number of angles = 1233 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1127 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 <- "35.272" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1124" Evaluating: 1124-13 Parameter: NUMWAT <- "1111" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1111" Comparing "1075" and "1111". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.272" Parameter: BOX -> "35.272" Parameter: BOX -> "35.272" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.27200 B = 35.27200 C = 35.27200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9427 2 1 -1 -2 -1 13.3084 3 1 -1 -1 -1 2.3725 4 1 -1 0 -1 0.4039 5 1 0 -1 -1 3.3483 6 1 0 0 -1 2.4459 7 1 -1 -1 0 2.9461 8 1 -1 0 0 6.1066 9 1 0 -1 0 2.7478 10 1 0 1 0 2.7478 11 1 0 0 1 2.4459 12 1 0 1 1 3.3483 13 1 2 1 1 9.9427 14 1 1 2 1 13.3084 15 1 1 1 1 2.3725 16 1 1 0 1 0.4039 17 1 1 1 0 2.9461 18 1 1 0 0 6.1066 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3409 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 186 62 62 5.90 2 C002 has 36 12 12 11.31 3 C003 has 2637 879 879 0.00 4 C004 has 822 274 274 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1134 378 378 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1209 403 403 0.00 9 C009 has 1203 401 401 0.00 Total of12307 atoms and 4095 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 3409 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3409 Number of groups = 1129 Number of bonds = 3403 Number of angles = 1233 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1127 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 = 3409 Number of groups = 1129 Number of bonds = 3403 Number of angles = 1233 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1127 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 <- "35.27" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1124" Evaluating: 1124-13 Parameter: NUMWAT <- "1111" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1111" Comparing "1075" and "1111". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.27" Parameter: BOX -> "35.27" Parameter: BOX -> "35.27" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.27000 B = 35.27000 C = 35.27000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9402 2 1 -1 -2 -1 13.3053 3 1 -1 -1 -1 2.3705 4 1 -1 0 -1 0.4042 5 1 0 -1 -1 3.3487 6 1 0 0 -1 2.4448 7 1 -1 -1 0 2.9447 8 1 -1 0 0 6.1059 9 1 0 -1 0 2.7469 10 1 0 1 0 2.7469 11 1 0 0 1 2.4448 12 1 0 1 1 3.3487 13 1 2 1 1 9.9402 14 1 1 2 1 13.3053 15 1 1 1 1 2.3705 16 1 1 0 1 0.4042 17 1 1 1 0 2.9447 18 1 1 0 0 6.1059 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3409 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 189 63 63 5.90 2 C002 has 36 12 12 11.30 3 C003 has 2637 879 879 0.00 4 C004 has 822 274 274 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1134 378 378 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1209 403 403 0.00 9 C009 has 1203 401 401 0.00 Total of12310 atoms and 4096 groups and 4091 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3409 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3409 Number of groups = 1129 Number of bonds = 3403 Number of angles = 1233 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1127 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 = 3409 Number of groups = 1129 Number of bonds = 3403 Number of angles = 1233 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1127 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 <- "35.268" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1124" Evaluating: 1124-13 Parameter: NUMWAT <- "1111" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1111" Comparing "1075" and "1111". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.268" Parameter: BOX -> "35.268" Parameter: BOX -> "35.268" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.26800 B = 35.26800 C = 35.26800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9377 2 1 -1 -2 -1 13.3021 3 1 -1 -1 -1 2.3686 4 1 -1 0 -1 0.4046 5 1 0 -1 -1 3.3491 6 1 0 0 -1 2.4438 7 1 -1 -1 0 2.9434 8 1 -1 0 0 6.1052 9 1 0 -1 0 2.7460 10 1 0 1 0 2.7460 11 1 0 0 1 2.4438 12 1 0 1 1 3.3491 13 1 2 1 1 9.9377 14 1 1 2 1 13.3021 15 1 1 1 1 2.3686 16 1 1 0 1 0.4046 17 1 1 1 0 2.9434 18 1 1 0 0 6.1052 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3409 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 1011 OPERATED ON BY TRANSFORMATION C003 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 189 63 63 5.89 2 C002 has 36 12 12 11.30 3 C003 has 2634 878 878 0.00 4 C004 has 825 275 275 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1134 378 378 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1206 402 402 0.00 9 C009 has 1200 400 400 0.00 Total of12304 atoms and 4094 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> 3 atoms have been selected out of 3409 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 = 3406 Number of groups = 1128 Number of bonds = 3400 Number of angles = 1232 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1126 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 = 3406 Number of groups = 1128 Number of bonds = 3400 Number of angles = 1232 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1126 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 <- "35.266" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1123" Evaluating: 1123-13 Parameter: NUMWAT <- "1110" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1110" Comparing "1075" and "1110". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.266" Parameter: BOX -> "35.266" Parameter: BOX -> "35.266" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.26600 B = 35.26600 C = 35.26600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9352 2 1 -1 -2 -1 13.2990 3 1 -1 -1 -1 2.3666 4 1 -1 0 -1 0.4049 5 1 0 -1 -1 3.3495 6 1 0 0 -1 2.4427 7 1 -1 -1 0 2.9420 8 1 -1 0 0 6.1045 9 1 0 -1 0 2.7451 10 1 0 1 0 2.7451 11 1 0 0 1 2.4427 12 1 0 1 1 3.3495 13 1 2 1 1 9.9352 14 1 1 2 1 13.2990 15 1 1 1 1 2.3666 16 1 1 0 1 0.4049 17 1 1 1 0 2.9420 18 1 1 0 0 6.1045 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3406 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 189 63 63 5.89 2 C002 has 36 12 12 11.30 3 C003 has 2634 878 878 0.00 4 C004 has 825 275 275 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1134 378 378 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1206 402 402 0.00 9 C009 has 1200 400 400 0.00 Total of12301 atoms and 4093 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 3406 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3406 Number of groups = 1128 Number of bonds = 3400 Number of angles = 1232 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1126 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 = 3406 Number of groups = 1128 Number of bonds = 3400 Number of angles = 1232 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1126 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 <- "35.264" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1123" Evaluating: 1123-13 Parameter: NUMWAT <- "1110" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1110" Comparing "1075" and "1110". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.264" Parameter: BOX -> "35.264" Parameter: BOX -> "35.264" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.26400 B = 35.26400 C = 35.26400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9327 2 1 -1 -2 -1 13.2959 3 1 -1 -1 -1 2.3646 4 1 -1 0 -1 0.4053 5 1 0 -1 -1 3.3500 6 1 0 0 -1 2.4416 7 1 -1 -1 0 2.9407 8 1 -1 0 0 6.1038 9 1 0 -1 0 2.7442 10 1 0 1 0 2.7442 11 1 0 0 1 2.4416 12 1 0 1 1 3.3500 13 1 2 1 1 9.9327 14 1 1 2 1 13.2959 15 1 1 1 1 2.3646 16 1 1 0 1 0.4053 17 1 1 1 0 2.9407 18 1 1 0 0 6.1038 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3406 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 189 63 63 5.89 2 C002 has 36 12 12 11.30 3 C003 has 2634 878 878 0.00 4 C004 has 825 275 275 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1206 402 402 0.00 9 C009 has 1200 400 400 0.00 Total of12304 atoms and 4094 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 3406 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3406 Number of groups = 1128 Number of bonds = 3400 Number of angles = 1232 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1126 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 = 3406 Number of groups = 1128 Number of bonds = 3400 Number of angles = 1232 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1126 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 <- "35.262" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1123" Evaluating: 1123-13 Parameter: NUMWAT <- "1110" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1110" Comparing "1075" and "1110". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.262" Parameter: BOX -> "35.262" Parameter: BOX -> "35.262" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.26200 B = 35.26200 C = 35.26200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9302 2 1 -1 -2 -1 13.2928 3 1 -1 -1 -1 2.3626 4 1 -1 0 -1 0.4056 5 1 0 -1 -1 3.3504 6 1 0 0 -1 2.4406 7 1 -1 -1 0 2.9393 8 1 -1 0 0 6.1031 9 1 0 -1 0 2.7432 10 1 0 1 0 2.7432 11 1 0 0 1 2.4406 12 1 0 1 1 3.3504 13 1 2 1 1 9.9302 14 1 1 2 1 13.2928 15 1 1 1 1 2.3626 16 1 1 0 1 0.4056 17 1 1 1 0 2.9393 18 1 1 0 0 6.1031 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3406 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 189 63 63 5.89 2 C002 has 36 12 12 11.29 3 C003 has 2634 878 878 0.00 4 C004 has 825 275 275 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 819 273 273 0.00 8 C008 has 1206 402 402 0.00 9 C009 has 1200 400 400 0.00 Total of12304 atoms and 4094 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 3406 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3406 Number of groups = 1128 Number of bonds = 3400 Number of angles = 1232 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1126 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 = 3406 Number of groups = 1128 Number of bonds = 3400 Number of angles = 1232 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1126 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 <- "35.26" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1123" Evaluating: 1123-13 Parameter: NUMWAT <- "1110" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1110" Comparing "1075" and "1110". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.26" Parameter: BOX -> "35.26" Parameter: BOX -> "35.26" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.26000 B = 35.26000 C = 35.26000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9277 2 1 -1 -2 -1 13.2897 3 1 -1 -1 -1 2.3606 4 1 -1 0 -1 0.4060 5 1 0 -1 -1 3.3508 6 1 0 0 -1 2.4395 7 1 -1 -1 0 2.9379 8 1 -1 0 0 6.1024 9 1 0 -1 0 2.7423 10 1 0 1 0 2.7423 11 1 0 0 1 2.4395 12 1 0 1 1 3.3508 13 1 2 1 1 9.9277 14 1 1 2 1 13.2897 15 1 1 1 1 2.3606 16 1 1 0 1 0.4060 17 1 1 1 0 2.9379 18 1 1 0 0 6.1024 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3406 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 189 63 63 5.88 2 C002 has 36 12 12 11.29 3 C003 has 2634 878 878 0.00 4 C004 has 825 275 275 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1206 402 402 0.00 9 C009 has 1200 400 400 0.00 Total of12307 atoms and 4095 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 3406 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3406 Number of groups = 1128 Number of bonds = 3400 Number of angles = 1232 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1126 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 = 3406 Number of groups = 1128 Number of bonds = 3400 Number of angles = 1232 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1126 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 <- "35.258" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1123" Evaluating: 1123-13 Parameter: NUMWAT <- "1110" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1110" Comparing "1075" and "1110". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.258" Parameter: BOX -> "35.258" Parameter: BOX -> "35.258" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.25800 B = 35.25800 C = 35.25800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9252 2 1 -1 -2 -1 13.2865 3 1 -1 -1 -1 2.3586 4 1 -1 0 -1 0.4064 5 1 0 -1 -1 3.3513 6 1 0 0 -1 2.4384 7 1 -1 -1 0 2.9366 8 1 -1 0 0 6.1017 9 1 0 -1 0 2.7414 10 1 0 1 0 2.7414 11 1 0 0 1 2.4384 12 1 0 1 1 3.3513 13 1 2 1 1 9.9252 14 1 1 2 1 13.2865 15 1 1 1 1 2.3586 16 1 1 0 1 0.4064 17 1 1 1 0 2.9366 18 1 1 0 0 6.1017 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3406 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 189 63 63 5.88 2 C002 has 36 12 12 11.29 3 C003 has 2634 878 878 0.00 4 C004 has 828 276 276 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1209 403 403 0.00 9 C009 has 1200 400 400 0.00 Total of12313 atoms and 4097 groups and 4092 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3406 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3406 Number of groups = 1128 Number of bonds = 3400 Number of angles = 1232 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1126 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 = 3406 Number of groups = 1128 Number of bonds = 3400 Number of angles = 1232 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1126 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 <- "35.256" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1123" Evaluating: 1123-13 Parameter: NUMWAT <- "1110" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1110" Comparing "1075" and "1110". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.256" Parameter: BOX -> "35.256" Parameter: BOX -> "35.256" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.25600 B = 35.25600 C = 35.25600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9227 2 1 -1 -2 -1 13.2834 3 1 -1 -1 -1 2.3566 4 1 -1 0 -1 0.4068 5 1 0 -1 -1 3.3517 6 1 0 0 -1 2.4373 7 1 -1 -1 0 2.9352 8 1 -1 0 0 6.1010 9 1 0 -1 0 2.7405 10 1 0 1 0 2.7405 11 1 0 0 1 2.4373 12 1 0 1 1 3.3517 13 1 2 1 1 9.9227 14 1 1 2 1 13.2834 15 1 1 1 1 2.3566 16 1 1 0 1 0.4068 17 1 1 1 0 2.9352 18 1 1 0 0 6.1010 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3406 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 918 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.88 2 C002 has 36 12 12 11.28 3 C003 has 2631 877 877 0.00 4 C004 has 828 276 276 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1134 378 378 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1197 399 399 0.00 Total of12313 atoms and 4097 groups and 4092 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3406 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 = 3403 Number of groups = 1127 Number of bonds = 3397 Number of angles = 1231 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1125 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 = 3403 Number of groups = 1127 Number of bonds = 3397 Number of angles = 1231 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1125 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 <- "35.254" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1122" Evaluating: 1122-13 Parameter: NUMWAT <- "1109" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1109" Comparing "1075" and "1109". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.254" Parameter: BOX -> "35.254" Parameter: BOX -> "35.254" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.25400 B = 35.25400 C = 35.25400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9202 2 1 -1 -2 -1 13.2803 3 1 -1 -1 -1 2.3547 4 1 -1 0 -1 0.4072 5 1 0 -1 -1 3.3522 6 1 0 0 -1 2.4363 7 1 -1 -1 0 2.9339 8 1 -1 0 0 6.1003 9 1 0 -1 0 2.7396 10 1 0 1 0 2.7396 11 1 0 0 1 2.4363 12 1 0 1 1 3.3522 13 1 2 1 1 9.9202 14 1 1 2 1 13.2803 15 1 1 1 1 2.3547 16 1 1 0 1 0.4072 17 1 1 1 0 2.9339 18 1 1 0 0 6.1003 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3403 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.87 2 C002 has 36 12 12 11.28 3 C003 has 2631 877 877 0.00 4 C004 has 828 276 276 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1215 405 405 0.00 9 C009 has 1197 399 399 0.00 Total of12316 atoms and 4098 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 3403 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3403 Number of groups = 1127 Number of bonds = 3397 Number of angles = 1231 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1125 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 = 3403 Number of groups = 1127 Number of bonds = 3397 Number of angles = 1231 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1125 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 <- "35.252" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1122" Evaluating: 1122-13 Parameter: NUMWAT <- "1109" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1109" Comparing "1075" and "1109". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.252" Parameter: BOX -> "35.252" Parameter: BOX -> "35.252" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.25200 B = 35.25200 C = 35.25200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9177 2 1 -1 -2 -1 13.2772 3 1 -1 -1 -1 2.3527 4 1 -1 0 -1 0.4077 5 1 0 -1 -1 3.3526 6 1 0 0 -1 2.4352 7 1 -1 -1 0 2.9325 8 1 -1 0 0 6.0996 9 1 0 -1 0 2.7387 10 1 0 1 0 2.7387 11 1 0 0 1 2.4352 12 1 0 1 1 3.3526 13 1 2 1 1 9.9177 14 1 1 2 1 13.2772 15 1 1 1 1 2.3527 16 1 1 0 1 0.4077 17 1 1 1 0 2.9325 18 1 1 0 0 6.0996 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3403 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 C015 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.87 2 C002 has 36 12 12 11.28 3 C003 has 2637 879 879 0.00 4 C004 has 828 276 276 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1143 381 381 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1215 405 405 0.00 9 C009 has 1200 400 400 0.00 Total of12334 atoms and 4104 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> 3 atoms have been selected out of 3403 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 = 1121 Number of atoms = 3400 Number of groups = 1126 Number of bonds = 3394 Number of angles = 1230 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2224 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1121 Number of atoms = 3400 Number of groups = 1126 Number of bonds = 3394 Number of angles = 1230 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2224 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.25" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1121" Evaluating: 1121-13 Parameter: NUMWAT <- "1108" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1108" Comparing "1075" and "1108". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.25" Parameter: BOX -> "35.25" Parameter: BOX -> "35.25" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.25000 B = 35.25000 C = 35.25000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9152 2 1 -1 -2 -1 13.2741 3 1 -1 -1 -1 2.3507 4 1 -1 0 -1 0.4081 5 1 0 -1 -1 3.3530 6 1 0 0 -1 2.4341 7 1 -1 -1 0 2.9311 8 1 -1 0 0 6.0989 9 1 0 -1 0 2.7378 10 1 0 1 0 2.7378 11 1 0 0 1 2.4341 12 1 0 1 1 3.3530 13 1 2 1 1 9.9152 14 1 1 2 1 13.2741 15 1 1 1 1 2.3507 16 1 1 0 1 0.4081 17 1 1 1 0 2.9311 18 1 1 0 0 6.0989 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3324 atoms have been selected out of 3400 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.87 2 C002 has 36 12 12 11.27 3 C003 has 2634 878 878 0.00 4 C004 has 828 276 276 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1215 405 405 0.00 9 C009 has 1197 399 399 0.00 Total of12316 atoms and 4098 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 3400 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1121 Number of atoms = 3400 Number of groups = 1126 Number of bonds = 3394 Number of angles = 1230 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2224 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1121 Number of atoms = 3400 Number of groups = 1126 Number of bonds = 3394 Number of angles = 1230 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2224 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.248" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1121" Evaluating: 1121-13 Parameter: NUMWAT <- "1108" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1108" Comparing "1075" and "1108". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.248" Parameter: BOX -> "35.248" Parameter: BOX -> "35.248" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.24800 B = 35.24800 C = 35.24800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9127 2 1 -1 -2 -1 13.2710 3 1 -1 -1 -1 2.3487 4 1 -1 0 -1 0.4086 5 1 0 -1 -1 3.3535 6 1 0 0 -1 2.4331 7 1 -1 -1 0 2.9298 8 1 -1 0 0 6.0982 9 1 0 -1 0 2.7369 10 1 0 1 0 2.7369 11 1 0 0 1 2.4331 12 1 0 1 1 3.3535 13 1 2 1 1 9.9127 14 1 1 2 1 13.2710 15 1 1 1 1 2.3487 16 1 1 0 1 0.4086 17 1 1 1 0 2.9298 18 1 1 0 0 6.0982 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3324 atoms have been selected out of 3400 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.86 2 C002 has 36 12 12 11.27 3 C003 has 2634 878 878 0.00 4 C004 has 828 276 276 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1143 381 381 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1215 405 405 0.00 9 C009 has 1197 399 399 0.00 Total of12322 atoms and 4100 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 3400 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1121 Number of atoms = 3400 Number of groups = 1126 Number of bonds = 3394 Number of angles = 1230 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2224 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1121 Number of atoms = 3400 Number of groups = 1126 Number of bonds = 3394 Number of angles = 1230 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2224 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.246" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1121" Evaluating: 1121-13 Parameter: NUMWAT <- "1108" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1108" Comparing "1075" and "1108". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.246" Parameter: BOX -> "35.246" Parameter: BOX -> "35.246" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.24600 B = 35.24600 C = 35.24600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9102 2 1 -1 -2 -1 13.2678 3 1 -1 -1 -1 2.3467 4 1 -1 0 -1 0.4091 5 1 0 -1 -1 3.3539 6 1 0 0 -1 2.4320 7 1 -1 -1 0 2.9284 8 1 -1 0 0 6.0975 9 1 0 -1 0 2.7360 10 1 0 1 0 2.7360 11 1 0 0 1 2.4320 12 1 0 1 1 3.3539 13 1 2 1 1 9.9102 14 1 1 2 1 13.2678 15 1 1 1 1 2.3467 16 1 1 0 1 0.4091 17 1 1 1 0 2.9284 18 1 1 0 0 6.0975 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3324 atoms have been selected out of 3400 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.86 2 C002 has 36 12 12 11.27 3 C003 has 2634 878 878 0.00 4 C004 has 828 276 276 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1143 381 381 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1218 406 406 0.00 9 C009 has 1197 399 399 0.00 Total of12325 atoms and 4101 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 3400 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1121 Number of atoms = 3400 Number of groups = 1126 Number of bonds = 3394 Number of angles = 1230 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2224 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1121 Number of atoms = 3400 Number of groups = 1126 Number of bonds = 3394 Number of angles = 1230 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2224 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.244" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1121" Evaluating: 1121-13 Parameter: NUMWAT <- "1108" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1108" Comparing "1075" and "1108". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.244" Parameter: BOX -> "35.244" Parameter: BOX -> "35.244" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.24400 B = 35.24400 C = 35.24400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9077 2 1 -1 -2 -1 13.2647 3 1 -1 -1 -1 2.3447 4 1 -1 0 -1 0.4095 5 1 0 -1 -1 3.3544 6 1 0 0 -1 2.4310 7 1 -1 -1 0 2.9271 8 1 -1 0 0 6.0968 9 1 0 -1 0 2.7351 10 1 0 1 0 2.7351 11 1 0 0 1 2.4310 12 1 0 1 1 3.3544 13 1 2 1 1 9.9077 14 1 1 2 1 13.2647 15 1 1 1 1 2.3447 16 1 1 0 1 0.4095 17 1 1 1 0 2.9271 18 1 1 0 0 6.0968 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3324 atoms have been selected out of 3400 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.86 2 C002 has 36 12 12 11.26 3 C003 has 2634 878 878 0.00 4 C004 has 828 276 276 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1143 381 381 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1218 406 406 0.00 9 C009 has 1200 400 400 0.00 Total of12328 atoms and 4102 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 3400 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1121 Number of atoms = 3400 Number of groups = 1126 Number of bonds = 3394 Number of angles = 1230 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2224 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1121 Number of atoms = 3400 Number of groups = 1126 Number of bonds = 3394 Number of angles = 1230 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2224 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.242" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1121" Evaluating: 1121-13 Parameter: NUMWAT <- "1108" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1108" Comparing "1075" and "1108". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.242" Parameter: BOX -> "35.242" Parameter: BOX -> "35.242" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.24200 B = 35.24200 C = 35.24200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9052 2 1 -1 -2 -1 13.2616 3 1 -1 -1 -1 2.3427 4 1 -1 0 -1 0.4100 5 1 0 -1 -1 3.3548 6 1 0 0 -1 2.4299 7 1 -1 -1 0 2.9257 8 1 -1 0 0 6.0962 9 1 0 -1 0 2.7342 10 1 0 1 0 2.7342 11 1 0 0 1 2.4299 12 1 0 1 1 3.3548 13 1 2 1 1 9.9052 14 1 1 2 1 13.2616 15 1 1 1 1 2.3427 16 1 1 0 1 0.4100 17 1 1 1 0 2.9257 18 1 1 0 0 6.0962 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3324 atoms have been selected out of 3400 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.85 2 C002 has 36 12 12 11.26 3 C003 has 2634 878 878 0.00 4 C004 has 828 276 276 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1143 381 381 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1218 406 406 0.00 9 C009 has 1200 400 400 0.00 Total of12328 atoms and 4102 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 3400 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1121 Number of atoms = 3400 Number of groups = 1126 Number of bonds = 3394 Number of angles = 1230 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2224 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1121 Number of atoms = 3400 Number of groups = 1126 Number of bonds = 3394 Number of angles = 1230 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2224 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.24" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1121" Evaluating: 1121-13 Parameter: NUMWAT <- "1108" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1108" Comparing "1075" and "1108". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.24" Parameter: BOX -> "35.24" Parameter: BOX -> "35.24" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.24000 B = 35.24000 C = 35.24000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9027 2 1 -1 -2 -1 13.2585 3 1 -1 -1 -1 2.3408 4 1 -1 0 -1 0.4105 5 1 0 -1 -1 3.3553 6 1 0 0 -1 2.4288 7 1 -1 -1 0 2.9244 8 1 -1 0 0 6.0955 9 1 0 -1 0 2.7332 10 1 0 1 0 2.7332 11 1 0 0 1 2.4288 12 1 0 1 1 3.3553 13 1 2 1 1 9.9027 14 1 1 2 1 13.2585 15 1 1 1 1 2.3408 16 1 1 0 1 0.4105 17 1 1 1 0 2.9244 18 1 1 0 0 6.0955 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3324 atoms have been selected out of 3400 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.85 2 C002 has 36 12 12 11.26 3 C003 has 2634 878 878 0.00 4 C004 has 828 276 276 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1143 381 381 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1218 406 406 0.00 9 C009 has 1200 400 400 0.00 Total of12328 atoms and 4102 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 3400 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1121 Number of atoms = 3400 Number of groups = 1126 Number of bonds = 3394 Number of angles = 1230 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2224 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1121 Number of atoms = 3400 Number of groups = 1126 Number of bonds = 3394 Number of angles = 1230 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1124 Number of HB donors = 2224 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.238" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1121" Evaluating: 1121-13 Parameter: NUMWAT <- "1108" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1108" Comparing "1075" and "1108". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.238" Parameter: BOX -> "35.238" Parameter: BOX -> "35.238" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.23800 B = 35.23800 C = 35.23800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.9002 2 1 -1 -2 -1 13.2554 3 1 -1 -1 -1 2.3388 4 1 -1 0 -1 0.4111 5 1 0 -1 -1 3.3557 6 1 0 0 -1 2.4278 7 1 -1 -1 0 2.9230 8 1 -1 0 0 6.0948 9 1 0 -1 0 2.7323 10 1 0 1 0 2.7323 11 1 0 0 1 2.4278 12 1 0 1 1 3.3557 13 1 2 1 1 9.9002 14 1 1 2 1 13.2554 15 1 1 1 1 2.3388 16 1 1 0 1 0.4111 17 1 1 1 0 2.9230 18 1 1 0 0 6.0948 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3324 atoms have been selected out of 3400 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 183 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.85 2 C002 has 36 12 12 11.26 3 C003 has 2634 878 878 0.00 4 C004 has 828 276 276 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1143 381 381 0.00 7 C007 has 828 276 276 0.00 8 C008 has 1215 405 405 0.00 9 C009 has 1203 401 401 0.00 Total of12331 atoms and 4103 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> 3 atoms have been selected out of 3400 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 = 1120 Number of atoms = 3397 Number of groups = 1125 Number of bonds = 3391 Number of angles = 1229 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1123 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 = 3397 Number of groups = 1125 Number of bonds = 3391 Number of angles = 1229 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1123 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 <- "35.236" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1120" Evaluating: 1120-13 Parameter: NUMWAT <- "1107" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1107" Comparing "1075" and "1107". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.236" Parameter: BOX -> "35.236" Parameter: BOX -> "35.236" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.23600 B = 35.23600 C = 35.23600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8977 2 1 -1 -2 -1 13.2523 3 1 -1 -1 -1 2.3368 4 1 -1 0 -1 0.4116 5 1 0 -1 -1 3.3562 6 1 0 0 -1 2.4267 7 1 -1 -1 0 2.9217 8 1 -1 0 0 6.0941 9 1 0 -1 0 2.7314 10 1 0 1 0 2.7314 11 1 0 0 1 2.4267 12 1 0 1 1 3.3562 13 1 2 1 1 9.8977 14 1 1 2 1 13.2523 15 1 1 1 1 2.3368 16 1 1 0 1 0.4116 17 1 1 1 0 2.9217 18 1 1 0 0 6.0941 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3397 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.85 2 C002 has 36 12 12 11.25 3 C003 has 2634 878 878 0.00 4 C004 has 828 276 276 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1143 381 381 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1215 405 405 0.00 9 C009 has 1200 400 400 0.00 Total of12322 atoms and 4100 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 3397 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3397 Number of groups = 1125 Number of bonds = 3391 Number of angles = 1229 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1123 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 = 3397 Number of groups = 1125 Number of bonds = 3391 Number of angles = 1229 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1123 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 <- "35.234" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1120" Evaluating: 1120-13 Parameter: NUMWAT <- "1107" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1107" Comparing "1075" and "1107". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.234" Parameter: BOX -> "35.234" Parameter: BOX -> "35.234" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.23400 B = 35.23400 C = 35.23400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8952 2 1 -1 -2 -1 13.2491 3 1 -1 -1 -1 2.3348 4 1 -1 0 -1 0.4121 5 1 0 -1 -1 3.3566 6 1 0 0 -1 2.4257 7 1 -1 -1 0 2.9203 8 1 -1 0 0 6.0934 9 1 0 -1 0 2.7305 10 1 0 1 0 2.7305 11 1 0 0 1 2.4257 12 1 0 1 1 3.3566 13 1 2 1 1 9.8952 14 1 1 2 1 13.2491 15 1 1 1 1 2.3348 16 1 1 0 1 0.4121 17 1 1 1 0 2.9203 18 1 1 0 0 6.0934 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3397 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 807 OPERATED ON BY TRANSFORMATION C004 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.84 2 C002 has 36 12 12 11.25 3 C003 has 2631 877 877 0.00 4 C004 has 828 276 276 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1203 401 401 0.00 Total of12316 atoms and 4098 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> 3 atoms have been selected out of 3397 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 = 1119 Number of atoms = 3394 Number of groups = 1124 Number of bonds = 3388 Number of angles = 1228 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2220 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1119 Number of atoms = 3394 Number of groups = 1124 Number of bonds = 3388 Number of angles = 1228 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2220 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.232" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1119" Evaluating: 1119-13 Parameter: NUMWAT <- "1106" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1106" Comparing "1075" and "1106". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.232" Parameter: BOX -> "35.232" Parameter: BOX -> "35.232" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.23200 B = 35.23200 C = 35.23200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8927 2 1 -1 -2 -1 13.2460 3 1 -1 -1 -1 2.3328 4 1 -1 0 -1 0.4127 5 1 0 -1 -1 3.3571 6 1 0 0 -1 2.4246 7 1 -1 -1 0 2.9190 8 1 -1 0 0 6.0927 9 1 0 -1 0 2.7296 10 1 0 1 0 2.7296 11 1 0 0 1 2.4246 12 1 0 1 1 3.3571 13 1 2 1 1 9.8927 14 1 1 2 1 13.2460 15 1 1 1 1 2.3328 16 1 1 0 1 0.4127 17 1 1 1 0 2.9190 18 1 1 0 0 6.0927 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3318 atoms have been selected out of 3394 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.84 2 C002 has 36 12 12 11.25 3 C003 has 2631 877 877 0.00 4 C004 has 825 275 275 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1200 400 400 0.00 Total of12310 atoms and 4096 groups and 4091 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3394 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1119 Number of atoms = 3394 Number of groups = 1124 Number of bonds = 3388 Number of angles = 1228 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2220 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1119 Number of atoms = 3394 Number of groups = 1124 Number of bonds = 3388 Number of angles = 1228 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2220 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.23" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1119" Evaluating: 1119-13 Parameter: NUMWAT <- "1106" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1106" Comparing "1075" and "1106". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.23" Parameter: BOX -> "35.23" Parameter: BOX -> "35.23" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.23000 B = 35.23000 C = 35.23000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8902 2 1 -1 -2 -1 13.2429 3 1 -1 -1 -1 2.3308 4 1 -1 0 -1 0.4133 5 1 0 -1 -1 3.3575 6 1 0 0 -1 2.4236 7 1 -1 -1 0 2.9177 8 1 -1 0 0 6.0920 9 1 0 -1 0 2.7288 10 1 0 1 0 2.7288 11 1 0 0 1 2.4236 12 1 0 1 1 3.3575 13 1 2 1 1 9.8902 14 1 1 2 1 13.2429 15 1 1 1 1 2.3308 16 1 1 0 1 0.4133 17 1 1 1 0 2.9177 18 1 1 0 0 6.0920 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3318 atoms have been selected out of 3394 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.84 2 C002 has 36 12 12 11.24 3 C003 has 2631 877 877 0.00 4 C004 has 825 275 275 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1200 400 400 0.00 Total of12310 atoms and 4096 groups and 4091 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3394 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1119 Number of atoms = 3394 Number of groups = 1124 Number of bonds = 3388 Number of angles = 1228 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2220 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1119 Number of atoms = 3394 Number of groups = 1124 Number of bonds = 3388 Number of angles = 1228 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2220 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.228" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1119" Evaluating: 1119-13 Parameter: NUMWAT <- "1106" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1106" Comparing "1075" and "1106". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.228" Parameter: BOX -> "35.228" Parameter: BOX -> "35.228" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.22800 B = 35.22800 C = 35.22800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8877 2 1 -1 -2 -1 13.2398 3 1 -1 -1 -1 2.3289 4 1 -1 0 -1 0.4139 5 1 0 -1 -1 3.3580 6 1 0 0 -1 2.4225 7 1 -1 -1 0 2.9163 8 1 -1 0 0 6.0913 9 1 0 -1 0 2.7279 10 1 0 1 0 2.7279 11 1 0 0 1 2.4225 12 1 0 1 1 3.3580 13 1 2 1 1 9.8877 14 1 1 2 1 13.2398 15 1 1 1 1 2.3289 16 1 1 0 1 0.4139 17 1 1 1 0 2.9163 18 1 1 0 0 6.0913 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3318 atoms have been selected out of 3394 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.83 2 C002 has 36 12 12 11.24 3 C003 has 2631 877 877 0.00 4 C004 has 825 275 275 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1200 400 400 0.00 Total of12310 atoms and 4096 groups and 4091 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3394 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1119 Number of atoms = 3394 Number of groups = 1124 Number of bonds = 3388 Number of angles = 1228 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2220 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1119 Number of atoms = 3394 Number of groups = 1124 Number of bonds = 3388 Number of angles = 1228 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1122 Number of HB donors = 2220 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.226" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1119" Evaluating: 1119-13 Parameter: NUMWAT <- "1106" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1106" Comparing "1075" and "1106". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.226" Parameter: BOX -> "35.226" Parameter: BOX -> "35.226" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.22600 B = 35.22600 C = 35.22600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8852 2 1 -1 -2 -1 13.2367 3 1 -1 -1 -1 2.3269 4 1 -1 0 -1 0.4144 5 1 0 -1 -1 3.3585 6 1 0 0 -1 2.4215 7 1 -1 -1 0 2.9150 8 1 -1 0 0 6.0906 9 1 0 -1 0 2.7270 10 1 0 1 0 2.7270 11 1 0 0 1 2.4215 12 1 0 1 1 3.3585 13 1 2 1 1 9.8852 14 1 1 2 1 13.2367 15 1 1 1 1 2.3269 16 1 1 0 1 0.4144 17 1 1 1 0 2.9150 18 1 1 0 0 6.0906 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3318 atoms have been selected out of 3394 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 784 OPERATED ON BY TRANSFORMATION C006 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.83 2 C002 has 36 12 12 11.24 3 C003 has 2628 876 876 0.00 4 C004 has 822 274 274 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1152 384 384 0.00 7 C007 has 828 276 276 0.00 8 C008 has 1215 405 405 0.00 9 C009 has 1200 400 400 0.00 Total of12322 atoms and 4100 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 3394 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 = 1118 Number of atoms = 3391 Number of groups = 1123 Number of bonds = 3385 Number of angles = 1227 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1121 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 = 3391 Number of groups = 1123 Number of bonds = 3385 Number of angles = 1227 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1121 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 <- "35.224" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1118" Evaluating: 1118-13 Parameter: NUMWAT <- "1105" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1105" Comparing "1075" and "1105". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.224" Parameter: BOX -> "35.224" Parameter: BOX -> "35.224" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.22400 B = 35.22400 C = 35.22400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8827 2 1 -1 -2 -1 13.2336 3 1 -1 -1 -1 2.3249 4 1 -1 0 -1 0.4151 5 1 0 -1 -1 3.3589 6 1 0 0 -1 2.4204 7 1 -1 -1 0 2.9136 8 1 -1 0 0 6.0900 9 1 0 -1 0 2.7261 10 1 0 1 0 2.7261 11 1 0 0 1 2.4204 12 1 0 1 1 3.3589 13 1 2 1 1 9.8827 14 1 1 2 1 13.2336 15 1 1 1 1 2.3249 16 1 1 0 1 0.4151 17 1 1 1 0 2.9136 18 1 1 0 0 6.0900 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3391 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 909 OPERATED ON BY TRANSFORMATION C009 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.83 2 C002 has 33 11 11 11.23 3 C003 has 2628 876 876 0.00 4 C004 has 825 275 275 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1215 405 405 0.00 9 C009 has 1203 401 401 0.00 Total of12301 atoms and 4093 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> 3 atoms have been selected out of 3391 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 = 1117 Number of atoms = 3388 Number of groups = 1122 Number of bonds = 3382 Number of angles = 1226 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2216 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1117 Number of atoms = 3388 Number of groups = 1122 Number of bonds = 3382 Number of angles = 1226 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2216 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.222" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1117" Evaluating: 1117-13 Parameter: NUMWAT <- "1104" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1104" Comparing "1075" and "1104". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.222" Parameter: BOX -> "35.222" Parameter: BOX -> "35.222" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.22200 B = 35.22200 C = 35.22200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8802 2 1 -1 -2 -1 13.2304 3 1 -1 -1 -1 2.3229 4 1 -1 0 -1 0.4157 5 1 0 -1 -1 3.3594 6 1 0 0 -1 2.4194 7 1 -1 -1 0 2.9123 8 1 -1 0 0 6.0893 9 1 0 -1 0 2.7252 10 1 0 1 0 2.7252 11 1 0 0 1 2.4194 12 1 0 1 1 3.3594 13 1 2 1 1 9.8802 14 1 1 2 1 13.2304 15 1 1 1 1 2.3229 16 1 1 0 1 0.4157 17 1 1 1 0 2.9123 18 1 1 0 0 6.0893 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3312 atoms have been selected out of 3388 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.82 2 C002 has 33 11 11 11.23 3 C003 has 2625 875 875 0.00 4 C004 has 822 274 274 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1197 399 399 0.00 Total of12283 atoms and 4087 groups and 4082 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3388 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1117 Number of atoms = 3388 Number of groups = 1122 Number of bonds = 3382 Number of angles = 1226 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2216 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1117 Number of atoms = 3388 Number of groups = 1122 Number of bonds = 3382 Number of angles = 1226 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2216 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.22" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1117" Evaluating: 1117-13 Parameter: NUMWAT <- "1104" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1104" Comparing "1075" and "1104". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.22" Parameter: BOX -> "35.22" Parameter: BOX -> "35.22" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.22000 B = 35.22000 C = 35.22000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8777 2 1 -1 -2 -1 13.2273 3 1 -1 -1 -1 2.3209 4 1 -1 0 -1 0.4163 5 1 0 -1 -1 3.3598 6 1 0 0 -1 2.4183 7 1 -1 -1 0 2.9110 8 1 -1 0 0 6.0886 9 1 0 -1 0 2.7243 10 1 0 1 0 2.7243 11 1 0 0 1 2.4183 12 1 0 1 1 3.3598 13 1 2 1 1 9.8777 14 1 1 2 1 13.2273 15 1 1 1 1 2.3209 16 1 1 0 1 0.4163 17 1 1 1 0 2.9110 18 1 1 0 0 6.0886 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3312 atoms have been selected out of 3388 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.82 2 C002 has 33 11 11 11.23 3 C003 has 2625 875 875 0.00 4 C004 has 822 274 274 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1197 399 399 0.00 Total of12283 atoms and 4087 groups and 4082 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3388 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1117 Number of atoms = 3388 Number of groups = 1122 Number of bonds = 3382 Number of angles = 1226 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2216 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1117 Number of atoms = 3388 Number of groups = 1122 Number of bonds = 3382 Number of angles = 1226 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2216 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.218" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1117" Evaluating: 1117-13 Parameter: NUMWAT <- "1104" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1104" Comparing "1075" and "1104". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.218" Parameter: BOX -> "35.218" Parameter: BOX -> "35.218" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.21800 B = 35.21800 C = 35.21800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8752 2 1 -1 -2 -1 13.9982 3 1 -1 -1 -1 2.3189 4 1 -1 0 -1 0.4169 5 1 0 -1 -1 3.3603 6 1 0 0 -1 2.4173 7 1 -1 -1 0 2.9096 8 1 -1 0 0 6.0879 9 1 0 -1 0 2.7234 10 1 0 1 0 2.7234 11 1 0 0 1 2.4173 12 1 0 1 1 3.3603 13 1 2 1 1 9.8752 14 1 1 2 1 13.9982 15 1 1 1 1 2.3189 16 1 1 0 1 0.4169 17 1 1 1 0 2.9096 18 1 1 0 0 6.0879 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3312 atoms have been selected out of 3388 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.82 2 C002 has 33 11 11 11.22 3 C003 has 2625 875 875 0.00 4 C004 has 822 274 274 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1197 399 399 0.00 Total of12283 atoms and 4087 groups and 4082 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3388 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1117 Number of atoms = 3388 Number of groups = 1122 Number of bonds = 3382 Number of angles = 1226 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2216 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1117 Number of atoms = 3388 Number of groups = 1122 Number of bonds = 3382 Number of angles = 1226 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2216 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.216" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1117" Evaluating: 1117-13 Parameter: NUMWAT <- "1104" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1104" Comparing "1075" and "1104". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.216" Parameter: BOX -> "35.216" Parameter: BOX -> "35.216" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.21600 B = 35.21600 C = 35.21600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8727 2 1 -1 -2 -1 13.9952 3 1 -1 -1 -1 2.3169 4 1 -1 0 -1 0.4176 5 1 0 -1 -1 3.3608 6 1 0 0 -1 2.4162 7 1 -1 -1 0 2.9083 8 1 -1 0 0 6.0872 9 1 0 -1 0 2.7225 10 1 0 1 0 2.7225 11 1 0 0 1 2.4162 12 1 0 1 1 3.3608 13 1 2 1 1 9.8727 14 1 1 2 1 13.9952 15 1 1 1 1 2.3169 16 1 1 0 1 0.4176 17 1 1 1 0 2.9083 18 1 1 0 0 6.0872 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3312 atoms have been selected out of 3388 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.81 2 C002 has 33 11 11 11.22 3 C003 has 2625 875 875 0.00 4 C004 has 822 274 274 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1197 399 399 0.00 Total of12283 atoms and 4087 groups and 4082 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3388 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1117 Number of atoms = 3388 Number of groups = 1122 Number of bonds = 3382 Number of angles = 1226 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2216 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1117 Number of atoms = 3388 Number of groups = 1122 Number of bonds = 3382 Number of angles = 1226 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2216 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.214" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1117" Evaluating: 1117-13 Parameter: NUMWAT <- "1104" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1104" Comparing "1075" and "1104". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.214" Parameter: BOX -> "35.214" Parameter: BOX -> "35.214" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.21400 B = 35.21400 C = 35.21400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8703 2 1 -1 -2 -1 13.9921 3 1 -1 -1 -1 2.3150 4 1 -1 0 -1 0.4183 5 1 0 -1 -1 3.3613 6 1 0 0 -1 2.4152 7 1 -1 -1 0 2.9069 8 1 -1 0 0 6.0865 9 1 0 -1 0 2.7216 10 1 0 1 0 2.7216 11 1 0 0 1 2.4152 12 1 0 1 1 3.3613 13 1 2 1 1 9.8703 14 1 1 2 1 13.9921 15 1 1 1 1 2.3150 16 1 1 0 1 0.4183 17 1 1 1 0 2.9069 18 1 1 0 0 6.0865 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3312 atoms have been selected out of 3388 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.81 2 C002 has 33 11 11 11.22 3 C003 has 2625 875 875 0.00 4 C004 has 822 274 274 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1200 400 400 0.00 Total of12286 atoms and 4088 groups and 4083 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3388 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1117 Number of atoms = 3388 Number of groups = 1122 Number of bonds = 3382 Number of angles = 1226 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2216 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1117 Number of atoms = 3388 Number of groups = 1122 Number of bonds = 3382 Number of angles = 1226 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2216 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.212" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1117" Evaluating: 1117-13 Parameter: NUMWAT <- "1104" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1104" Comparing "1075" and "1104". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.212" Parameter: BOX -> "35.212" Parameter: BOX -> "35.212" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.21200 B = 35.21200 C = 35.21200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8678 2 1 -1 -2 -1 13.9891 3 1 -1 -1 -1 2.3130 4 1 -1 0 -1 0.4189 5 1 0 -1 -1 3.3617 6 1 0 0 -1 2.4141 7 1 -1 -1 0 2.9056 8 1 -1 0 0 6.0859 9 1 0 -1 0 2.7207 10 1 0 1 0 2.7207 11 1 0 0 1 2.4141 12 1 0 1 1 3.3617 13 1 2 1 1 9.8678 14 1 1 2 1 13.9891 15 1 1 1 1 2.3130 16 1 1 0 1 0.4189 17 1 1 1 0 2.9056 18 1 1 0 0 6.0859 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3312 atoms have been selected out of 3388 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.81 2 C002 has 33 11 11 11.22 3 C003 has 2625 875 875 0.00 4 C004 has 822 274 274 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1203 401 401 0.00 Total of12289 atoms and 4089 groups and 4084 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3388 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1117 Number of atoms = 3388 Number of groups = 1122 Number of bonds = 3382 Number of angles = 1226 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2216 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1117 Number of atoms = 3388 Number of groups = 1122 Number of bonds = 3382 Number of angles = 1226 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2216 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.21" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1117" Evaluating: 1117-13 Parameter: NUMWAT <- "1104" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1104" Comparing "1075" and "1104". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.21" Parameter: BOX -> "35.21" Parameter: BOX -> "35.21" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.21000 B = 35.21000 C = 35.21000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8653 2 1 -1 -2 -1 13.9860 3 1 -1 -1 -1 2.3110 4 1 -1 0 -1 0.4196 5 1 0 -1 -1 3.3622 6 1 0 0 -1 2.4131 7 1 -1 -1 0 2.9043 8 1 -1 0 0 6.0852 9 1 0 -1 0 2.7198 10 1 0 1 0 2.7198 11 1 0 0 1 2.4131 12 1 0 1 1 3.3622 13 1 2 1 1 9.8653 14 1 1 2 1 13.9860 15 1 1 1 1 2.3110 16 1 1 0 1 0.4196 17 1 1 1 0 2.9043 18 1 1 0 0 6.0852 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3312 atoms have been selected out of 3388 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.81 2 C002 has 33 11 11 11.21 3 C003 has 2625 875 875 0.00 4 C004 has 822 274 274 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1203 401 401 0.00 Total of12289 atoms and 4089 groups and 4084 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3388 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1117 Number of atoms = 3388 Number of groups = 1122 Number of bonds = 3382 Number of angles = 1226 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2216 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1117 Number of atoms = 3388 Number of groups = 1122 Number of bonds = 3382 Number of angles = 1226 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2216 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.208" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1117" Evaluating: 1117-13 Parameter: NUMWAT <- "1104" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1104" Comparing "1075" and "1104". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.208" Parameter: BOX -> "35.208" Parameter: BOX -> "35.208" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.20800 B = 35.20800 C = 35.20800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8628 2 1 -1 -2 -1 13.9830 3 1 -1 -1 -1 2.3090 4 1 -1 0 -1 0.4203 5 1 0 -1 -1 3.3627 6 1 0 0 -1 2.4121 7 1 -1 -1 0 2.9030 8 1 -1 0 0 6.0845 9 1 0 -1 0 2.7190 10 1 0 1 0 2.7190 11 1 0 0 1 2.4121 12 1 0 1 1 3.3627 13 1 2 1 1 9.8628 14 1 1 2 1 13.9830 15 1 1 1 1 2.3090 16 1 1 0 1 0.4203 17 1 1 1 0 2.9030 18 1 1 0 0 6.0845 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3312 atoms have been selected out of 3388 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.80 2 C002 has 33 11 11 11.21 3 C003 has 2628 876 876 0.00 4 C004 has 822 274 274 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1203 401 401 0.00 Total of12292 atoms and 4090 groups and 4085 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3388 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1117 Number of atoms = 3388 Number of groups = 1122 Number of bonds = 3382 Number of angles = 1226 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2216 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1117 Number of atoms = 3388 Number of groups = 1122 Number of bonds = 3382 Number of angles = 1226 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2216 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.206" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1117" Evaluating: 1117-13 Parameter: NUMWAT <- "1104" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1104" Comparing "1075" and "1104". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.206" Parameter: BOX -> "35.206" Parameter: BOX -> "35.206" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.20600 B = 35.20600 C = 35.20600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8603 2 1 -1 -2 -1 13.9799 3 1 -1 -1 -1 2.3070 4 1 -1 0 -1 0.4210 5 1 0 -1 -1 3.3631 6 1 0 0 -1 2.4110 7 1 -1 -1 0 2.9016 8 1 -1 0 0 6.0838 9 1 0 -1 0 2.7181 10 1 0 1 0 2.7181 11 1 0 0 1 2.4110 12 1 0 1 1 3.3631 13 1 2 1 1 9.8603 14 1 1 2 1 13.9799 15 1 1 1 1 2.3070 16 1 1 0 1 0.4210 17 1 1 1 0 2.9016 18 1 1 0 0 6.0838 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3312 atoms have been selected out of 3388 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.80 2 C002 has 33 11 11 11.21 3 C003 has 2631 877 877 0.00 4 C004 has 822 274 274 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1203 401 401 0.00 Total of12295 atoms and 4091 groups and 4086 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3388 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1117 Number of atoms = 3388 Number of groups = 1122 Number of bonds = 3382 Number of angles = 1226 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2216 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1117 Number of atoms = 3388 Number of groups = 1122 Number of bonds = 3382 Number of angles = 1226 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2216 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.204" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1117" Evaluating: 1117-13 Parameter: NUMWAT <- "1104" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1104" Comparing "1075" and "1104". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.204" Parameter: BOX -> "35.204" Parameter: BOX -> "35.204" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.20400 B = 35.20400 C = 35.20400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8578 2 1 -1 -2 -1 13.9768 3 1 -1 -1 -1 2.3050 4 1 -1 0 -1 0.4218 5 1 0 -1 -1 3.3636 6 1 0 0 -1 2.4100 7 1 -1 -1 0 2.9003 8 1 -1 0 0 6.0831 9 1 0 -1 0 2.7172 10 1 0 1 0 2.7172 11 1 0 0 1 2.4100 12 1 0 1 1 3.3636 13 1 2 1 1 9.8578 14 1 1 2 1 13.9768 15 1 1 1 1 2.3050 16 1 1 0 1 0.4218 17 1 1 1 0 2.9003 18 1 1 0 0 6.0831 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3312 atoms have been selected out of 3388 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.80 2 C002 has 33 11 11 11.20 3 C003 has 2631 877 877 0.00 4 C004 has 822 274 274 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1203 401 401 0.00 Total of12295 atoms and 4091 groups and 4086 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3388 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1117 Number of atoms = 3388 Number of groups = 1122 Number of bonds = 3382 Number of angles = 1226 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2216 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1117 Number of atoms = 3388 Number of groups = 1122 Number of bonds = 3382 Number of angles = 1226 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2216 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.202" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1117" Evaluating: 1117-13 Parameter: NUMWAT <- "1104" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1104" Comparing "1075" and "1104". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.202" Parameter: BOX -> "35.202" Parameter: BOX -> "35.202" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.20200 B = 35.20200 C = 35.20200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8553 2 1 -1 -2 -1 13.9738 3 1 -1 -1 -1 2.3030 4 1 -1 0 -1 0.4225 5 1 0 -1 -1 3.3641 6 1 0 0 -1 2.4090 7 1 -1 -1 0 2.8990 8 1 -1 0 0 6.0825 9 1 0 -1 0 2.7163 10 1 0 1 0 2.7163 11 1 0 0 1 2.4090 12 1 0 1 1 3.3641 13 1 2 1 1 9.8553 14 1 1 2 1 13.9738 15 1 1 1 1 2.3030 16 1 1 0 1 0.4225 17 1 1 1 0 2.8990 18 1 1 0 0 6.0825 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3312 atoms have been selected out of 3388 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.79 2 C002 has 33 11 11 11.20 3 C003 has 2631 877 877 0.00 4 C004 has 822 274 274 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1143 381 381 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1203 401 401 0.00 Total of12298 atoms and 4092 groups and 4087 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3388 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1117 Number of atoms = 3388 Number of groups = 1122 Number of bonds = 3382 Number of angles = 1226 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2216 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1117 Number of atoms = 3388 Number of groups = 1122 Number of bonds = 3382 Number of angles = 1226 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1120 Number of HB donors = 2216 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.2" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1117" Evaluating: 1117-13 Parameter: NUMWAT <- "1104" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1104" Comparing "1075" and "1104". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.2" Parameter: BOX -> "35.2" Parameter: BOX -> "35.2" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.20000 B = 35.20000 C = 35.20000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8528 2 1 -1 -2 -1 13.9707 3 1 -1 -1 -1 2.3011 4 1 -1 0 -1 0.4232 5 1 0 -1 -1 3.3646 6 1 0 0 -1 2.4079 7 1 -1 -1 0 2.8976 8 1 -1 0 0 6.0818 9 1 0 -1 0 2.7154 10 1 0 1 0 2.7154 11 1 0 0 1 2.4079 12 1 0 1 1 3.3646 13 1 2 1 1 9.8528 14 1 1 2 1 13.9707 15 1 1 1 1 2.3011 16 1 1 0 1 0.4232 17 1 1 1 0 2.8976 18 1 1 0 0 6.0818 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3312 atoms have been selected out of 3388 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 867 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.79 2 C002 has 33 11 11 11.20 3 C003 has 2628 876 876 0.00 4 C004 has 822 274 274 0.00 5 C005 has 846 282 282 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1215 405 405 0.00 9 C009 has 1203 401 401 0.00 Total of12292 atoms and 4090 groups and 4085 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3388 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 = 1116 Number of atoms = 3385 Number of groups = 1121 Number of bonds = 3379 Number of angles = 1225 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1119 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 = 3385 Number of groups = 1121 Number of bonds = 3379 Number of angles = 1225 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1119 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 <- "35.198" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1116" Evaluating: 1116-13 Parameter: NUMWAT <- "1103" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1103" Comparing "1075" and "1103". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.198" Parameter: BOX -> "35.198" Parameter: BOX -> "35.198" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.19800 B = 35.19800 C = 35.19800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8503 2 1 -1 -2 -1 13.9677 3 1 -1 -1 -1 2.2991 4 1 -1 0 -1 0.4240 5 1 0 -1 -1 3.3651 6 1 0 0 -1 2.4069 7 1 -1 -1 0 2.8963 8 1 -1 0 0 6.0811 9 1 0 -1 0 2.7146 10 1 0 1 0 2.7146 11 1 0 0 1 2.4069 12 1 0 1 1 3.3651 13 1 2 1 1 9.8503 14 1 1 2 1 13.9677 15 1 1 1 1 2.2991 16 1 1 0 1 0.4240 17 1 1 1 0 2.8963 18 1 1 0 0 6.0811 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3385 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.79 2 C002 has 33 11 11 11.19 3 C003 has 2628 876 876 0.00 4 C004 has 822 274 274 0.00 5 C005 has 846 282 282 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1203 401 401 0.00 Total of12286 atoms and 4088 groups and 4083 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3385 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3385 Number of groups = 1121 Number of bonds = 3379 Number of angles = 1225 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1119 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 = 3385 Number of groups = 1121 Number of bonds = 3379 Number of angles = 1225 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1119 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 <- "35.196" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1116" Evaluating: 1116-13 Parameter: NUMWAT <- "1103" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1103" Comparing "1075" and "1103". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.196" Parameter: BOX -> "35.196" Parameter: BOX -> "35.196" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.19600 B = 35.19600 C = 35.19600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8478 2 1 -1 -2 -1 13.9646 3 1 -1 -1 -1 2.2971 4 1 -1 0 -1 0.4248 5 1 0 -1 -1 3.3655 6 1 0 0 -1 2.4059 7 1 -1 -1 0 2.8950 8 1 -1 0 0 6.0804 9 1 0 -1 0 2.7137 10 1 0 1 0 2.7137 11 1 0 0 1 2.4059 12 1 0 1 1 3.3655 13 1 2 1 1 9.8478 14 1 1 2 1 13.9646 15 1 1 1 1 2.2971 16 1 1 0 1 0.4248 17 1 1 1 0 2.8950 18 1 1 0 0 6.0804 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3385 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 901 OPERATED ON BY TRANSFORMATION C005 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.78 2 C002 has 33 11 11 11.19 3 C003 has 2625 875 875 0.00 4 C004 has 822 274 274 0.00 5 C005 has 861 287 287 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1215 405 405 0.00 9 C009 has 1203 401 401 0.00 Total of12298 atoms and 4092 groups and 4087 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3385 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 = 3382 Number of groups = 1120 Number of bonds = 3376 Number of angles = 1224 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1118 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 = 3382 Number of groups = 1120 Number of bonds = 3376 Number of angles = 1224 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1118 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 <- "35.194" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1115" Evaluating: 1115-13 Parameter: NUMWAT <- "1102" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1102" Comparing "1075" and "1102". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.194" Parameter: BOX -> "35.194" Parameter: BOX -> "35.194" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.19400 B = 35.19400 C = 35.19400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8454 2 1 -1 -2 -1 13.9616 3 1 -1 -1 -1 2.2951 4 1 -1 0 -1 0.4255 5 1 0 -1 -1 3.3660 6 1 0 0 -1 2.4048 7 1 -1 -1 0 2.8937 8 1 -1 0 0 6.0797 9 1 0 -1 0 2.7128 10 1 0 1 0 2.7128 11 1 0 0 1 2.4048 12 1 0 1 1 3.3660 13 1 2 1 1 9.8454 14 1 1 2 1 13.9616 15 1 1 1 1 2.2951 16 1 1 0 1 0.4255 17 1 1 1 0 2.8937 18 1 1 0 0 6.0797 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3382 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.78 2 C002 has 33 11 11 11.19 3 C003 has 2625 875 875 0.00 4 C004 has 822 274 274 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1200 400 400 0.00 Total of12271 atoms and 4083 groups and 4078 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3382 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3382 Number of groups = 1120 Number of bonds = 3376 Number of angles = 1224 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1118 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 = 3382 Number of groups = 1120 Number of bonds = 3376 Number of angles = 1224 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1118 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 <- "35.192" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1115" Evaluating: 1115-13 Parameter: NUMWAT <- "1102" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1102" Comparing "1075" and "1102". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.192" Parameter: BOX -> "35.192" Parameter: BOX -> "35.192" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.19200 B = 35.19200 C = 35.19200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8429 2 1 -1 -2 -1 13.9585 3 1 -1 -1 -1 2.2931 4 1 -1 0 -1 0.4263 5 1 0 -1 -1 3.3665 6 1 0 0 -1 2.4038 7 1 -1 -1 0 2.8924 8 1 -1 0 0 6.0791 9 1 0 -1 0 2.7119 10 1 0 1 0 2.7119 11 1 0 0 1 2.4038 12 1 0 1 1 3.3665 13 1 2 1 1 9.8429 14 1 1 2 1 13.9585 15 1 1 1 1 2.2931 16 1 1 0 1 0.4263 17 1 1 1 0 2.8924 18 1 1 0 0 6.0791 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3382 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.78 2 C002 has 33 11 11 11.18 3 C003 has 2625 875 875 0.00 4 C004 has 822 274 274 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1200 400 400 0.00 Total of12274 atoms and 4084 groups and 4079 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3382 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3382 Number of groups = 1120 Number of bonds = 3376 Number of angles = 1224 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1118 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 = 3382 Number of groups = 1120 Number of bonds = 3376 Number of angles = 1224 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1118 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 <- "35.19" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1115" Evaluating: 1115-13 Parameter: NUMWAT <- "1102" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1102" Comparing "1075" and "1102". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.19" Parameter: BOX -> "35.19" Parameter: BOX -> "35.19" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.19000 B = 35.19000 C = 35.19000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8404 2 1 -1 -2 -1 13.9555 3 1 -1 -1 -1 2.2911 4 1 -1 0 -1 0.4271 5 1 0 -1 -1 3.3670 6 1 0 0 -1 2.4028 7 1 -1 -1 0 2.8910 8 1 -1 0 0 6.0784 9 1 0 -1 0 2.7111 10 1 0 1 0 2.7111 11 1 0 0 1 2.4028 12 1 0 1 1 3.3670 13 1 2 1 1 9.8404 14 1 1 2 1 13.9555 15 1 1 1 1 2.2911 16 1 1 0 1 0.4271 17 1 1 1 0 2.8910 18 1 1 0 0 6.0784 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3382 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.77 2 C002 has 33 11 11 11.18 3 C003 has 2625 875 875 0.00 4 C004 has 822 274 274 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1203 401 401 0.00 Total of12277 atoms and 4085 groups and 4080 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3382 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3382 Number of groups = 1120 Number of bonds = 3376 Number of angles = 1224 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1118 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 = 3382 Number of groups = 1120 Number of bonds = 3376 Number of angles = 1224 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1118 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 <- "35.188" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1115" Evaluating: 1115-13 Parameter: NUMWAT <- "1102" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1102" Comparing "1075" and "1102". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.188" Parameter: BOX -> "35.188" Parameter: BOX -> "35.188" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.18800 B = 35.18800 C = 35.18800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8379 2 1 -1 -2 -1 13.9524 3 1 -1 -1 -1 2.2892 4 1 -1 0 -1 0.4280 5 1 0 -1 -1 3.3675 6 1 0 0 -1 2.4017 7 1 -1 -1 0 2.8897 8 1 -1 0 0 6.0777 9 1 0 -1 0 2.7102 10 1 0 1 0 2.7102 11 1 0 0 1 2.4017 12 1 0 1 1 3.3675 13 1 2 1 1 9.8379 14 1 1 2 1 13.9524 15 1 1 1 1 2.2892 16 1 1 0 1 0.4280 17 1 1 1 0 2.8897 18 1 1 0 0 6.0777 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3382 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.77 2 C002 has 33 11 11 11.18 3 C003 has 2625 875 875 0.00 4 C004 has 822 274 274 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1206 402 402 0.00 Total of12280 atoms and 4086 groups and 4081 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3382 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3382 Number of groups = 1120 Number of bonds = 3376 Number of angles = 1224 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1118 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 = 3382 Number of groups = 1120 Number of bonds = 3376 Number of angles = 1224 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1118 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 <- "35.186" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1115" Evaluating: 1115-13 Parameter: NUMWAT <- "1102" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1102" Comparing "1075" and "1102". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.186" Parameter: BOX -> "35.186" Parameter: BOX -> "35.186" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.18600 B = 35.18600 C = 35.18600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8354 2 1 -1 -2 -1 13.9493 3 1 -1 -1 -1 2.2872 4 1 -1 0 -1 0.4288 5 1 0 -1 -1 3.3680 6 1 0 0 -1 2.4007 7 1 -1 -1 0 2.8884 8 1 -1 0 0 6.0770 9 1 0 -1 0 2.7093 10 1 0 1 0 2.7093 11 1 0 0 1 2.4007 12 1 0 1 1 3.3680 13 1 2 1 1 9.8354 14 1 1 2 1 13.9493 15 1 1 1 1 2.2872 16 1 1 0 1 0.4288 17 1 1 1 0 2.8884 18 1 1 0 0 6.0770 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3382 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.77 2 C002 has 33 11 11 11.18 3 C003 has 2625 875 875 0.00 4 C004 has 822 274 274 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1206 402 402 0.00 Total of12280 atoms and 4086 groups and 4081 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3382 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3382 Number of groups = 1120 Number of bonds = 3376 Number of angles = 1224 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1118 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 = 3382 Number of groups = 1120 Number of bonds = 3376 Number of angles = 1224 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1118 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 <- "35.184" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1115" Evaluating: 1115-13 Parameter: NUMWAT <- "1102" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1102" Comparing "1075" and "1102". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.184" Parameter: BOX -> "35.184" Parameter: BOX -> "35.184" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.18400 B = 35.18400 C = 35.18400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8329 2 1 -1 -2 -1 13.9463 3 1 -1 -1 -1 2.2852 4 1 -1 0 -1 0.4296 5 1 0 -1 -1 3.3685 6 1 0 0 -1 2.3997 7 1 -1 -1 0 2.8871 8 1 -1 0 0 6.0764 9 1 0 -1 0 2.7084 10 1 0 1 0 2.7084 11 1 0 0 1 2.3997 12 1 0 1 1 3.3685 13 1 2 1 1 9.8329 14 1 1 2 1 13.9463 15 1 1 1 1 2.2852 16 1 1 0 1 0.4296 17 1 1 1 0 2.8871 18 1 1 0 0 6.0764 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3382 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 195 65 65 5.77 2 C002 has 33 11 11 11.17 3 C003 has 2625 875 875 0.00 4 C004 has 822 274 274 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1206 402 402 0.00 Total of12280 atoms and 4086 groups and 4081 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3382 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3382 Number of groups = 1120 Number of bonds = 3376 Number of angles = 1224 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1118 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 = 3382 Number of groups = 1120 Number of bonds = 3376 Number of angles = 1224 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1118 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 <- "35.182" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1115" Evaluating: 1115-13 Parameter: NUMWAT <- "1102" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1102" Comparing "1075" and "1102". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.182" Parameter: BOX -> "35.182" Parameter: BOX -> "35.182" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.18200 B = 35.18200 C = 35.18200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8304 2 1 -1 -2 -1 13.9432 3 1 -1 -1 -1 2.2832 4 1 -1 0 -1 0.4305 5 1 0 -1 -1 3.3690 6 1 0 0 -1 2.3987 7 1 -1 -1 0 2.8858 8 1 -1 0 0 6.0757 9 1 0 -1 0 2.7076 10 1 0 1 0 2.7076 11 1 0 0 1 2.3987 12 1 0 1 1 3.3690 13 1 2 1 1 9.8304 14 1 1 2 1 13.9432 15 1 1 1 1 2.2832 16 1 1 0 1 0.4305 17 1 1 1 0 2.8858 18 1 1 0 0 6.0757 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3382 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 C009 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.76 2 C002 has 30 10 10 11.17 3 C003 has 2625 875 875 0.00 4 C004 has 825 275 275 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1215 405 405 0.00 9 C009 has 1203 401 401 0.00 Total of12280 atoms and 4086 groups and 4081 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3382 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 = 3379 Number of groups = 1119 Number of bonds = 3373 Number of angles = 1223 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1117 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 = 3379 Number of groups = 1119 Number of bonds = 3373 Number of angles = 1223 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1117 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 <- "35.18" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1114" Evaluating: 1114-13 Parameter: NUMWAT <- "1101" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1101" Comparing "1075" and "1101". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.18" Parameter: BOX -> "35.18" Parameter: BOX -> "35.18" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.18000 B = 35.18000 C = 35.18000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8280 2 1 -1 -2 -1 13.9402 3 1 -1 -1 -1 2.2812 4 1 -1 0 -1 0.4313 5 1 0 -1 -1 3.3695 6 1 0 0 -1 2.3976 7 1 -1 -1 0 2.8845 8 1 -1 0 0 6.0750 9 1 0 -1 0 2.7067 10 1 0 1 0 2.7067 11 1 0 0 1 2.3976 12 1 0 1 1 3.3695 13 1 2 1 1 9.8280 14 1 1 2 1 13.9402 15 1 1 1 1 2.2812 16 1 1 0 1 0.4313 17 1 1 1 0 2.8845 18 1 1 0 0 6.0750 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3379 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.76 2 C002 has 30 10 10 11.17 3 C003 has 2622 874 874 0.00 4 C004 has 822 274 274 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 822 274 274 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1203 401 401 0.00 Total of12268 atoms and 4082 groups and 4077 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3379 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3379 Number of groups = 1119 Number of bonds = 3373 Number of angles = 1223 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1117 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 = 3379 Number of groups = 1119 Number of bonds = 3373 Number of angles = 1223 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1117 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 <- "35.178" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1114" Evaluating: 1114-13 Parameter: NUMWAT <- "1101" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1101" Comparing "1075" and "1101". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.178" Parameter: BOX -> "35.178" Parameter: BOX -> "35.178" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.17800 B = 35.17800 C = 35.17800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8255 2 1 -1 -2 -1 13.9371 3 1 -1 -1 -1 2.2792 4 1 -1 0 -1 0.4322 5 1 0 -1 -1 3.3700 6 1 0 0 -1 2.3966 7 1 -1 -1 0 2.8831 8 1 -1 0 0 6.0743 9 1 0 -1 0 2.7058 10 1 0 1 0 2.7058 11 1 0 0 1 2.3966 12 1 0 1 1 3.3700 13 1 2 1 1 9.8255 14 1 1 2 1 13.9371 15 1 1 1 1 2.2792 16 1 1 0 1 0.4322 17 1 1 1 0 2.8831 18 1 1 0 0 6.0743 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3379 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 906 OPERATED ON BY TRANSFORMATION C009 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.76 2 C002 has 27 9 9 11.16 3 C003 has 2622 874 874 0.00 4 C004 has 825 275 275 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1206 402 402 0.00 Total of12277 atoms and 4085 groups and 4080 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3379 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 = 3376 Number of groups = 1118 Number of bonds = 3370 Number of angles = 1222 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1116 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 = 3376 Number of groups = 1118 Number of bonds = 3370 Number of angles = 1222 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1116 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 <- "35.176" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1113" Evaluating: 1113-13 Parameter: NUMWAT <- "1100" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1100" Comparing "1075" and "1100". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.176" Parameter: BOX -> "35.176" Parameter: BOX -> "35.176" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.17600 B = 35.17600 C = 35.17600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8230 2 1 -1 -2 -1 13.9341 3 1 -1 -1 -1 2.2773 4 1 -1 0 -1 0.4331 5 1 0 -1 -1 3.3705 6 1 0 0 -1 2.3956 7 1 -1 -1 0 2.8818 8 1 -1 0 0 6.0737 9 1 0 -1 0 2.7050 10 1 0 1 0 2.7050 11 1 0 0 1 2.3956 12 1 0 1 1 3.3705 13 1 2 1 1 9.8230 14 1 1 2 1 13.9341 15 1 1 1 1 2.2773 16 1 1 0 1 0.4331 17 1 1 1 0 2.8818 18 1 1 0 0 6.0737 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3376 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.75 2 C002 has 27 9 9 11.16 3 C003 has 2619 873 873 0.00 4 C004 has 822 274 274 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1200 400 400 0.00 Total of12259 atoms and 4079 groups and 4074 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3376 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3376 Number of groups = 1118 Number of bonds = 3370 Number of angles = 1222 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1116 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 = 3376 Number of groups = 1118 Number of bonds = 3370 Number of angles = 1222 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1116 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 <- "35.174" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1113" Evaluating: 1113-13 Parameter: NUMWAT <- "1100" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1100" Comparing "1075" and "1100". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.174" Parameter: BOX -> "35.174" Parameter: BOX -> "35.174" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.17400 B = 35.17400 C = 35.17400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8205 2 1 -1 -2 -1 13.9310 3 1 -1 -1 -1 2.2753 4 1 -1 0 -1 0.4339 5 1 0 -1 -1 3.3710 6 1 0 0 -1 2.3946 7 1 -1 -1 0 2.8805 8 1 -1 0 0 6.0730 9 1 0 -1 0 2.7041 10 1 0 1 0 2.7041 11 1 0 0 1 2.3946 12 1 0 1 1 3.3710 13 1 2 1 1 9.8205 14 1 1 2 1 13.9310 15 1 1 1 1 2.2753 16 1 1 0 1 0.4339 17 1 1 1 0 2.8805 18 1 1 0 0 6.0730 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3376 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.75 2 C002 has 27 9 9 11.16 3 C003 has 2619 873 873 0.00 4 C004 has 822 274 274 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1200 400 400 0.00 Total of12259 atoms and 4079 groups and 4074 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3376 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3376 Number of groups = 1118 Number of bonds = 3370 Number of angles = 1222 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1116 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 = 3376 Number of groups = 1118 Number of bonds = 3370 Number of angles = 1222 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1116 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 <- "35.172" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1113" Evaluating: 1113-13 Parameter: NUMWAT <- "1100" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1100" Comparing "1075" and "1100". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.172" Parameter: BOX -> "35.172" Parameter: BOX -> "35.172" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.17200 B = 35.17200 C = 35.17200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8180 2 1 -1 -2 -1 13.9280 3 1 -1 -1 -1 2.2733 4 1 -1 0 -1 0.4348 5 1 0 -1 -1 3.3715 6 1 0 0 -1 2.3936 7 1 -1 -1 0 2.8792 8 1 -1 0 0 6.0723 9 1 0 -1 0 2.7032 10 1 0 1 0 2.7032 11 1 0 0 1 2.3936 12 1 0 1 1 3.3715 13 1 2 1 1 9.8180 14 1 1 2 1 13.9280 15 1 1 1 1 2.2733 16 1 1 0 1 0.4348 17 1 1 1 0 2.8792 18 1 1 0 0 6.0723 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3376 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.75 2 C002 has 27 9 9 11.15 3 C003 has 2619 873 873 0.00 4 C004 has 822 274 274 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1215 405 405 0.00 9 C009 has 1200 400 400 0.00 Total of12262 atoms and 4080 groups and 4075 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3376 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3376 Number of groups = 1118 Number of bonds = 3370 Number of angles = 1222 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1116 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 = 3376 Number of groups = 1118 Number of bonds = 3370 Number of angles = 1222 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1116 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 <- "35.17" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1113" Evaluating: 1113-13 Parameter: NUMWAT <- "1100" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1100" Comparing "1075" and "1100". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.17" Parameter: BOX -> "35.17" Parameter: BOX -> "35.17" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.17000 B = 35.17000 C = 35.17000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8155 2 1 -1 -2 -1 13.9249 3 1 -1 -1 -1 2.2713 4 1 -1 0 -1 0.4357 5 1 0 -1 -1 3.3720 6 1 0 0 -1 2.3925 7 1 -1 -1 0 2.8779 8 1 -1 0 0 6.0717 9 1 0 -1 0 2.7024 10 1 0 1 0 2.7024 11 1 0 0 1 2.3925 12 1 0 1 1 3.3720 13 1 2 1 1 9.8155 14 1 1 2 1 13.9249 15 1 1 1 1 2.2713 16 1 1 0 1 0.4357 17 1 1 1 0 2.8779 18 1 1 0 0 6.0717 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3376 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.74 2 C002 has 27 9 9 11.15 3 C003 has 2619 873 873 0.00 4 C004 has 822 274 274 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1215 405 405 0.00 9 C009 has 1200 400 400 0.00 Total of12262 atoms and 4080 groups and 4075 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3376 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3376 Number of groups = 1118 Number of bonds = 3370 Number of angles = 1222 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1116 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 = 3376 Number of groups = 1118 Number of bonds = 3370 Number of angles = 1222 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1116 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 <- "35.168" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1113" Evaluating: 1113-13 Parameter: NUMWAT <- "1100" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1100" Comparing "1075" and "1100". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.168" Parameter: BOX -> "35.168" Parameter: BOX -> "35.168" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.16800 B = 35.16800 C = 35.16800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8131 2 1 -1 -2 -1 13.9218 3 1 -1 -1 -1 2.2693 4 1 -1 0 -1 0.4367 5 1 0 -1 -1 3.3725 6 1 0 0 -1 2.3915 7 1 -1 -1 0 2.8766 8 1 -1 0 0 6.0705 9 1 0 -1 0 2.7015 10 1 0 1 0 2.7015 11 1 0 0 1 2.3915 12 1 0 1 1 3.3725 13 1 2 1 1 9.8131 14 1 1 2 1 13.9218 15 1 1 1 1 2.2693 16 1 1 0 1 0.4367 17 1 1 1 0 2.8766 18 1 1 0 0 6.0705 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3376 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.74 2 C002 has 27 9 9 11.15 3 C003 has 2619 873 873 0.00 4 C004 has 822 274 274 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1143 381 381 0.00 7 C007 has 825 275 275 0.00 8 C008 has 1215 405 405 0.00 9 C009 has 1200 400 400 0.00 Total of12268 atoms and 4082 groups and 4077 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3376 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3376 Number of groups = 1118 Number of bonds = 3370 Number of angles = 1222 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1116 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 = 3376 Number of groups = 1118 Number of bonds = 3370 Number of angles = 1222 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1116 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 <- "35.166" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1113" Evaluating: 1113-13 Parameter: NUMWAT <- "1100" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1100" Comparing "1075" and "1100". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.166" Parameter: BOX -> "35.166" Parameter: BOX -> "35.166" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.16600 B = 35.16600 C = 35.16600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8106 2 1 -1 -2 -1 13.9188 3 1 -1 -1 -1 2.2673 4 1 -1 0 -1 0.4376 5 1 0 -1 -1 3.3730 6 1 0 0 -1 2.3905 7 1 -1 -1 0 2.8753 8 1 -1 0 0 6.0689 9 1 0 -1 0 2.7007 10 1 0 1 0 2.7007 11 1 0 0 1 2.3905 12 1 0 1 1 3.3730 13 1 2 1 1 9.8106 14 1 1 2 1 13.9188 15 1 1 1 1 2.2673 16 1 1 0 1 0.4376 17 1 1 1 0 2.8753 18 1 1 0 0 6.0689 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3376 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 C018 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.74 2 C002 has 27 9 9 11.14 3 C003 has 2625 875 875 0.00 4 C004 has 825 275 275 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1143 381 381 0.00 7 C007 has 801 267 267 0.00 8 C008 has 1209 403 403 0.00 9 C009 has 1209 403 403 0.00 Total of12256 atoms and 4078 groups and 4073 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3376 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 = 1112 Number of atoms = 3373 Number of groups = 1117 Number of bonds = 3367 Number of angles = 1221 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1115 Number of HB donors = 2206 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1112 Number of atoms = 3373 Number of groups = 1117 Number of bonds = 3367 Number of angles = 1221 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1115 Number of HB donors = 2206 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.164" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1112" Evaluating: 1112-13 Parameter: NUMWAT <- "1099" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1099" Comparing "1075" and "1099". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.164" Parameter: BOX -> "35.164" Parameter: BOX -> "35.164" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.16400 B = 35.16400 C = 35.16400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8081 2 1 -1 -2 -1 13.9157 3 1 -1 -1 -1 2.2653 4 1 -1 0 -1 0.4385 5 1 0 -1 -1 3.3735 6 1 0 0 -1 2.3895 7 1 -1 -1 0 2.8740 8 1 -1 0 0 6.0697 9 1 0 -1 0 2.6998 10 1 0 1 0 2.6998 11 1 0 0 1 2.3895 12 1 0 1 1 3.3735 13 1 2 1 1 9.8081 14 1 1 2 1 13.9157 15 1 1 1 1 2.2653 16 1 1 0 1 0.4385 17 1 1 1 0 2.8740 18 1 1 0 0 6.0697 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3297 atoms have been selected out of 3373 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.73 2 C002 has 27 9 9 11.14 3 C003 has 2622 874 874 0.00 4 C004 has 822 274 274 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1143 381 381 0.00 7 C007 has 801 267 267 0.00 8 C008 has 1206 402 402 0.00 9 C009 has 1200 400 400 0.00 Total of12235 atoms and 4071 groups and 4066 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3373 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1112 Number of atoms = 3373 Number of groups = 1117 Number of bonds = 3367 Number of angles = 1221 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1115 Number of HB donors = 2206 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1112 Number of atoms = 3373 Number of groups = 1117 Number of bonds = 3367 Number of angles = 1221 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1115 Number of HB donors = 2206 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.162" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1112" Evaluating: 1112-13 Parameter: NUMWAT <- "1099" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1099" Comparing "1075" and "1099". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.162" Parameter: BOX -> "35.162" Parameter: BOX -> "35.162" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.16200 B = 35.16200 C = 35.16200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8056 2 1 -1 -2 -1 13.9127 3 1 -1 -1 -1 2.2634 4 1 -1 0 -1 0.4395 5 1 0 -1 -1 3.3740 6 1 0 0 -1 2.3885 7 1 -1 -1 0 2.8727 8 1 -1 0 0 6.0690 9 1 0 -1 0 2.6989 10 1 0 1 0 2.6989 11 1 0 0 1 2.3885 12 1 0 1 1 3.3740 13 1 2 1 1 9.8056 14 1 1 2 1 13.9127 15 1 1 1 1 2.2634 16 1 1 0 1 0.4395 17 1 1 1 0 2.8727 18 1 1 0 0 6.0690 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3297 atoms have been selected out of 3373 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 806 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 201 67 67 5.73 2 C002 has 30 10 10 11.14 3 C003 has 2622 874 874 0.00 4 C004 has 819 273 273 0.00 5 C005 has 846 282 282 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 804 268 268 0.00 8 C008 has 1203 401 401 0.00 9 C009 has 1200 400 400 0.00 Total of12238 atoms and 4072 groups and 4067 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3373 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 = 1111 Number of atoms = 3370 Number of groups = 1116 Number of bonds = 3364 Number of angles = 1220 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1114 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 = 3370 Number of groups = 1116 Number of bonds = 3364 Number of angles = 1220 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1114 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 <- "35.16" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1111" Evaluating: 1111-13 Parameter: NUMWAT <- "1098" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1098" Comparing "1075" and "1098". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.16" Parameter: BOX -> "35.16" Parameter: BOX -> "35.16" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.16000 B = 35.16000 C = 35.16000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8031 2 1 -1 -2 -1 13.9096 3 1 -1 -1 -1 2.2614 4 1 -1 0 -1 0.4404 5 1 0 -1 -1 3.3745 6 1 0 0 -1 2.3875 7 1 -1 -1 0 2.8714 8 1 -1 0 0 6.0683 9 1 0 -1 0 2.6981 10 1 0 1 0 2.6981 11 1 0 0 1 2.3875 12 1 0 1 1 3.3745 13 1 2 1 1 9.8031 14 1 1 2 1 13.9096 15 1 1 1 1 2.2614 16 1 1 0 1 0.4404 17 1 1 1 0 2.8714 18 1 1 0 0 6.0683 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3370 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 201 67 67 5.73 2 C002 has 27 9 9 11.14 3 C003 has 2619 873 873 0.00 4 C004 has 819 273 273 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 801 267 267 0.00 8 C008 has 1203 401 401 0.00 9 C009 has 1197 399 399 0.00 Total of12220 atoms and 4066 groups and 4061 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3370 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3370 Number of groups = 1116 Number of bonds = 3364 Number of angles = 1220 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1114 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 = 3370 Number of groups = 1116 Number of bonds = 3364 Number of angles = 1220 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1114 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 <- "35.158" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1111" Evaluating: 1111-13 Parameter: NUMWAT <- "1098" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1098" Comparing "1075" and "1098". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.158" Parameter: BOX -> "35.158" Parameter: BOX -> "35.158" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.15800 B = 35.15800 C = 35.15800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.8007 2 1 -1 -2 -1 13.9066 3 1 -1 -1 -1 2.2594 4 1 -1 0 -1 0.4414 5 1 0 -1 -1 3.3750 6 1 0 0 -1 2.3865 7 1 -1 -1 0 2.8701 8 1 -1 0 0 6.0677 9 1 0 -1 0 2.6972 10 1 0 1 0 2.6972 11 1 0 0 1 2.3865 12 1 0 1 1 3.3750 13 1 2 1 1 9.8007 14 1 1 2 1 13.9066 15 1 1 1 1 2.2594 16 1 1 0 1 0.4414 17 1 1 1 0 2.8701 18 1 1 0 0 6.0677 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3370 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 201 67 67 5.73 2 C002 has 27 9 9 11.13 3 C003 has 2619 873 873 0.00 4 C004 has 819 273 273 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 801 267 267 0.00 8 C008 has 1206 402 402 0.00 9 C009 has 1197 399 399 0.00 Total of12223 atoms and 4067 groups and 4062 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3370 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3370 Number of groups = 1116 Number of bonds = 3364 Number of angles = 1220 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1114 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 = 3370 Number of groups = 1116 Number of bonds = 3364 Number of angles = 1220 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1114 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 <- "35.156" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1111" Evaluating: 1111-13 Parameter: NUMWAT <- "1098" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1098" Comparing "1075" and "1098". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.156" Parameter: BOX -> "35.156" Parameter: BOX -> "35.156" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.15600 B = 35.15600 C = 35.15600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7982 2 1 -1 -2 -1 13.9035 3 1 -1 -1 -1 2.2574 4 1 -1 0 -1 0.4424 5 1 0 -1 -1 3.3755 6 1 0 0 -1 2.3855 7 1 -1 -1 0 2.8688 8 1 -1 0 0 6.0670 9 1 0 -1 0 2.6964 10 1 0 1 0 2.6964 11 1 0 0 1 2.3855 12 1 0 1 1 3.3755 13 1 2 1 1 9.7982 14 1 1 2 1 13.9035 15 1 1 1 1 2.2574 16 1 1 0 1 0.4424 17 1 1 1 0 2.8688 18 1 1 0 0 6.0670 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3370 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 573 OPERATED ON BY TRANSFORMATION C017 RESIDUE 1101 OPERATED ON BY TRANSFORMATION C006 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 204 68 68 5.72 2 C002 has 27 9 9 11.13 3 C003 has 2619 873 873 0.00 4 C004 has 813 271 271 0.00 5 C005 has 840 280 280 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 786 262 262 0.00 8 C008 has 1212 404 404 0.00 9 C009 has 1203 401 401 0.00 Total of12214 atoms and 4064 groups and 4059 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3370 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 = 1109 Number of atoms = 3364 Number of groups = 1114 Number of bonds = 3358 Number of angles = 1218 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1112 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 = 3364 Number of groups = 1114 Number of bonds = 3358 Number of angles = 1218 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1112 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 <- "35.154" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1109" Evaluating: 1109-13 Parameter: NUMWAT <- "1096" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1096" Comparing "1075" and "1096". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.154" Parameter: BOX -> "35.154" Parameter: BOX -> "35.154" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.15400 B = 35.15400 C = 35.15400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7957 2 1 -1 -2 -1 13.9005 3 1 -1 -1 -1 2.2554 4 1 -1 0 -1 0.4434 5 1 0 -1 -1 4.4317 6 1 0 0 -1 5.7922 7 1 -1 -1 0 2.8675 8 1 -1 0 0 6.0663 9 1 0 -1 0 2.6955 10 1 0 1 0 2.6955 11 1 0 0 1 5.7922 12 1 0 1 1 4.4317 13 1 2 1 1 9.7957 14 1 1 2 1 13.9005 15 1 1 1 1 2.2554 16 1 1 0 1 0.4434 17 1 1 1 0 2.8675 18 1 1 0 0 6.0663 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3364 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 902 OPERATED ON BY TRANSFORMATION C018 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 204 68 68 5.72 2 C002 has 27 9 9 11.13 3 C003 has 2616 872 872 0.00 4 C004 has 816 272 272 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1131 377 377 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1197 399 399 0.00 9 C009 has 1197 399 399 0.00 Total of12169 atoms and 4049 groups and 4044 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3364 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 = 3361 Number of groups = 1113 Number of bonds = 3355 Number of angles = 1217 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1111 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 = 3361 Number of groups = 1113 Number of bonds = 3355 Number of angles = 1217 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1111 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 <- "35.152" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1108" Evaluating: 1108-13 Parameter: NUMWAT <- "1095" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1095" Comparing "1075" and "1095". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.152" Parameter: BOX -> "35.152" Parameter: BOX -> "35.152" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.15200 B = 35.15200 C = 35.15200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7932 2 1 -1 -2 -1 13.8974 3 1 -1 -1 -1 2.2534 4 1 -1 0 -1 0.4444 5 1 0 -1 -1 4.4321 6 1 0 0 -1 5.7906 7 1 -1 -1 0 2.8662 8 1 -1 0 0 6.0657 9 1 0 -1 0 2.6947 10 1 0 1 0 2.6947 11 1 0 0 1 5.7906 12 1 0 1 1 4.4321 13 1 2 1 1 9.7932 14 1 1 2 1 13.8974 15 1 1 1 1 2.2534 16 1 1 0 1 0.4444 17 1 1 1 0 2.8662 18 1 1 0 0 6.0657 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3361 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 C015 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 201 67 67 5.72 2 C002 has 27 9 9 11.12 3 C003 has 2616 872 872 0.00 4 C004 has 813 271 271 0.00 5 C005 has 840 280 280 0.00 6 C006 has 1134 378 378 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1194 398 398 0.00 9 C009 has 1200 400 400 0.00 Total of12166 atoms and 4048 groups and 4043 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3361 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 = 3358 Number of groups = 1112 Number of bonds = 3352 Number of angles = 1216 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1110 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 = 3358 Number of groups = 1112 Number of bonds = 3352 Number of angles = 1216 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1110 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 <- "35.15" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1107" Evaluating: 1107-13 Parameter: NUMWAT <- "1094" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1094" Comparing "1075" and "1094". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.15" Parameter: BOX -> "35.15" Parameter: BOX -> "35.15" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.15000 B = 35.15000 C = 35.15000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7908 2 1 -1 -2 -1 13.8943 3 1 -1 -1 -1 2.2515 4 1 -1 0 -1 0.4454 5 1 0 -1 -1 4.4326 6 1 0 0 -1 5.7889 7 1 -1 -1 0 2.8649 8 1 -1 0 0 6.0650 9 1 0 -1 0 2.6938 10 1 0 1 0 2.6938 11 1 0 0 1 5.7889 12 1 0 1 1 4.4326 13 1 2 1 1 9.7908 14 1 1 2 1 13.8943 15 1 1 1 1 2.2515 16 1 1 0 1 0.4454 17 1 1 1 0 2.8649 18 1 1 0 0 6.0650 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3358 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 201 67 67 5.71 2 C002 has 27 9 9 11.12 3 C003 has 2613 871 871 0.00 4 C004 has 813 271 271 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1194 398 398 0.00 9 C009 has 1197 399 399 0.00 Total of12157 atoms and 4045 groups and 4040 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3358 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3358 Number of groups = 1112 Number of bonds = 3352 Number of angles = 1216 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1110 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 = 3358 Number of groups = 1112 Number of bonds = 3352 Number of angles = 1216 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1110 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 <- "35.148" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1107" Evaluating: 1107-13 Parameter: NUMWAT <- "1094" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1094" Comparing "1075" and "1094". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.148" Parameter: BOX -> "35.148" Parameter: BOX -> "35.148" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.14800 B = 35.14800 C = 35.14800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7883 2 1 -1 -2 -1 13.8913 3 1 -1 -1 -1 2.2495 4 1 -1 0 -1 0.4464 5 1 0 -1 -1 4.4330 6 1 0 0 -1 5.7872 7 1 -1 -1 0 2.8636 8 1 -1 0 0 6.0643 9 1 0 -1 0 2.6930 10 1 0 1 0 2.6930 11 1 0 0 1 5.7872 12 1 0 1 1 4.4330 13 1 2 1 1 9.7883 14 1 1 2 1 13.8913 15 1 1 1 1 2.2495 16 1 1 0 1 0.4464 17 1 1 1 0 2.8636 18 1 1 0 0 6.0643 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3358 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 C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.71 2 C002 has 27 9 9 11.12 3 C003 has 2613 871 871 0.00 4 C004 has 813 271 271 0.00 5 C005 has 840 280 280 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1194 398 398 0.00 9 C009 has 1200 400 400 0.00 Total of12157 atoms and 4045 groups and 4040 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3358 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 = 3355 Number of groups = 1111 Number of bonds = 3349 Number of angles = 1215 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1109 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 = 3355 Number of groups = 1111 Number of bonds = 3349 Number of angles = 1215 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1109 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 <- "35.146" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1106" Evaluating: 1106-13 Parameter: NUMWAT <- "1093" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1093" Comparing "1075" and "1093". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.146" Parameter: BOX -> "35.146" Parameter: BOX -> "35.146" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.14600 B = 35.14600 C = 35.14600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7858 2 1 -1 -2 -1 13.8882 3 1 -1 -1 -1 2.2475 4 1 -1 0 -1 0.4474 5 1 0 -1 -1 4.4335 6 1 0 0 -1 5.7856 7 1 -1 -1 0 2.8623 8 1 -1 0 0 6.0637 9 1 0 -1 0 2.6921 10 1 0 1 0 2.6921 11 1 0 0 1 5.7856 12 1 0 1 1 4.4335 13 1 2 1 1 9.7858 14 1 1 2 1 13.8882 15 1 1 1 1 2.2475 16 1 1 0 1 0.4474 17 1 1 1 0 2.8623 18 1 1 0 0 6.0637 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3355 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.71 2 C002 has 27 9 9 11.11 3 C003 has 2610 870 870 0.00 4 C004 has 813 271 271 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1191 397 397 0.00 9 C009 has 1197 399 399 0.00 Total of12142 atoms and 4040 groups and 4035 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3355 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3355 Number of groups = 1111 Number of bonds = 3349 Number of angles = 1215 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1109 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 = 3355 Number of groups = 1111 Number of bonds = 3349 Number of angles = 1215 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1109 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 <- "35.144" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1106" Evaluating: 1106-13 Parameter: NUMWAT <- "1093" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1093" Comparing "1075" and "1093". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.144" Parameter: BOX -> "35.144" Parameter: BOX -> "35.144" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.14400 B = 35.14400 C = 35.14400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7833 2 1 -1 -2 -1 13.8852 3 1 -1 -1 -1 2.2455 4 1 -1 0 -1 0.4485 5 1 0 -1 -1 4.4339 6 1 0 0 -1 5.7839 7 1 -1 -1 0 2.8610 8 1 -1 0 0 6.0630 9 1 0 -1 0 2.6913 10 1 0 1 0 2.6913 11 1 0 0 1 5.7839 12 1 0 1 1 4.4339 13 1 2 1 1 9.7833 14 1 1 2 1 13.8852 15 1 1 1 1 2.2455 16 1 1 0 1 0.4485 17 1 1 1 0 2.8610 18 1 1 0 0 6.0630 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3355 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.70 2 C002 has 27 9 9 11.11 3 C003 has 2613 871 871 0.00 4 C004 has 813 271 271 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1191 397 397 0.00 9 C009 has 1197 399 399 0.00 Total of12145 atoms and 4041 groups and 4036 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3355 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3355 Number of groups = 1111 Number of bonds = 3349 Number of angles = 1215 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1109 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 = 3355 Number of groups = 1111 Number of bonds = 3349 Number of angles = 1215 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1109 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 <- "35.142" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1106" Evaluating: 1106-13 Parameter: NUMWAT <- "1093" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1093" Comparing "1075" and "1093". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.142" Parameter: BOX -> "35.142" Parameter: BOX -> "35.142" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.14200 B = 35.14200 C = 35.14200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7808 2 1 -1 -2 -1 13.8821 3 1 -1 -1 -1 2.2435 4 1 -1 0 -1 0.4495 5 1 0 -1 -1 4.4344 6 1 0 0 -1 5.7822 7 1 -1 -1 0 2.8598 8 1 -1 0 0 6.0623 9 1 0 -1 0 2.6904 10 1 0 1 0 2.6904 11 1 0 0 1 5.7822 12 1 0 1 1 4.4344 13 1 2 1 1 9.7808 14 1 1 2 1 13.8821 15 1 1 1 1 2.2435 16 1 1 0 1 0.4495 17 1 1 1 0 2.8598 18 1 1 0 0 6.0623 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3355 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.70 2 C002 has 27 9 9 11.11 3 C003 has 2613 871 871 0.00 4 C004 has 813 271 271 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1191 397 397 0.00 9 C009 has 1197 399 399 0.00 Total of12145 atoms and 4041 groups and 4036 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3355 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3355 Number of groups = 1111 Number of bonds = 3349 Number of angles = 1215 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1109 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 = 3355 Number of groups = 1111 Number of bonds = 3349 Number of angles = 1215 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1109 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 <- "35.14" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1106" Evaluating: 1106-13 Parameter: NUMWAT <- "1093" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1093" Comparing "1075" and "1093". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.14" Parameter: BOX -> "35.14" Parameter: BOX -> "35.14" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.14000 B = 35.14000 C = 35.14000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7784 2 1 -1 -2 -1 13.8791 3 1 -1 -1 -1 2.2415 4 1 -1 0 -1 0.4506 5 1 0 -1 -1 4.4349 6 1 0 0 -1 5.7806 7 1 -1 -1 0 2.8585 8 1 -1 0 0 6.0617 9 1 0 -1 0 2.6896 10 1 0 1 0 2.6896 11 1 0 0 1 5.7806 12 1 0 1 1 4.4349 13 1 2 1 1 9.7784 14 1 1 2 1 13.8791 15 1 1 1 1 2.2415 16 1 1 0 1 0.4506 17 1 1 1 0 2.8585 18 1 1 0 0 6.0617 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3355 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.70 2 C002 has 27 9 9 11.10 3 C003 has 2616 872 872 0.00 4 C004 has 813 271 271 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1191 397 397 0.00 9 C009 has 1197 399 399 0.00 Total of12151 atoms and 4043 groups and 4038 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3355 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3355 Number of groups = 1111 Number of bonds = 3349 Number of angles = 1215 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1109 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 = 3355 Number of groups = 1111 Number of bonds = 3349 Number of angles = 1215 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1109 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 <- "35.138" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1106" Evaluating: 1106-13 Parameter: NUMWAT <- "1093" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1093" Comparing "1075" and "1093". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.138" Parameter: BOX -> "35.138" Parameter: BOX -> "35.138" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.13800 B = 35.13800 C = 35.13800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7759 2 1 -1 -2 -1 13.8760 3 1 -1 -1 -1 2.2396 4 1 -1 0 -1 0.4516 5 1 0 -1 -1 4.4353 6 1 0 0 -1 5.7789 7 1 -1 -1 0 2.8572 8 1 -1 0 0 6.0610 9 1 0 -1 0 2.6888 10 1 0 1 0 2.6888 11 1 0 0 1 5.7789 12 1 0 1 1 4.4353 13 1 2 1 1 9.7759 14 1 1 2 1 13.8760 15 1 1 1 1 2.2396 16 1 1 0 1 0.4516 17 1 1 1 0 2.8572 18 1 1 0 0 6.0610 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3355 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.69 2 C002 has 27 9 9 11.10 3 C003 has 2616 872 872 0.00 4 C004 has 813 271 271 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1191 397 397 0.00 9 C009 has 1197 399 399 0.00 Total of12151 atoms and 4043 groups and 4038 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3355 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3355 Number of groups = 1111 Number of bonds = 3349 Number of angles = 1215 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1109 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 = 3355 Number of groups = 1111 Number of bonds = 3349 Number of angles = 1215 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1109 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 <- "35.136" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1106" Evaluating: 1106-13 Parameter: NUMWAT <- "1093" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1093" Comparing "1075" and "1093". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.136" Parameter: BOX -> "35.136" Parameter: BOX -> "35.136" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.13600 B = 35.13600 C = 35.13600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7734 2 1 -1 -2 -1 13.8730 3 1 -1 -1 -1 2.2376 4 1 -1 0 -1 0.4527 5 1 0 -1 -1 4.4358 6 1 0 0 -1 5.7773 7 1 -1 -1 0 2.8559 8 1 -1 0 0 6.0604 9 1 0 -1 0 2.6879 10 1 0 1 0 2.6879 11 1 0 0 1 5.7773 12 1 0 1 1 4.4358 13 1 2 1 1 9.7734 14 1 1 2 1 13.8730 15 1 1 1 1 2.2376 16 1 1 0 1 0.4527 17 1 1 1 0 2.8559 18 1 1 0 0 6.0604 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3355 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 201 67 67 5.69 2 C002 has 27 9 9 11.10 3 C003 has 2616 872 872 0.00 4 C004 has 813 271 271 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1191 397 397 0.00 9 C009 has 1197 399 399 0.00 Total of12154 atoms and 4044 groups and 4039 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3355 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3355 Number of groups = 1111 Number of bonds = 3349 Number of angles = 1215 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1109 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 = 3355 Number of groups = 1111 Number of bonds = 3349 Number of angles = 1215 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1109 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 <- "35.134" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1106" Evaluating: 1106-13 Parameter: NUMWAT <- "1093" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1093" Comparing "1075" and "1093". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.134" Parameter: BOX -> "35.134" Parameter: BOX -> "35.134" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.13400 B = 35.13400 C = 35.13400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7710 2 1 -1 -2 -1 13.8699 3 1 -1 -1 -1 2.2356 4 1 -1 0 -1 0.4538 5 1 0 -1 -1 4.4363 6 1 0 0 -1 5.7756 7 1 -1 -1 0 2.8546 8 1 -1 0 0 6.0597 9 1 0 -1 0 2.6871 10 1 0 1 0 2.6871 11 1 0 0 1 5.7756 12 1 0 1 1 4.4363 13 1 2 1 1 9.7710 14 1 1 2 1 13.8699 15 1 1 1 1 2.2356 16 1 1 0 1 0.4538 17 1 1 1 0 2.8546 18 1 1 0 0 6.0597 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3355 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 161 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 201 67 67 5.69 2 C002 has 27 9 9 11.10 3 C003 has 2616 872 872 0.00 4 C004 has 813 271 271 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1194 398 398 0.00 9 C009 has 1197 399 399 0.00 Total of12154 atoms and 4044 groups and 4039 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3355 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 = 3352 Number of groups = 1110 Number of bonds = 3346 Number of angles = 1214 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1108 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 = 3352 Number of groups = 1110 Number of bonds = 3346 Number of angles = 1214 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1108 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 <- "35.132" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1105" Evaluating: 1105-13 Parameter: NUMWAT <- "1092" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1092" Comparing "1075" and "1092". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.132" Parameter: BOX -> "35.132" Parameter: BOX -> "35.132" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.13200 B = 35.13200 C = 35.13200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7685 2 1 -1 -2 -1 13.8669 3 1 -1 -1 -1 2.2336 4 1 -1 0 -1 0.4549 5 1 0 -1 -1 4.4367 6 1 0 0 -1 5.7739 7 1 -1 -1 0 2.8533 8 1 -1 0 0 6.0590 9 1 0 -1 0 2.6862 10 1 0 1 0 2.6862 11 1 0 0 1 5.7739 12 1 0 1 1 4.4367 13 1 2 1 1 9.7685 14 1 1 2 1 13.8669 15 1 1 1 1 2.2336 16 1 1 0 1 0.4549 17 1 1 1 0 2.8533 18 1 1 0 0 6.0590 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3352 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 201 67 67 5.69 2 C002 has 27 9 9 11.09 3 C003 has 2616 872 872 0.00 4 C004 has 813 271 271 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1188 396 396 0.00 9 C009 has 1197 399 399 0.00 Total of12145 atoms and 4041 groups and 4036 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3352 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3352 Number of groups = 1110 Number of bonds = 3346 Number of angles = 1214 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1108 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 = 3352 Number of groups = 1110 Number of bonds = 3346 Number of angles = 1214 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1108 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 <- "35.13" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1105" Evaluating: 1105-13 Parameter: NUMWAT <- "1092" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1092" Comparing "1075" and "1092". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.13" Parameter: BOX -> "35.13" Parameter: BOX -> "35.13" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.13000 B = 35.13000 C = 35.13000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7660 2 1 -1 -2 -1 13.9976 3 1 -1 -1 -1 2.2316 4 1 -1 0 -1 0.4560 5 1 0 -1 -1 4.4372 6 1 0 0 -1 5.7723 7 1 -1 -1 0 2.8521 8 1 -1 0 0 6.0584 9 1 0 -1 0 2.6854 10 1 0 1 0 2.6854 11 1 0 0 1 5.7723 12 1 0 1 1 4.4372 13 1 2 1 1 9.7660 14 1 1 2 1 13.9976 15 1 1 1 1 2.2316 16 1 1 0 1 0.4560 17 1 1 1 0 2.8521 18 1 1 0 0 6.0584 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3352 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 597 OPERATED ON BY TRANSFORMATION C010 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 201 67 67 5.68 2 C002 has 27 9 9 11.09 3 C003 has 2619 873 873 0.00 4 C004 has 813 271 271 0.00 5 C005 has 840 280 280 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1188 396 396 0.00 9 C009 has 1197 399 399 0.00 Total of12154 atoms and 4044 groups and 4039 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3352 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 = 1104 Number of atoms = 3349 Number of groups = 1109 Number of bonds = 3343 Number of angles = 1213 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1107 Number of HB donors = 2190 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1104 Number of atoms = 3349 Number of groups = 1109 Number of bonds = 3343 Number of angles = 1213 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1107 Number of HB donors = 2190 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.128" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1104" Evaluating: 1104-13 Parameter: NUMWAT <- "1091" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1091" Comparing "1075" and "1091". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.128" Parameter: BOX -> "35.128" Parameter: BOX -> "35.128" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.12800 B = 35.12800 C = 35.12800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7635 2 1 -1 -2 -1 13.9946 3 1 -1 -1 -1 2.2296 4 1 -1 0 -1 0.4571 5 1 0 -1 -1 4.4377 6 1 0 0 -1 5.7706 7 1 -1 -1 0 2.8508 8 1 -1 0 0 6.0577 9 1 0 -1 0 2.6846 10 1 0 1 0 2.6846 11 1 0 0 1 5.7706 12 1 0 1 1 4.4377 13 1 2 1 1 9.7635 14 1 1 2 1 13.9946 15 1 1 1 1 2.2296 16 1 1 0 1 0.4571 17 1 1 1 0 2.8508 18 1 1 0 0 6.0577 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3273 atoms have been selected out of 3349 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 201 67 67 5.68 2 C002 has 27 9 9 11.09 3 C003 has 2616 872 872 0.00 4 C004 has 810 270 270 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1188 396 396 0.00 9 C009 has 1197 399 399 0.00 Total of12142 atoms and 4040 groups and 4035 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3349 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1104 Number of atoms = 3349 Number of groups = 1109 Number of bonds = 3343 Number of angles = 1213 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1107 Number of HB donors = 2190 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1104 Number of atoms = 3349 Number of groups = 1109 Number of bonds = 3343 Number of angles = 1213 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1107 Number of HB donors = 2190 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.126" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1104" Evaluating: 1104-13 Parameter: NUMWAT <- "1091" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1091" Comparing "1075" and "1091". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.126" Parameter: BOX -> "35.126" Parameter: BOX -> "35.126" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.12600 B = 35.12600 C = 35.12600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7611 2 1 -1 -2 -1 13.9917 3 1 -1 -1 -1 2.2277 4 1 -1 0 -1 0.4582 5 1 0 -1 -1 4.4381 6 1 0 0 -1 5.7689 7 1 -1 -1 0 2.8495 8 1 -1 0 0 6.0571 9 1 0 -1 0 2.6837 10 1 0 1 0 2.6837 11 1 0 0 1 5.7689 12 1 0 1 1 4.4381 13 1 2 1 1 9.7611 14 1 1 2 1 13.9917 15 1 1 1 1 2.2277 16 1 1 0 1 0.4582 17 1 1 1 0 2.8495 18 1 1 0 0 6.0571 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3273 atoms have been selected out of 3349 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 201 67 67 5.68 2 C002 has 27 9 9 11.08 3 C003 has 2616 872 872 0.00 4 C004 has 810 270 270 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1188 396 396 0.00 9 C009 has 1197 399 399 0.00 Total of12142 atoms and 4040 groups and 4035 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3349 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1104 Number of atoms = 3349 Number of groups = 1109 Number of bonds = 3343 Number of angles = 1213 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1107 Number of HB donors = 2190 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1104 Number of atoms = 3349 Number of groups = 1109 Number of bonds = 3343 Number of angles = 1213 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1107 Number of HB donors = 2190 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.124" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1104" Evaluating: 1104-13 Parameter: NUMWAT <- "1091" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1091" Comparing "1075" and "1091". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.124" Parameter: BOX -> "35.124" Parameter: BOX -> "35.124" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.12400 B = 35.12400 C = 35.12400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7586 2 1 -1 -2 -1 13.9887 3 1 -1 -1 -1 2.2257 4 1 -1 0 -1 0.4594 5 1 0 -1 -1 4.4386 6 1 0 0 -1 5.7673 7 1 -1 -1 0 2.8482 8 1 -1 0 0 6.0564 9 1 0 -1 0 2.6829 10 1 0 1 0 2.6829 11 1 0 0 1 5.7673 12 1 0 1 1 4.4386 13 1 2 1 1 9.7586 14 1 1 2 1 13.9887 15 1 1 1 1 2.2257 16 1 1 0 1 0.4594 17 1 1 1 0 2.8482 18 1 1 0 0 6.0564 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3273 atoms have been selected out of 3349 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 201 67 67 5.67 2 C002 has 27 9 9 11.08 3 C003 has 2616 872 872 0.00 4 C004 has 810 270 270 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1188 396 396 0.00 9 C009 has 1197 399 399 0.00 Total of12142 atoms and 4040 groups and 4035 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3349 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1104 Number of atoms = 3349 Number of groups = 1109 Number of bonds = 3343 Number of angles = 1213 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1107 Number of HB donors = 2190 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1104 Number of atoms = 3349 Number of groups = 1109 Number of bonds = 3343 Number of angles = 1213 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1107 Number of HB donors = 2190 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.122" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1104" Evaluating: 1104-13 Parameter: NUMWAT <- "1091" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1091" Comparing "1075" and "1091". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.122" Parameter: BOX -> "35.122" Parameter: BOX -> "35.122" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.12200 B = 35.12200 C = 35.12200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7561 2 1 -1 -2 -1 13.9857 3 1 -1 -1 -1 2.2237 4 1 -1 0 -1 0.4605 5 1 0 -1 -1 4.4391 6 1 0 0 -1 5.7656 7 1 -1 -1 0 2.8469 8 1 -1 0 0 6.0558 9 1 0 -1 0 2.6821 10 1 0 1 0 2.6821 11 1 0 0 1 5.7656 12 1 0 1 1 4.4391 13 1 2 1 1 9.7561 14 1 1 2 1 13.9857 15 1 1 1 1 2.2237 16 1 1 0 1 0.4605 17 1 1 1 0 2.8469 18 1 1 0 0 6.0558 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3273 atoms have been selected out of 3349 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 201 67 67 5.67 2 C002 has 27 9 9 11.08 3 C003 has 2616 872 872 0.00 4 C004 has 813 271 271 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1188 396 396 0.00 9 C009 has 1200 400 400 0.00 Total of12148 atoms and 4042 groups and 4037 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3349 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1104 Number of atoms = 3349 Number of groups = 1109 Number of bonds = 3343 Number of angles = 1213 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1107 Number of HB donors = 2190 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1104 Number of atoms = 3349 Number of groups = 1109 Number of bonds = 3343 Number of angles = 1213 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1107 Number of HB donors = 2190 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.12" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1104" Evaluating: 1104-13 Parameter: NUMWAT <- "1091" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1091" Comparing "1075" and "1091". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.12" Parameter: BOX -> "35.12" Parameter: BOX -> "35.12" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.12000 B = 35.12000 C = 35.12000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7536 2 1 -1 -2 -1 13.9828 3 1 -1 -1 -1 2.2217 4 1 -1 0 -1 0.4616 5 1 0 -1 -1 4.4395 6 1 0 0 -1 5.7639 7 1 -1 -1 0 2.8457 8 1 -1 0 0 6.0551 9 1 0 -1 0 2.6812 10 1 0 1 0 2.6812 11 1 0 0 1 5.7639 12 1 0 1 1 4.4395 13 1 2 1 1 9.7536 14 1 1 2 1 13.9828 15 1 1 1 1 2.2217 16 1 1 0 1 0.4616 17 1 1 1 0 2.8457 18 1 1 0 0 6.0551 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3273 atoms have been selected out of 3349 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 201 67 67 5.67 2 C002 has 27 9 9 11.07 3 C003 has 2619 873 873 0.00 4 C004 has 813 271 271 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1188 396 396 0.00 9 C009 has 1200 400 400 0.00 Total of12151 atoms and 4043 groups and 4038 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3349 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1104 Number of atoms = 3349 Number of groups = 1109 Number of bonds = 3343 Number of angles = 1213 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1107 Number of HB donors = 2190 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1104 Number of atoms = 3349 Number of groups = 1109 Number of bonds = 3343 Number of angles = 1213 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1107 Number of HB donors = 2190 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.118" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1104" Evaluating: 1104-13 Parameter: NUMWAT <- "1091" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1091" Comparing "1075" and "1091". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.118" Parameter: BOX -> "35.118" Parameter: BOX -> "35.118" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.11800 B = 35.11800 C = 35.11800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7512 2 1 -1 -2 -1 13.9798 3 1 -1 -1 -1 2.2197 4 1 -1 0 -1 0.4628 5 1 0 -1 -1 4.4400 6 1 0 0 -1 5.7623 7 1 -1 -1 0 2.8444 8 1 -1 0 0 6.0544 9 1 0 -1 0 2.6804 10 1 0 1 0 2.6804 11 1 0 0 1 5.7623 12 1 0 1 1 4.4400 13 1 2 1 1 9.7512 14 1 1 2 1 13.9798 15 1 1 1 1 2.2197 16 1 1 0 1 0.4628 17 1 1 1 0 2.8444 18 1 1 0 0 6.0544 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3273 atoms have been selected out of 3349 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 969 OPERATED ON BY TRANSFORMATION C003 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 201 67 67 5.66 2 C002 has 27 9 9 11.07 3 C003 has 2616 872 872 0.00 4 C004 has 813 271 271 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1188 396 396 0.00 9 C009 has 1197 399 399 0.00 Total of12139 atoms and 4039 groups and 4034 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3349 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 = 1103 Number of atoms = 3346 Number of groups = 1108 Number of bonds = 3340 Number of angles = 1212 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1106 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 = 3346 Number of groups = 1108 Number of bonds = 3340 Number of angles = 1212 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1106 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 <- "35.116" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1103" Evaluating: 1103-13 Parameter: NUMWAT <- "1090" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1090" Comparing "1075" and "1090". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.116" Parameter: BOX -> "35.116" Parameter: BOX -> "35.116" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.11600 B = 35.11600 C = 35.11600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7487 2 1 -1 -2 -1 13.9768 3 1 -1 -1 -1 2.2177 4 1 -1 0 -1 0.4640 5 1 0 -1 -1 4.4405 6 1 0 0 -1 5.7606 7 1 -1 -1 0 2.8431 8 1 -1 0 0 6.0538 9 1 0 -1 0 2.6796 10 1 0 1 0 2.6796 11 1 0 0 1 5.7606 12 1 0 1 1 4.4405 13 1 2 1 1 9.7487 14 1 1 2 1 13.9768 15 1 1 1 1 2.2177 16 1 1 0 1 0.4640 17 1 1 1 0 2.8431 18 1 1 0 0 6.0538 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3346 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 201 67 67 5.66 2 C002 has 30 10 10 11.07 3 C003 has 2616 872 872 0.00 4 C004 has 813 271 271 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1188 396 396 0.00 9 C009 has 1197 399 399 0.00 Total of12139 atoms and 4039 groups and 4034 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3346 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3346 Number of groups = 1108 Number of bonds = 3340 Number of angles = 1212 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1106 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 = 3346 Number of groups = 1108 Number of bonds = 3340 Number of angles = 1212 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1106 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 <- "35.114" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1103" Evaluating: 1103-13 Parameter: NUMWAT <- "1090" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1090" Comparing "1075" and "1090". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.114" Parameter: BOX -> "35.114" Parameter: BOX -> "35.114" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.11400 B = 35.11400 C = 35.11400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7462 2 1 -1 -2 -1 13.9739 3 1 -1 -1 -1 2.2157 4 1 -1 0 -1 0.4651 5 1 0 -1 -1 4.4410 6 1 0 0 -1 5.7590 7 1 -1 -1 0 2.8419 8 1 -1 0 0 6.0531 9 1 0 -1 0 2.6787 10 1 0 1 0 2.6787 11 1 0 0 1 5.7590 12 1 0 1 1 4.4410 13 1 2 1 1 9.7462 14 1 1 2 1 13.9739 15 1 1 1 1 2.2157 16 1 1 0 1 0.4651 17 1 1 1 0 2.8419 18 1 1 0 0 6.0531 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3346 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 201 67 67 5.66 2 C002 has 30 10 10 11.06 3 C003 has 2616 872 872 0.00 4 C004 has 813 271 271 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1188 396 396 0.00 9 C009 has 1197 399 399 0.00 Total of12139 atoms and 4039 groups and 4034 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3346 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3346 Number of groups = 1108 Number of bonds = 3340 Number of angles = 1212 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1106 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 = 3346 Number of groups = 1108 Number of bonds = 3340 Number of angles = 1212 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1106 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 <- "35.112" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1103" Evaluating: 1103-13 Parameter: NUMWAT <- "1090" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1090" Comparing "1075" and "1090". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.112" Parameter: BOX -> "35.112" Parameter: BOX -> "35.112" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.11200 B = 35.11200 C = 35.11200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7438 2 1 -1 -2 -1 13.9709 3 1 -1 -1 -1 2.2138 4 1 -1 0 -1 0.4663 5 1 0 -1 -1 4.4414 6 1 0 0 -1 5.7573 7 1 -1 -1 0 2.8406 8 1 -1 0 0 6.0525 9 1 0 -1 0 2.6779 10 1 0 1 0 2.6779 11 1 0 0 1 5.7573 12 1 0 1 1 4.4414 13 1 2 1 1 9.7438 14 1 1 2 1 13.9709 15 1 1 1 1 2.2138 16 1 1 0 1 0.4663 17 1 1 1 0 2.8406 18 1 1 0 0 6.0525 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3346 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 201 67 67 5.65 2 C002 has 30 10 10 11.06 3 C003 has 2616 872 872 0.00 4 C004 has 813 271 271 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1188 396 396 0.00 9 C009 has 1197 399 399 0.00 Total of12139 atoms and 4039 groups and 4034 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3346 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3346 Number of groups = 1108 Number of bonds = 3340 Number of angles = 1212 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1106 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 = 3346 Number of groups = 1108 Number of bonds = 3340 Number of angles = 1212 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1106 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 <- "35.11" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1103" Evaluating: 1103-13 Parameter: NUMWAT <- "1090" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1090" Comparing "1075" and "1090". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.11" Parameter: BOX -> "35.11" Parameter: BOX -> "35.11" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.11000 B = 35.11000 C = 35.11000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7413 2 1 -1 -2 -1 13.9679 3 1 -1 -1 -1 2.2118 4 1 -1 0 -1 0.4675 5 1 0 -1 -1 4.4419 6 1 0 0 -1 5.7556 7 1 -1 -1 0 2.8393 8 1 -1 0 0 6.0518 9 1 0 -1 0 2.6771 10 1 0 1 0 2.6771 11 1 0 0 1 5.7556 12 1 0 1 1 4.4419 13 1 2 1 1 9.7413 14 1 1 2 1 13.9679 15 1 1 1 1 2.2118 16 1 1 0 1 0.4675 17 1 1 1 0 2.8393 18 1 1 0 0 6.0518 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3346 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 468 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.65 2 C002 has 30 10 10 11.06 3 C003 has 2616 872 872 0.00 4 C004 has 813 271 271 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1188 396 396 0.00 9 C009 has 1200 400 400 0.00 Total of12139 atoms and 4039 groups and 4034 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3346 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 = 3343 Number of groups = 1107 Number of bonds = 3337 Number of angles = 1211 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1105 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 = 3343 Number of groups = 1107 Number of bonds = 3337 Number of angles = 1211 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1105 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 <- "35.108" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1102" Evaluating: 1102-13 Parameter: NUMWAT <- "1089" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1089" Comparing "1075" and "1089". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.108" Parameter: BOX -> "35.108" Parameter: BOX -> "35.108" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.10800 B = 35.10800 C = 35.10800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7388 2 1 -1 -2 -1 13.9650 3 1 -1 -1 -1 2.2098 4 1 -1 0 -1 0.4687 5 1 0 -1 -1 4.4424 6 1 0 0 -1 5.7540 7 1 -1 -1 0 2.8380 8 1 -1 0 0 6.0512 9 1 0 -1 0 2.6763 10 1 0 1 0 2.6763 11 1 0 0 1 5.7540 12 1 0 1 1 4.4424 13 1 2 1 1 9.7388 14 1 1 2 1 13.9650 15 1 1 1 1 2.2098 16 1 1 0 1 0.4687 17 1 1 1 0 2.8380 18 1 1 0 0 6.0512 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3343 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.65 2 C002 has 30 10 10 11.06 3 C003 has 2616 872 872 0.00 4 C004 has 813 271 271 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1185 395 395 0.00 9 C009 has 1197 399 399 0.00 Total of12127 atoms and 4035 groups and 4030 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3343 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3343 Number of groups = 1107 Number of bonds = 3337 Number of angles = 1211 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1105 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 = 3343 Number of groups = 1107 Number of bonds = 3337 Number of angles = 1211 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1105 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 <- "35.106" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1102" Evaluating: 1102-13 Parameter: NUMWAT <- "1089" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1089" Comparing "1075" and "1089". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.106" Parameter: BOX -> "35.106" Parameter: BOX -> "35.106" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.10600 B = 35.10600 C = 35.10600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7364 2 1 -1 -2 -1 13.9620 3 1 -1 -1 -1 2.2078 4 1 -1 0 -1 0.4699 5 1 0 -1 -1 4.4429 6 1 0 0 -1 5.7523 7 1 -1 -1 0 2.8368 8 1 -1 0 0 6.0505 9 1 0 -1 0 2.6754 10 1 0 1 0 2.6754 11 1 0 0 1 5.7523 12 1 0 1 1 4.4429 13 1 2 1 1 9.7364 14 1 1 2 1 13.9620 15 1 1 1 1 2.2078 16 1 1 0 1 0.4699 17 1 1 1 0 2.8368 18 1 1 0 0 6.0505 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3343 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.65 2 C002 has 30 10 10 11.05 3 C003 has 2616 872 872 0.00 4 C004 has 813 271 271 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1188 396 396 0.00 9 C009 has 1197 399 399 0.00 Total of12130 atoms and 4036 groups and 4031 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3343 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3343 Number of groups = 1107 Number of bonds = 3337 Number of angles = 1211 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1105 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 = 3343 Number of groups = 1107 Number of bonds = 3337 Number of angles = 1211 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1105 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 <- "35.104" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1102" Evaluating: 1102-13 Parameter: NUMWAT <- "1089" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1089" Comparing "1075" and "1089". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.104" Parameter: BOX -> "35.104" Parameter: BOX -> "35.104" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.10400 B = 35.10400 C = 35.10400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7339 2 1 -1 -2 -1 13.9591 3 1 -1 -1 -1 2.2058 4 1 -1 0 -1 0.4711 5 1 0 -1 -1 4.4434 6 1 0 0 -1 5.7506 7 1 -1 -1 0 2.8355 8 1 -1 0 0 6.0499 9 1 0 -1 0 2.6746 10 1 0 1 0 2.6746 11 1 0 0 1 5.7506 12 1 0 1 1 4.4434 13 1 2 1 1 9.7339 14 1 1 2 1 13.9591 15 1 1 1 1 2.2058 16 1 1 0 1 0.4711 17 1 1 1 0 2.8355 18 1 1 0 0 6.0499 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3343 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.64 2 C002 has 30 10 10 11.05 3 C003 has 2616 872 872 0.00 4 C004 has 813 271 271 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1188 396 396 0.00 9 C009 has 1197 399 399 0.00 Total of12130 atoms and 4036 groups and 4031 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3343 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3343 Number of groups = 1107 Number of bonds = 3337 Number of angles = 1211 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1105 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 = 3343 Number of groups = 1107 Number of bonds = 3337 Number of angles = 1211 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1105 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 <- "35.102" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1102" Evaluating: 1102-13 Parameter: NUMWAT <- "1089" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1089" Comparing "1075" and "1089". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.102" Parameter: BOX -> "35.102" Parameter: BOX -> "35.102" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.10200 B = 35.10200 C = 35.10200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7314 2 1 -1 -2 -1 13.9561 3 1 -1 -1 -1 2.2038 4 1 -1 0 -1 0.4723 5 1 0 -1 -1 4.4439 6 1 0 0 -1 5.7490 7 1 -1 -1 0 2.8343 8 1 -1 0 0 6.0492 9 1 0 -1 0 2.6738 10 1 0 1 0 2.6738 11 1 0 0 1 5.7490 12 1 0 1 1 4.4439 13 1 2 1 1 9.7314 14 1 1 2 1 13.9561 15 1 1 1 1 2.2038 16 1 1 0 1 0.4723 17 1 1 1 0 2.8343 18 1 1 0 0 6.0492 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3343 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.64 2 C002 has 30 10 10 11.05 3 C003 has 2616 872 872 0.00 4 C004 has 813 271 271 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1137 379 379 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1188 396 396 0.00 9 C009 has 1197 399 399 0.00 Total of12130 atoms and 4036 groups and 4031 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3343 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3343 Number of groups = 1107 Number of bonds = 3337 Number of angles = 1211 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1105 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 = 3343 Number of groups = 1107 Number of bonds = 3337 Number of angles = 1211 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1105 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 <- "35.1" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1102" Evaluating: 1102-13 Parameter: NUMWAT <- "1089" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1089" Comparing "1075" and "1089". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.1" Parameter: BOX -> "35.1" Parameter: BOX -> "35.1" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.10000 B = 35.10000 C = 35.10000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7290 2 1 -1 -2 -1 13.9531 3 1 -1 -1 -1 2.2019 4 1 -1 0 -1 0.4736 5 1 0 -1 -1 4.4443 6 1 0 0 -1 5.7473 7 1 -1 -1 0 2.8330 8 1 -1 0 0 6.0486 9 1 0 -1 0 2.6730 10 1 0 1 0 2.6730 11 1 0 0 1 5.7473 12 1 0 1 1 4.4443 13 1 2 1 1 9.7290 14 1 1 2 1 13.9531 15 1 1 1 1 2.2019 16 1 1 0 1 0.4736 17 1 1 1 0 2.8330 18 1 1 0 0 6.0486 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3343 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.64 2 C002 has 30 10 10 11.04 3 C003 has 2616 872 872 0.00 4 C004 has 813 271 271 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1188 396 396 0.00 9 C009 has 1197 399 399 0.00 Total of12133 atoms and 4037 groups and 4032 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3343 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3343 Number of groups = 1107 Number of bonds = 3337 Number of angles = 1211 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1105 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 = 3343 Number of groups = 1107 Number of bonds = 3337 Number of angles = 1211 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1105 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 <- "35.098" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1102" Evaluating: 1102-13 Parameter: NUMWAT <- "1089" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1089" Comparing "1075" and "1089". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.098" Parameter: BOX -> "35.098" Parameter: BOX -> "35.098" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.09800 B = 35.09800 C = 35.09800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7265 2 1 -1 -2 -1 13.9502 3 1 -1 -1 -1 2.1999 4 1 -1 0 -1 0.4748 5 1 0 -1 -1 4.4448 6 1 0 0 -1 5.7457 7 1 -1 -1 0 2.8317 8 1 -1 0 0 6.0479 9 1 0 -1 0 2.6722 10 1 0 1 0 2.6722 11 1 0 0 1 5.7457 12 1 0 1 1 4.4448 13 1 2 1 1 9.7265 14 1 1 2 1 13.9502 15 1 1 1 1 2.1999 16 1 1 0 1 0.4748 17 1 1 1 0 2.8317 18 1 1 0 0 6.0479 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3343 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.63 2 C002 has 30 10 10 11.04 3 C003 has 2616 872 872 0.00 4 C004 has 813 271 271 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1188 396 396 0.00 9 C009 has 1197 399 399 0.00 Total of12136 atoms and 4038 groups and 4033 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3343 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3343 Number of groups = 1107 Number of bonds = 3337 Number of angles = 1211 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1105 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 = 3343 Number of groups = 1107 Number of bonds = 3337 Number of angles = 1211 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1105 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 <- "35.096" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1102" Evaluating: 1102-13 Parameter: NUMWAT <- "1089" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1089" Comparing "1075" and "1089". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.096" Parameter: BOX -> "35.096" Parameter: BOX -> "35.096" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.09600 B = 35.09600 C = 35.09600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7240 2 1 -1 -2 -1 13.9472 3 1 -1 -1 -1 2.1979 4 1 -1 0 -1 0.4761 5 1 0 -1 -1 4.4453 6 1 0 0 -1 5.7440 7 1 -1 -1 0 2.8305 8 1 -1 0 0 6.0473 9 1 0 -1 0 2.6714 10 1 0 1 0 2.6714 11 1 0 0 1 5.7440 12 1 0 1 1 4.4453 13 1 2 1 1 9.7240 14 1 1 2 1 13.9472 15 1 1 1 1 2.1979 16 1 1 0 1 0.4761 17 1 1 1 0 2.8305 18 1 1 0 0 6.0473 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3343 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.63 2 C002 has 30 10 10 11.04 3 C003 has 2616 872 872 0.00 4 C004 has 813 271 271 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1188 396 396 0.00 9 C009 has 1197 399 399 0.00 Total of12136 atoms and 4038 groups and 4033 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3343 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3343 Number of groups = 1107 Number of bonds = 3337 Number of angles = 1211 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1105 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 = 3343 Number of groups = 1107 Number of bonds = 3337 Number of angles = 1211 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1105 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 <- "35.094" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1102" Evaluating: 1102-13 Parameter: NUMWAT <- "1089" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1089" Comparing "1075" and "1089". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.094" Parameter: BOX -> "35.094" Parameter: BOX -> "35.094" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.09400 B = 35.09400 C = 35.09400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7216 2 1 -1 -2 -1 13.9442 3 1 -1 -1 -1 2.1959 4 1 -1 0 -1 0.4773 5 1 0 -1 -1 4.4458 6 1 0 0 -1 5.7423 7 1 -1 -1 0 2.8292 8 1 -1 0 0 6.0466 9 1 0 -1 0 2.6705 10 1 0 1 0 2.6705 11 1 0 0 1 5.7423 12 1 0 1 1 4.4458 13 1 2 1 1 9.7216 14 1 1 2 1 13.9442 15 1 1 1 1 2.1959 16 1 1 0 1 0.4773 17 1 1 1 0 2.8292 18 1 1 0 0 6.0466 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3343 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.63 2 C002 has 30 10 10 11.03 3 C003 has 2616 872 872 0.00 4 C004 has 813 271 271 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1140 380 380 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1188 396 396 0.00 9 C009 has 1197 399 399 0.00 Total of12136 atoms and 4038 groups and 4033 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3343 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3343 Number of groups = 1107 Number of bonds = 3337 Number of angles = 1211 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1105 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 = 3343 Number of groups = 1107 Number of bonds = 3337 Number of angles = 1211 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1105 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 <- "35.092" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1102" Evaluating: 1102-13 Parameter: NUMWAT <- "1089" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1089" Comparing "1075" and "1089". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.092" Parameter: BOX -> "35.092" Parameter: BOX -> "35.092" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.09200 B = 35.09200 C = 35.09200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7191 2 1 -1 -2 -1 13.9413 3 1 -1 -1 -1 2.1939 4 1 -1 0 -1 0.4786 5 1 0 -1 -1 4.4463 6 1 0 0 -1 5.7407 7 1 -1 -1 0 2.8280 8 1 -1 0 0 6.0460 9 1 0 -1 0 2.6697 10 1 0 1 0 2.6697 11 1 0 0 1 5.7407 12 1 0 1 1 4.4463 13 1 2 1 1 9.7191 14 1 1 2 1 13.9413 15 1 1 1 1 2.1939 16 1 1 0 1 0.4786 17 1 1 1 0 2.8280 18 1 1 0 0 6.0460 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3343 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.62 2 C002 has 30 10 10 11.03 3 C003 has 2619 873 873 0.00 4 C004 has 813 271 271 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1143 381 381 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1188 396 396 0.00 9 C009 has 1197 399 399 0.00 Total of12142 atoms and 4040 groups and 4035 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3343 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3343 Number of groups = 1107 Number of bonds = 3337 Number of angles = 1211 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1105 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 = 3343 Number of groups = 1107 Number of bonds = 3337 Number of angles = 1211 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1105 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 <- "35.09" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1102" Evaluating: 1102-13 Parameter: NUMWAT <- "1089" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1089" Comparing "1075" and "1089". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.09" Parameter: BOX -> "35.09" Parameter: BOX -> "35.09" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.09000 B = 35.09000 C = 35.09000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7166 2 1 -1 -2 -1 13.9383 3 1 -1 -1 -1 2.1920 4 1 -1 0 -1 0.4798 5 1 0 -1 -1 4.4468 6 1 0 0 -1 5.7390 7 1 -1 -1 0 2.8267 8 1 -1 0 0 6.0453 9 1 0 -1 0 2.6689 10 1 0 1 0 2.6689 11 1 0 0 1 5.7390 12 1 0 1 1 4.4468 13 1 2 1 1 9.7166 14 1 1 2 1 13.9383 15 1 1 1 1 2.1920 16 1 1 0 1 0.4798 17 1 1 1 0 2.8267 18 1 1 0 0 6.0453 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3343 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.62 2 C002 has 30 10 10 11.03 3 C003 has 2619 873 873 0.00 4 C004 has 813 271 271 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1143 381 381 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1188 396 396 0.00 9 C009 has 1197 399 399 0.00 Total of12142 atoms and 4040 groups and 4035 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3343 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3343 Number of groups = 1107 Number of bonds = 3337 Number of angles = 1211 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1105 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 = 3343 Number of groups = 1107 Number of bonds = 3337 Number of angles = 1211 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1105 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 <- "35.088" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1102" Evaluating: 1102-13 Parameter: NUMWAT <- "1089" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1089" Comparing "1075" and "1089". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.088" Parameter: BOX -> "35.088" Parameter: BOX -> "35.088" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.08800 B = 35.08800 C = 35.08800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7142 2 1 -1 -2 -1 13.9353 3 1 -1 -1 -1 2.1900 4 1 -1 0 -1 0.4811 5 1 0 -1 -1 4.4473 6 1 0 0 -1 5.7374 7 1 -1 -1 0 2.8255 8 1 -1 0 0 6.0447 9 1 0 -1 0 2.6681 10 1 0 1 0 2.6681 11 1 0 0 1 5.7374 12 1 0 1 1 4.4473 13 1 2 1 1 9.7142 14 1 1 2 1 13.9353 15 1 1 1 1 2.1900 16 1 1 0 1 0.4811 17 1 1 1 0 2.8255 18 1 1 0 0 6.0447 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3343 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.62 2 C002 has 30 10 10 11.02 3 C003 has 2619 873 873 0.00 4 C004 has 813 271 271 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1143 381 381 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1188 396 396 0.00 9 C009 has 1197 399 399 0.00 Total of12142 atoms and 4040 groups and 4035 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3343 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3343 Number of groups = 1107 Number of bonds = 3337 Number of angles = 1211 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1105 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 = 3343 Number of groups = 1107 Number of bonds = 3337 Number of angles = 1211 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1105 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 <- "35.086" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1102" Evaluating: 1102-13 Parameter: NUMWAT <- "1089" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1089" Comparing "1075" and "1089". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.086" Parameter: BOX -> "35.086" Parameter: BOX -> "35.086" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.08600 B = 35.08600 C = 35.08600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7117 2 1 -1 -2 -1 13.9324 3 1 -1 -1 -1 2.1880 4 1 -1 0 -1 0.4824 5 1 0 -1 -1 4.4478 6 1 0 0 -1 5.7357 7 1 -1 -1 0 2.8242 8 1 -1 0 0 6.0441 9 1 0 -1 0 2.6673 10 1 0 1 0 2.6673 11 1 0 0 1 5.7357 12 1 0 1 1 4.4478 13 1 2 1 1 9.7117 14 1 1 2 1 13.9324 15 1 1 1 1 2.1880 16 1 1 0 1 0.4824 17 1 1 1 0 2.8242 18 1 1 0 0 6.0441 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3343 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 C012 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.61 2 C002 has 30 10 10 11.02 3 C003 has 2622 874 874 0.00 4 C004 has 813 271 271 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1146 382 382 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1185 395 395 0.00 9 C009 has 1200 400 400 0.00 Total of12151 atoms and 4043 groups and 4038 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3343 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 = 1101 Number of atoms = 3340 Number of groups = 1106 Number of bonds = 3334 Number of angles = 1210 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1104 Number of HB donors = 2184 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1101 Number of atoms = 3340 Number of groups = 1106 Number of bonds = 3334 Number of angles = 1210 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1104 Number of HB donors = 2184 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.084" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1101" Evaluating: 1101-13 Parameter: NUMWAT <- "1088" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1088" Comparing "1075" and "1088". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.084" Parameter: BOX -> "35.084" Parameter: BOX -> "35.084" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.08400 B = 35.08400 C = 35.08400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7093 2 1 -1 -2 -1 13.9294 3 1 -1 -1 -1 2.1860 4 1 -1 0 -1 0.4837 5 1 0 -1 -1 4.4483 6 1 0 0 -1 5.7340 7 1 -1 -1 0 2.8230 8 1 -1 0 0 6.0434 9 1 0 -1 0 2.6665 10 1 0 1 0 2.6665 11 1 0 0 1 5.7340 12 1 0 1 1 4.4483 13 1 2 1 1 9.7093 14 1 1 2 1 13.9294 15 1 1 1 1 2.1860 16 1 1 0 1 0.4837 17 1 1 1 0 2.8230 18 1 1 0 0 6.0434 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3264 atoms have been selected out of 3340 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.61 2 C002 has 30 10 10 11.02 3 C003 has 2619 873 873 0.00 4 C004 has 813 271 271 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1146 382 382 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1185 395 395 0.00 9 C009 has 1197 399 399 0.00 Total of12139 atoms and 4039 groups and 4034 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3340 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1101 Number of atoms = 3340 Number of groups = 1106 Number of bonds = 3334 Number of angles = 1210 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1104 Number of HB donors = 2184 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1101 Number of atoms = 3340 Number of groups = 1106 Number of bonds = 3334 Number of angles = 1210 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1104 Number of HB donors = 2184 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.082" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1101" Evaluating: 1101-13 Parameter: NUMWAT <- "1088" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1088" Comparing "1075" and "1088". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.082" Parameter: BOX -> "35.082" Parameter: BOX -> "35.082" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.08200 B = 35.08200 C = 35.08200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7068 2 1 -1 -2 -1 13.9264 3 1 -1 -1 -1 2.1840 4 1 -1 0 -1 0.4850 5 1 0 -1 -1 4.4488 6 1 0 0 -1 5.7324 7 1 -1 -1 0 2.8217 8 1 -1 0 0 6.0428 9 1 0 -1 0 2.6657 10 1 0 1 0 2.6657 11 1 0 0 1 5.7324 12 1 0 1 1 4.4488 13 1 2 1 1 9.7068 14 1 1 2 1 13.9264 15 1 1 1 1 2.1840 16 1 1 0 1 0.4850 17 1 1 1 0 2.8217 18 1 1 0 0 6.0428 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3264 atoms have been selected out of 3340 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.61 2 C002 has 30 10 10 11.01 3 C003 has 2619 873 873 0.00 4 C004 has 813 271 271 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1146 382 382 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1185 395 395 0.00 9 C009 has 1197 399 399 0.00 Total of12139 atoms and 4039 groups and 4034 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3340 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1101 Number of atoms = 3340 Number of groups = 1106 Number of bonds = 3334 Number of angles = 1210 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1104 Number of HB donors = 2184 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1101 Number of atoms = 3340 Number of groups = 1106 Number of bonds = 3334 Number of angles = 1210 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1104 Number of HB donors = 2184 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.08" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1101" Evaluating: 1101-13 Parameter: NUMWAT <- "1088" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1088" Comparing "1075" and "1088". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.08" Parameter: BOX -> "35.08" Parameter: BOX -> "35.08" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.08000 B = 35.08000 C = 35.08000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7043 2 1 -1 -2 -1 13.9235 3 1 -1 -1 -1 2.1820 4 1 -1 0 -1 0.4863 5 1 0 -1 -1 4.4492 6 1 0 0 -1 5.7307 7 1 -1 -1 0 2.8205 8 1 -1 0 0 6.0421 9 1 0 -1 0 2.6649 10 1 0 1 0 2.6649 11 1 0 0 1 5.7307 12 1 0 1 1 4.4492 13 1 2 1 1 9.7043 14 1 1 2 1 13.9235 15 1 1 1 1 2.1820 16 1 1 0 1 0.4863 17 1 1 1 0 2.8205 18 1 1 0 0 6.0421 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3264 atoms have been selected out of 3340 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.61 2 C002 has 30 10 10 11.01 3 C003 has 2619 873 873 0.00 4 C004 has 813 271 271 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1146 382 382 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1185 395 395 0.00 9 C009 has 1197 399 399 0.00 Total of12139 atoms and 4039 groups and 4034 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3340 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1101 Number of atoms = 3340 Number of groups = 1106 Number of bonds = 3334 Number of angles = 1210 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1104 Number of HB donors = 2184 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1101 Number of atoms = 3340 Number of groups = 1106 Number of bonds = 3334 Number of angles = 1210 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1104 Number of HB donors = 2184 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.078" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1101" Evaluating: 1101-13 Parameter: NUMWAT <- "1088" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1088" Comparing "1075" and "1088". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.078" Parameter: BOX -> "35.078" Parameter: BOX -> "35.078" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.07800 B = 35.07800 C = 35.07800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.7019 2 1 -1 -2 -1 13.9205 3 1 -1 -1 -1 2.1801 4 1 -1 0 -1 0.4876 5 1 0 -1 -1 4.4497 6 1 0 0 -1 5.7291 7 1 -1 -1 0 2.8192 8 1 -1 0 0 6.0415 9 1 0 -1 0 2.6641 10 1 0 1 0 2.6641 11 1 0 0 1 5.7291 12 1 0 1 1 4.4497 13 1 2 1 1 9.7019 14 1 1 2 1 13.9205 15 1 1 1 1 2.1801 16 1 1 0 1 0.4876 17 1 1 1 0 2.8192 18 1 1 0 0 6.0415 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3264 atoms have been selected out of 3340 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 436 OPERATED ON BY TRANSFORMATION C009 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 198 66 66 5.60 2 C002 has 27 9 9 11.01 3 C003 has 2619 873 873 0.00 4 C004 has 816 272 272 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1191 397 397 0.00 9 C009 has 1194 398 398 0.00 Total of12139 atoms and 4039 groups and 4034 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3340 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 = 1100 Number of atoms = 3337 Number of groups = 1105 Number of bonds = 3331 Number of angles = 1209 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1103 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 = 3337 Number of groups = 1105 Number of bonds = 3331 Number of angles = 1209 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1103 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 <- "35.076" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1100" Evaluating: 1100-13 Parameter: NUMWAT <- "1087" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1087" Comparing "1075" and "1087". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.076" Parameter: BOX -> "35.076" Parameter: BOX -> "35.076" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.07600 B = 35.07600 C = 35.07600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6994 2 1 -1 -2 -1 13.9176 3 1 -1 -1 -1 2.1781 4 1 -1 0 -1 0.4890 5 1 0 -1 -1 4.4502 6 1 0 0 -1 5.7274 7 1 -1 -1 0 2.8180 8 1 -1 0 0 6.0408 9 1 0 -1 0 2.6633 10 1 0 1 0 2.6633 11 1 0 0 1 5.7274 12 1 0 1 1 4.4502 13 1 2 1 1 9.6994 14 1 1 2 1 13.9176 15 1 1 1 1 2.1781 16 1 1 0 1 0.4890 17 1 1 1 0 2.8180 18 1 1 0 0 6.0408 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3337 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 201 67 67 5.60 2 C002 has 27 9 9 11.01 3 C003 has 2616 872 872 0.00 4 C004 has 813 271 271 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1146 382 382 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1188 396 396 0.00 9 C009 has 1194 398 398 0.00 Total of12127 atoms and 4035 groups and 4030 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3337 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3337 Number of groups = 1105 Number of bonds = 3331 Number of angles = 1209 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1103 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 = 3337 Number of groups = 1105 Number of bonds = 3331 Number of angles = 1209 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1103 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 <- "35.074" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1100" Evaluating: 1100-13 Parameter: NUMWAT <- "1087" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1087" Comparing "1075" and "1087". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.074" Parameter: BOX -> "35.074" Parameter: BOX -> "35.074" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.07400 B = 35.07400 C = 35.07400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6970 2 1 -1 -2 -1 13.9146 3 1 -1 -1 -1 2.1761 4 1 -1 0 -1 0.4903 5 1 0 -1 -1 4.4507 6 1 0 0 -1 5.7257 7 1 -1 -1 0 2.8167 8 1 -1 0 0 6.0402 9 1 0 -1 0 2.6625 10 1 0 1 0 2.6625 11 1 0 0 1 5.7257 12 1 0 1 1 4.4507 13 1 2 1 1 9.6970 14 1 1 2 1 13.9146 15 1 1 1 1 2.1761 16 1 1 0 1 0.4903 17 1 1 1 0 2.8167 18 1 1 0 0 6.0402 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3337 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 201 67 67 5.60 2 C002 has 27 9 9 11.00 3 C003 has 2616 872 872 0.00 4 C004 has 813 271 271 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1146 382 382 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1188 396 396 0.00 9 C009 has 1194 398 398 0.00 Total of12127 atoms and 4035 groups and 4030 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3337 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3337 Number of groups = 1105 Number of bonds = 3331 Number of angles = 1209 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1103 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 = 3337 Number of groups = 1105 Number of bonds = 3331 Number of angles = 1209 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1103 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 <- "35.072" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1100" Evaluating: 1100-13 Parameter: NUMWAT <- "1087" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1087" Comparing "1075" and "1087". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.072" Parameter: BOX -> "35.072" Parameter: BOX -> "35.072" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.07200 B = 35.07200 C = 35.07200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6945 2 1 -1 -2 -1 13.9116 3 1 -1 -1 -1 2.1741 4 1 -1 0 -1 0.4916 5 1 0 -1 -1 4.4512 6 1 0 0 -1 5.7241 7 1 -1 -1 0 2.8155 8 1 -1 0 0 6.0396 9 1 0 -1 0 2.6617 10 1 0 1 0 2.6617 11 1 0 0 1 5.7241 12 1 0 1 1 4.4512 13 1 2 1 1 9.6945 14 1 1 2 1 13.9116 15 1 1 1 1 2.1741 16 1 1 0 1 0.4916 17 1 1 1 0 2.8155 18 1 1 0 0 6.0396 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3337 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 204 68 68 5.59 2 C002 has 27 9 9 11.00 3 C003 has 2616 872 872 0.00 4 C004 has 813 271 271 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1146 382 382 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1188 396 396 0.00 9 C009 has 1194 398 398 0.00 Total of12136 atoms and 4038 groups and 4033 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3337 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3337 Number of groups = 1105 Number of bonds = 3331 Number of angles = 1209 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1103 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 = 3337 Number of groups = 1105 Number of bonds = 3331 Number of angles = 1209 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1103 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 <- "35.07" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1100" Evaluating: 1100-13 Parameter: NUMWAT <- "1087" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1087" Comparing "1075" and "1087". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.07" Parameter: BOX -> "35.07" Parameter: BOX -> "35.07" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.07000 B = 35.07000 C = 35.07000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6920 2 1 -1 -2 -1 13.9087 3 1 -1 -1 -1 2.1721 4 1 -1 0 -1 0.4930 5 1 0 -1 -1 4.4517 6 1 0 0 -1 5.7224 7 1 -1 -1 0 2.8142 8 1 -1 0 0 6.0389 9 1 0 -1 0 2.6609 10 1 0 1 0 2.6609 11 1 0 0 1 5.7224 12 1 0 1 1 4.4517 13 1 2 1 1 9.6920 14 1 1 2 1 13.9087 15 1 1 1 1 2.1721 16 1 1 0 1 0.4930 17 1 1 1 0 2.8142 18 1 1 0 0 6.0389 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3337 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 204 68 68 5.59 2 C002 has 27 9 9 11.00 3 C003 has 2616 872 872 0.00 4 C004 has 813 271 271 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1146 382 382 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1188 396 396 0.00 9 C009 has 1197 399 399 0.00 Total of12139 atoms and 4039 groups and 4034 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3337 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3337 Number of groups = 1105 Number of bonds = 3331 Number of angles = 1209 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1103 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 = 3337 Number of groups = 1105 Number of bonds = 3331 Number of angles = 1209 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1103 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 <- "35.068" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1100" Evaluating: 1100-13 Parameter: NUMWAT <- "1087" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1087" Comparing "1075" and "1087". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.068" Parameter: BOX -> "35.068" Parameter: BOX -> "35.068" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.06800 B = 35.06800 C = 35.06800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6896 2 1 -1 -2 -1 13.9057 3 1 -1 -1 -1 2.1701 4 1 -1 0 -1 0.4943 5 1 0 -1 -1 4.4522 6 1 0 0 -1 5.7208 7 1 -1 -1 0 2.8130 8 1 -1 0 0 6.0383 9 1 0 -1 0 2.6601 10 1 0 1 0 2.6601 11 1 0 0 1 5.7208 12 1 0 1 1 4.4522 13 1 2 1 1 9.6896 14 1 1 2 1 13.9057 15 1 1 1 1 2.1701 16 1 1 0 1 0.4943 17 1 1 1 0 2.8130 18 1 1 0 0 6.0383 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3337 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 152 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 204 68 68 5.59 2 C002 has 27 9 9 10.99 3 C003 has 2616 872 872 0.00 4 C004 has 816 272 272 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1146 382 382 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1194 398 398 0.00 9 C009 has 1200 400 400 0.00 Total of12148 atoms and 4042 groups and 4037 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3337 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 = 3334 Number of groups = 1104 Number of bonds = 3328 Number of angles = 1208 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1102 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 = 3334 Number of groups = 1104 Number of bonds = 3328 Number of angles = 1208 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1102 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 <- "35.066" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1099" Evaluating: 1099-13 Parameter: NUMWAT <- "1086" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1086" Comparing "1075" and "1086". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.066" Parameter: BOX -> "35.066" Parameter: BOX -> "35.066" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.06600 B = 35.06600 C = 35.06600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6871 2 1 -1 -2 -1 13.9027 3 1 -1 -1 -1 2.1682 4 1 -1 0 -1 0.4957 5 1 0 -1 -1 4.4528 6 1 0 0 -1 5.7191 7 1 -1 -1 0 2.8118 8 1 -1 0 0 6.0376 9 1 0 -1 0 2.6593 10 1 0 1 0 2.6593 11 1 0 0 1 5.7191 12 1 0 1 1 4.4528 13 1 2 1 1 9.6871 14 1 1 2 1 13.9027 15 1 1 1 1 2.1682 16 1 1 0 1 0.4957 17 1 1 1 0 2.8118 18 1 1 0 0 6.0376 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3334 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 C007 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 204 68 68 5.58 2 C002 has 27 9 9 10.99 3 C003 has 2613 871 871 0.00 4 C004 has 813 271 271 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1194 398 398 0.00 Total of12121 atoms and 4033 groups and 4028 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3334 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 = 3331 Number of groups = 1103 Number of bonds = 3325 Number of angles = 1207 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1101 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 = 3331 Number of groups = 1103 Number of bonds = 3325 Number of angles = 1207 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1101 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 <- "35.064" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1098" Evaluating: 1098-13 Parameter: NUMWAT <- "1085" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1085" Comparing "1075" and "1085". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.064" Parameter: BOX -> "35.064" Parameter: BOX -> "35.064" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.06400 B = 35.06400 C = 35.06400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6847 2 1 -1 -2 -1 13.8998 3 1 -1 -1 -1 2.1662 4 1 -1 0 -1 0.4970 5 1 0 -1 -1 4.4533 6 1 0 0 -1 5.7175 7 1 -1 -1 0 2.8105 8 1 -1 0 0 5.9197 9 1 0 -1 0 2.6585 10 1 0 1 0 2.6585 11 1 0 0 1 5.7175 12 1 0 1 1 4.4533 13 1 2 1 1 9.6847 14 1 1 2 1 13.8998 15 1 1 1 1 2.1662 16 1 1 0 1 0.4970 17 1 1 1 0 2.8105 18 1 1 0 0 5.9197 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3331 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 914 OPERATED ON BY TRANSFORMATION C009 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 204 68 68 5.58 2 C002 has 27 9 9 10.99 3 C003 has 2610 870 870 0.00 4 C004 has 816 272 272 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1152 384 384 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1197 399 399 0.00 Total of12133 atoms and 4037 groups and 4032 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3331 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 <- "35.062" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1097" Evaluating: 1097-13 Parameter: NUMWAT <- "1084" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1084" Comparing "1075" and "1084". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.062" Parameter: BOX -> "35.062" Parameter: BOX -> "35.062" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.06200 B = 35.06200 C = 35.06200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6822 2 1 -1 -2 -1 13.8968 3 1 -1 -1 -1 2.1642 4 1 -1 0 -1 0.4984 5 1 0 -1 -1 4.4538 6 1 0 0 -1 5.7158 7 1 -1 -1 0 2.8093 8 1 -1 0 0 5.9189 9 1 0 -1 0 2.6577 10 1 0 1 0 2.6577 11 1 0 0 1 5.7158 12 1 0 1 1 4.4538 13 1 2 1 1 9.6822 14 1 1 2 1 13.8968 15 1 1 1 1 2.1642 16 1 1 0 1 0.4984 17 1 1 1 0 2.8093 18 1 1 0 0 5.9189 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3328 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.58 2 C002 has 27 9 9 10.98 3 C003 has 2610 870 870 0.00 4 C004 has 816 272 272 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 771 257 257 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1191 397 397 0.00 Total of12112 atoms and 4030 groups and 4025 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3328 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 <- "35.06" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1097" Evaluating: 1097-13 Parameter: NUMWAT <- "1084" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1084" Comparing "1075" and "1084". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.06" Parameter: BOX -> "35.06" Parameter: BOX -> "35.06" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.06000 B = 35.06000 C = 35.06000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6798 2 1 -1 -2 -1 13.8939 3 1 -1 -1 -1 2.1622 4 1 -1 0 -1 0.4998 5 1 0 -1 -1 4.4543 6 1 0 0 -1 5.7141 7 1 -1 -1 0 2.8080 8 1 -1 0 0 5.9182 9 1 0 -1 0 2.6569 10 1 0 1 0 2.6569 11 1 0 0 1 5.7141 12 1 0 1 1 4.4543 13 1 2 1 1 9.6798 14 1 1 2 1 13.8939 15 1 1 1 1 2.1622 16 1 1 0 1 0.4998 17 1 1 1 0 2.8080 18 1 1 0 0 5.9182 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3328 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.57 2 C002 has 27 9 9 10.98 3 C003 has 2610 870 870 0.00 4 C004 has 816 272 272 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1191 397 397 0.00 Total of12118 atoms and 4032 groups and 4027 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3328 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 <- "35.058" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1097" Evaluating: 1097-13 Parameter: NUMWAT <- "1084" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1084" Comparing "1075" and "1084". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.058" Parameter: BOX -> "35.058" Parameter: BOX -> "35.058" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.05800 B = 35.05800 C = 35.05800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6773 2 1 -1 -2 -1 13.8909 3 1 -1 -1 -1 2.1602 4 1 -1 0 -1 0.5012 5 1 0 -1 -1 4.4548 6 1 0 0 -1 5.7125 7 1 -1 -1 0 2.8068 8 1 -1 0 0 5.9174 9 1 0 -1 0 2.6561 10 1 0 1 0 2.6561 11 1 0 0 1 5.7125 12 1 0 1 1 4.4548 13 1 2 1 1 9.6773 14 1 1 2 1 13.8909 15 1 1 1 1 2.1602 16 1 1 0 1 0.5012 17 1 1 1 0 2.8068 18 1 1 0 0 5.9174 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3328 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.57 2 C002 has 27 9 9 10.98 3 C003 has 2610 870 870 0.00 4 C004 has 816 272 272 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1191 397 397 0.00 Total of12118 atoms and 4032 groups and 4027 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3328 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 <- "35.056" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1097" Evaluating: 1097-13 Parameter: NUMWAT <- "1084" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1084" Comparing "1075" and "1084". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.056" Parameter: BOX -> "35.056" Parameter: BOX -> "35.056" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.05600 B = 35.05600 C = 35.05600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6748 2 1 -1 -2 -1 13.8879 3 1 -1 -1 -1 2.1582 4 1 -1 0 -1 0.5026 5 1 0 -1 -1 4.4553 6 1 0 0 -1 5.7108 7 1 -1 -1 0 2.8056 8 1 -1 0 0 5.9167 9 1 0 -1 0 2.6553 10 1 0 1 0 2.6553 11 1 0 0 1 5.7108 12 1 0 1 1 4.4553 13 1 2 1 1 9.6748 14 1 1 2 1 13.8879 15 1 1 1 1 2.1582 16 1 1 0 1 0.5026 17 1 1 1 0 2.8056 18 1 1 0 0 5.9167 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3328 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.57 2 C002 has 27 9 9 10.97 3 C003 has 2610 870 870 0.00 4 C004 has 816 272 272 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1191 397 397 0.00 Total of12118 atoms and 4032 groups and 4027 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3328 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 <- "35.054" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1097" Evaluating: 1097-13 Parameter: NUMWAT <- "1084" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1084" Comparing "1075" and "1084". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.054" Parameter: BOX -> "35.054" Parameter: BOX -> "35.054" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.05400 B = 35.05400 C = 35.05400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6724 2 1 -1 -2 -1 13.8850 3 1 -1 -1 -1 2.1563 4 1 -1 0 -1 0.5040 5 1 0 -1 -1 4.4558 6 1 0 0 -1 5.7092 7 1 -1 -1 0 2.8044 8 1 -1 0 0 5.9159 9 1 0 -1 0 2.6545 10 1 0 1 0 2.6545 11 1 0 0 1 5.7092 12 1 0 1 1 4.4558 13 1 2 1 1 9.6724 14 1 1 2 1 13.8850 15 1 1 1 1 2.1563 16 1 1 0 1 0.5040 17 1 1 1 0 2.8044 18 1 1 0 0 5.9159 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3328 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.56 2 C002 has 27 9 9 10.97 3 C003 has 2610 870 870 0.00 4 C004 has 816 272 272 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1191 397 397 0.00 Total of12118 atoms and 4032 groups and 4027 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3328 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 <- "35.052" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1097" Evaluating: 1097-13 Parameter: NUMWAT <- "1084" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1084" Comparing "1075" and "1084". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.052" Parameter: BOX -> "35.052" Parameter: BOX -> "35.052" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.05200 B = 35.05200 C = 35.05200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6699 2 1 -1 -2 -1 13.8820 3 1 -1 -1 -1 2.1543 4 1 -1 0 -1 0.5054 5 1 0 -1 -1 4.4563 6 1 0 0 -1 5.7075 7 1 -1 -1 0 2.8031 8 1 -1 0 0 5.9152 9 1 0 -1 0 2.6537 10 1 0 1 0 2.6537 11 1 0 0 1 5.7075 12 1 0 1 1 4.4563 13 1 2 1 1 9.6699 14 1 1 2 1 13.8820 15 1 1 1 1 2.1543 16 1 1 0 1 0.5054 17 1 1 1 0 2.8031 18 1 1 0 0 5.9152 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3328 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.56 2 C002 has 27 9 9 10.97 3 C003 has 2610 870 870 0.00 4 C004 has 816 272 272 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1149 383 383 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1191 397 397 0.00 Total of12121 atoms and 4033 groups and 4028 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3328 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 <- "35.05" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1097" Evaluating: 1097-13 Parameter: NUMWAT <- "1084" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1084" Comparing "1075" and "1084". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.05" Parameter: BOX -> "35.05" Parameter: BOX -> "35.05" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.05000 B = 35.05000 C = 35.05000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6675 2 1 -1 -2 -1 13.8790 3 1 -1 -1 -1 2.1523 4 1 -1 0 -1 0.5068 5 1 0 -1 -1 4.4568 6 1 0 0 -1 5.7059 7 1 -1 -1 0 2.8019 8 1 -1 0 0 5.9145 9 1 0 -1 0 2.6529 10 1 0 1 0 2.6529 11 1 0 0 1 5.7059 12 1 0 1 1 4.4568 13 1 2 1 1 9.6675 14 1 1 2 1 13.8790 15 1 1 1 1 2.1523 16 1 1 0 1 0.5068 17 1 1 1 0 2.8019 18 1 1 0 0 5.9145 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3328 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.56 2 C002 has 27 9 9 10.97 3 C003 has 2610 870 870 0.00 4 C004 has 816 272 272 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1152 384 384 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1191 397 397 0.00 Total of12124 atoms and 4034 groups and 4029 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3328 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 <- "35.048" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1097" Evaluating: 1097-13 Parameter: NUMWAT <- "1084" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1084" Comparing "1075" and "1084". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.048" Parameter: BOX -> "35.048" Parameter: BOX -> "35.048" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.04800 B = 35.04800 C = 35.04800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6650 2 1 -1 -2 -1 13.8761 3 1 -1 -1 -1 2.1503 4 1 -1 0 -1 0.5082 5 1 0 -1 -1 4.4573 6 1 0 0 -1 5.7042 7 1 -1 -1 0 2.8007 8 1 -1 0 0 5.9137 9 1 0 -1 0 2.6521 10 1 0 1 0 2.6521 11 1 0 0 1 5.7042 12 1 0 1 1 4.4573 13 1 2 1 1 9.6650 14 1 1 2 1 13.8761 15 1 1 1 1 2.1503 16 1 1 0 1 0.5082 17 1 1 1 0 2.8007 18 1 1 0 0 5.9137 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3328 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.56 2 C002 has 27 9 9 10.96 3 C003 has 2610 870 870 0.00 4 C004 has 816 272 272 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1152 384 384 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1191 397 397 0.00 Total of12124 atoms and 4034 groups and 4029 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3328 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 <- "35.046" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1097" Evaluating: 1097-13 Parameter: NUMWAT <- "1084" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1084" Comparing "1075" and "1084". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.046" Parameter: BOX -> "35.046" Parameter: BOX -> "35.046" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.04600 B = 35.04600 C = 35.04600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6626 2 1 -1 -2 -1 13.8731 3 1 -1 -1 -1 2.1483 4 1 -1 0 -1 0.5096 5 1 0 -1 -1 4.4579 6 1 0 0 -1 5.7025 7 1 -1 -1 0 2.7994 8 1 -1 0 0 5.9130 9 1 0 -1 0 2.6514 10 1 0 1 0 2.6514 11 1 0 0 1 5.7025 12 1 0 1 1 4.4579 13 1 2 1 1 9.6626 14 1 1 2 1 13.8731 15 1 1 1 1 2.1483 16 1 1 0 1 0.5096 17 1 1 1 0 2.7994 18 1 1 0 0 5.9130 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3328 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.55 2 C002 has 27 9 9 10.96 3 C003 has 2610 870 870 0.00 4 C004 has 816 272 272 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1152 384 384 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1191 397 397 0.00 Total of12124 atoms and 4034 groups and 4029 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3328 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 <- "35.044" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1097" Evaluating: 1097-13 Parameter: NUMWAT <- "1084" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1084" Comparing "1075" and "1084". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.044" Parameter: BOX -> "35.044" Parameter: BOX -> "35.044" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.04400 B = 35.04400 C = 35.04400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6601 2 1 -1 -2 -1 13.8702 3 1 -1 -1 -1 2.1463 4 1 -1 0 -1 0.5111 5 1 0 -1 -1 4.4584 6 1 0 0 -1 5.7009 7 1 -1 -1 0 2.7982 8 1 -1 0 0 5.9122 9 1 0 -1 0 2.6506 10 1 0 1 0 2.6506 11 1 0 0 1 5.7009 12 1 0 1 1 4.4584 13 1 2 1 1 9.6601 14 1 1 2 1 13.8702 15 1 1 1 1 2.1463 16 1 1 0 1 0.5111 17 1 1 1 0 2.7982 18 1 1 0 0 5.9122 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3328 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.55 2 C002 has 27 9 9 10.96 3 C003 has 2610 870 870 0.00 4 C004 has 816 272 272 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1152 384 384 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1191 397 397 0.00 Total of12124 atoms and 4034 groups and 4029 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3328 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 <- "35.042" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1097" Evaluating: 1097-13 Parameter: NUMWAT <- "1084" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1084" Comparing "1075" and "1084". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.042" Parameter: BOX -> "35.042" Parameter: BOX -> "35.042" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.04200 B = 35.04200 C = 35.04200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6577 2 1 -1 -2 -1 13.8672 3 1 -1 -1 -1 2.1444 4 1 -1 0 -1 0.5125 5 1 0 -1 -1 4.4589 6 1 0 0 -1 5.6992 7 1 -1 -1 0 2.7970 8 1 -1 0 0 5.9115 9 1 0 -1 0 2.6498 10 1 0 1 0 2.6498 11 1 0 0 1 5.6992 12 1 0 1 1 4.4589 13 1 2 1 1 9.6577 14 1 1 2 1 13.8672 15 1 1 1 1 2.1444 16 1 1 0 1 0.5125 17 1 1 1 0 2.7970 18 1 1 0 0 5.9115 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3328 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.55 2 C002 has 27 9 9 10.95 3 C003 has 2610 870 870 0.00 4 C004 has 816 272 272 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1152 384 384 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1191 397 397 0.00 Total of12124 atoms and 4034 groups and 4029 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3328 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 <- "35.04" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1097" Evaluating: 1097-13 Parameter: NUMWAT <- "1084" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1084" Comparing "1075" and "1084". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.04" Parameter: BOX -> "35.04" Parameter: BOX -> "35.04" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.04000 B = 35.04000 C = 35.04000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6552 2 1 -1 -2 -1 13.8642 3 1 -1 -1 -1 2.1424 4 1 -1 0 -1 0.5140 5 1 0 -1 -1 4.4594 6 1 0 0 -1 5.6976 7 1 -1 -1 0 2.7958 8 1 -1 0 0 5.9108 9 1 0 -1 0 2.6490 10 1 0 1 0 2.6490 11 1 0 0 1 5.6976 12 1 0 1 1 4.4594 13 1 2 1 1 9.6552 14 1 1 2 1 13.8642 15 1 1 1 1 2.1424 16 1 1 0 1 0.5140 17 1 1 1 0 2.7958 18 1 1 0 0 5.9108 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3328 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.54 2 C002 has 27 9 9 10.95 3 C003 has 2610 870 870 0.00 4 C004 has 816 272 272 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1152 384 384 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1191 397 397 0.00 Total of12124 atoms and 4034 groups and 4029 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3328 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 <- "35.038" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1097" Evaluating: 1097-13 Parameter: NUMWAT <- "1084" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1084" Comparing "1075" and "1084". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.038" Parameter: BOX -> "35.038" Parameter: BOX -> "35.038" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.03800 B = 35.03800 C = 35.03800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6528 2 1 -1 -2 -1 13.8613 3 1 -1 -1 -1 2.1404 4 1 -1 0 -1 0.5154 5 1 0 -1 -1 4.4599 6 1 0 0 -1 5.6959 7 1 -1 -1 0 2.7946 8 1 -1 0 0 5.9100 9 1 0 -1 0 2.6482 10 1 0 1 0 2.6482 11 1 0 0 1 5.6959 12 1 0 1 1 4.4599 13 1 2 1 1 9.6528 14 1 1 2 1 13.8613 15 1 1 1 1 2.1404 16 1 1 0 1 0.5154 17 1 1 1 0 2.7946 18 1 1 0 0 5.9100 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3328 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.54 2 C002 has 27 9 9 10.95 3 C003 has 2610 870 870 0.00 4 C004 has 816 272 272 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1191 397 397 0.00 Total of12127 atoms and 4035 groups and 4030 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3328 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 <- "35.036" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1097" Evaluating: 1097-13 Parameter: NUMWAT <- "1084" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1084" Comparing "1075" and "1084". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.036" Parameter: BOX -> "35.036" Parameter: BOX -> "35.036" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.03600 B = 35.03600 C = 35.03600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6503 2 1 -1 -2 -1 13.8583 3 1 -1 -1 -1 2.1384 4 1 -1 0 -1 0.5169 5 1 0 -1 -1 4.4605 6 1 0 0 -1 5.6943 7 1 -1 -1 0 2.7933 8 1 -1 0 0 5.9093 9 1 0 -1 0 2.6474 10 1 0 1 0 2.6474 11 1 0 0 1 5.6943 12 1 0 1 1 4.4605 13 1 2 1 1 9.6503 14 1 1 2 1 13.8583 15 1 1 1 1 2.1384 16 1 1 0 1 0.5169 17 1 1 1 0 2.7933 18 1 1 0 0 5.9093 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3328 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.54 2 C002 has 27 9 9 10.94 3 C003 has 2610 870 870 0.00 4 C004 has 816 272 272 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1191 397 397 0.00 Total of12127 atoms and 4035 groups and 4030 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3328 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 <- "35.034" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1097" Evaluating: 1097-13 Parameter: NUMWAT <- "1084" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1084" Comparing "1075" and "1084". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.034" Parameter: BOX -> "35.034" Parameter: BOX -> "35.034" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.03400 B = 35.03400 C = 35.03400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6479 2 1 -1 -2 -1 13.8554 3 1 -1 -1 -1 2.1364 4 1 -1 0 -1 0.5183 5 1 0 -1 -1 4.4610 6 1 0 0 -1 5.6926 7 1 -1 -1 0 2.7921 8 1 -1 0 0 5.9085 9 1 0 -1 0 2.6467 10 1 0 1 0 2.6467 11 1 0 0 1 5.6926 12 1 0 1 1 4.4610 13 1 2 1 1 9.6479 14 1 1 2 1 13.8554 15 1 1 1 1 2.1364 16 1 1 0 1 0.5183 17 1 1 1 0 2.7921 18 1 1 0 0 5.9085 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3328 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.53 2 C002 has 27 9 9 10.94 3 C003 has 2610 870 870 0.00 4 C004 has 816 272 272 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1194 398 398 0.00 Total of12130 atoms and 4036 groups and 4031 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3328 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 <- "35.032" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1097" Evaluating: 1097-13 Parameter: NUMWAT <- "1084" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1084" Comparing "1075" and "1084". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.032" Parameter: BOX -> "35.032" Parameter: BOX -> "35.032" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.03200 B = 35.03200 C = 35.03200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6454 2 1 -1 -2 -1 13.8524 3 1 -1 -1 -1 2.1345 4 1 -1 0 -1 0.5198 5 1 0 -1 -1 4.4615 6 1 0 0 -1 5.6910 7 1 -1 -1 0 2.7909 8 1 -1 0 0 5.9078 9 1 0 -1 0 2.6459 10 1 0 1 0 2.6459 11 1 0 0 1 5.6910 12 1 0 1 1 4.4615 13 1 2 1 1 9.6454 14 1 1 2 1 13.8524 15 1 1 1 1 2.1345 16 1 1 0 1 0.5198 17 1 1 1 0 2.7909 18 1 1 0 0 5.9078 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3328 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.53 2 C002 has 27 9 9 10.94 3 C003 has 2610 870 870 0.00 4 C004 has 816 272 272 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1194 398 398 0.00 Total of12130 atoms and 4036 groups and 4031 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3328 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 = 3328 Number of groups = 1102 Number of bonds = 3322 Number of angles = 1206 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1100 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 <- "35.03" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1097" Evaluating: 1097-13 Parameter: NUMWAT <- "1084" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1084" Comparing "1075" and "1084". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.03" Parameter: BOX -> "35.03" Parameter: BOX -> "35.03" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.03000 B = 35.03000 C = 35.03000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6430 2 1 -1 -2 -1 13.8494 3 1 -1 -1 -1 2.1325 4 1 -1 0 -1 0.5213 5 1 0 -1 -1 4.4620 6 1 0 0 -1 5.6893 7 1 -1 -1 0 2.7897 8 1 -1 0 0 5.9071 9 1 0 -1 0 2.6451 10 1 0 1 0 2.6451 11 1 0 0 1 5.6893 12 1 0 1 1 4.4620 13 1 2 1 1 9.6430 14 1 1 2 1 13.8494 15 1 1 1 1 2.1325 16 1 1 0 1 0.5213 17 1 1 1 0 2.7897 18 1 1 0 0 5.9071 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3328 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 C015 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.53 2 C002 has 27 9 9 10.93 3 C003 has 2613 871 871 0.00 4 C004 has 819 273 273 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1158 386 386 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1197 399 399 0.00 Total of12145 atoms and 4041 groups and 4036 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3328 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 = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.028" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1096" Evaluating: 1096-13 Parameter: NUMWAT <- "1083" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1083" Comparing "1075" and "1083". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.028" Parameter: BOX -> "35.028" Parameter: BOX -> "35.028" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.02800 B = 35.02800 C = 35.02800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6405 2 1 -1 -2 -1 13.8465 3 1 -1 -1 -1 2.1305 4 1 -1 0 -1 0.5228 5 1 0 -1 -1 4.4625 6 1 0 0 -1 5.6877 7 1 -1 -1 0 2.7885 8 1 -1 0 0 5.9063 9 1 0 -1 0 2.6443 10 1 0 1 0 2.6443 11 1 0 0 1 5.6877 12 1 0 1 1 4.4625 13 1 2 1 1 9.6405 14 1 1 2 1 13.8465 15 1 1 1 1 2.1305 16 1 1 0 1 0.5228 17 1 1 1 0 2.7885 18 1 1 0 0 5.9063 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3249 atoms have been selected out of 3325 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.52 2 C002 has 27 9 9 10.93 3 C003 has 2610 870 870 0.00 4 C004 has 819 273 273 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1194 398 398 0.00 Total of12130 atoms and 4036 groups and 4031 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3325 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.026" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1096" Evaluating: 1096-13 Parameter: NUMWAT <- "1083" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1083" Comparing "1075" and "1083". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.026" Parameter: BOX -> "35.026" Parameter: BOX -> "35.026" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.02600 B = 35.02600 C = 35.02600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6381 2 1 -1 -2 -1 13.8435 3 1 -1 -1 -1 2.1285 4 1 -1 0 -1 0.5243 5 1 0 -1 -1 4.4631 6 1 0 0 -1 5.6860 7 1 -1 -1 0 2.7873 8 1 -1 0 0 5.9056 9 1 0 -1 0 2.6436 10 1 0 1 0 2.6436 11 1 0 0 1 5.6860 12 1 0 1 1 4.4631 13 1 2 1 1 9.6381 14 1 1 2 1 13.8435 15 1 1 1 1 2.1285 16 1 1 0 1 0.5243 17 1 1 1 0 2.7873 18 1 1 0 0 5.9056 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3249 atoms have been selected out of 3325 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.52 2 C002 has 27 9 9 10.93 3 C003 has 2610 870 870 0.00 4 C004 has 819 273 273 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1194 398 398 0.00 Total of12130 atoms and 4036 groups and 4031 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3325 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.024" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1096" Evaluating: 1096-13 Parameter: NUMWAT <- "1083" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1083" Comparing "1075" and "1083". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.024" Parameter: BOX -> "35.024" Parameter: BOX -> "35.024" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.02400 B = 35.02400 C = 35.02400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6356 2 1 -1 -2 -1 13.8406 3 1 -1 -1 -1 2.1265 4 1 -1 0 -1 0.5257 5 1 0 -1 -1 4.4636 6 1 0 0 -1 5.6844 7 1 -1 -1 0 2.7861 8 1 -1 0 0 5.9049 9 1 0 -1 0 2.6428 10 1 0 1 0 2.6428 11 1 0 0 1 5.6844 12 1 0 1 1 4.4636 13 1 2 1 1 9.6356 14 1 1 2 1 13.8406 15 1 1 1 1 2.1265 16 1 1 0 1 0.5257 17 1 1 1 0 2.7861 18 1 1 0 0 5.9049 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3249 atoms have been selected out of 3325 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.52 2 C002 has 27 9 9 10.93 3 C003 has 2610 870 870 0.00 4 C004 has 819 273 273 0.00 5 C005 has 831 277 277 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1194 398 398 0.00 Total of12133 atoms and 4037 groups and 4032 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3325 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.022" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1096" Evaluating: 1096-13 Parameter: NUMWAT <- "1083" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1083" Comparing "1075" and "1083". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.022" Parameter: BOX -> "35.022" Parameter: BOX -> "35.022" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.02200 B = 35.02200 C = 35.02200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6332 2 1 -1 -2 -1 13.8376 3 1 -1 -1 -1 2.1245 4 1 -1 0 -1 0.5272 5 1 0 -1 -1 4.4641 6 1 0 0 -1 5.6827 7 1 -1 -1 0 2.7849 8 1 -1 0 0 5.9041 9 1 0 -1 0 2.6420 10 1 0 1 0 2.6420 11 1 0 0 1 5.6827 12 1 0 1 1 4.4641 13 1 2 1 1 9.6332 14 1 1 2 1 13.8376 15 1 1 1 1 2.1245 16 1 1 0 1 0.5272 17 1 1 1 0 2.7849 18 1 1 0 0 5.9041 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3249 atoms have been selected out of 3325 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.52 2 C002 has 27 9 9 10.92 3 C003 has 2610 870 870 0.00 4 C004 has 819 273 273 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1194 398 398 0.00 Total of12139 atoms and 4039 groups and 4034 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3325 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.02" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1096" Evaluating: 1096-13 Parameter: NUMWAT <- "1083" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1083" Comparing "1075" and "1083". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.02" Parameter: BOX -> "35.02" Parameter: BOX -> "35.02" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.02000 B = 35.02000 C = 35.02000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6307 2 1 -1 -2 -1 13.8346 3 1 -1 -1 -1 2.1226 4 1 -1 0 -1 0.5288 5 1 0 -1 -1 4.4647 6 1 0 0 -1 5.6810 7 1 -1 -1 0 2.7836 8 1 -1 0 0 5.9034 9 1 0 -1 0 2.6413 10 1 0 1 0 2.6413 11 1 0 0 1 5.6810 12 1 0 1 1 4.4647 13 1 2 1 1 9.6307 14 1 1 2 1 13.8346 15 1 1 1 1 2.1226 16 1 1 0 1 0.5288 17 1 1 1 0 2.7836 18 1 1 0 0 5.9034 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3249 atoms have been selected out of 3325 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.51 2 C002 has 27 9 9 10.92 3 C003 has 2610 870 870 0.00 4 C004 has 819 273 273 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1194 398 398 0.00 Total of12139 atoms and 4039 groups and 4034 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3325 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.018" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1096" Evaluating: 1096-13 Parameter: NUMWAT <- "1083" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1083" Comparing "1075" and "1083". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.018" Parameter: BOX -> "35.018" Parameter: BOX -> "35.018" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.01800 B = 35.01800 C = 35.01800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6283 2 1 -1 -2 -1 13.8317 3 1 -1 -1 -1 2.1206 4 1 -1 0 -1 0.5303 5 1 0 -1 -1 4.4652 6 1 0 0 -1 5.6794 7 1 -1 -1 0 2.7824 8 1 -1 0 0 5.9027 9 1 0 -1 0 2.6405 10 1 0 1 0 2.6405 11 1 0 0 1 5.6794 12 1 0 1 1 4.4652 13 1 2 1 1 9.6283 14 1 1 2 1 13.8317 15 1 1 1 1 2.1206 16 1 1 0 1 0.5303 17 1 1 1 0 2.7824 18 1 1 0 0 5.9027 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3249 atoms have been selected out of 3325 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.51 2 C002 has 30 10 10 10.92 3 C003 has 2610 870 870 0.00 4 C004 has 819 273 273 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1185 395 395 0.00 9 C009 has 1194 398 398 0.00 Total of12145 atoms and 4041 groups and 4036 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3325 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.016" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1096" Evaluating: 1096-13 Parameter: NUMWAT <- "1083" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1083" Comparing "1075" and "1083". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.016" Parameter: BOX -> "35.016" Parameter: BOX -> "35.016" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.01600 B = 35.01600 C = 35.01600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6258 2 1 -1 -2 -1 13.8287 3 1 -1 -1 -1 2.1186 4 1 -1 0 -1 0.5318 5 1 0 -1 -1 4.4657 6 1 0 0 -1 5.6777 7 1 -1 -1 0 2.7812 8 1 -1 0 0 5.9019 9 1 0 -1 0 2.6397 10 1 0 1 0 2.6397 11 1 0 0 1 5.6777 12 1 0 1 1 4.4657 13 1 2 1 1 9.6258 14 1 1 2 1 13.8287 15 1 1 1 1 2.1186 16 1 1 0 1 0.5318 17 1 1 1 0 2.7812 18 1 1 0 0 5.9019 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3249 atoms have been selected out of 3325 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.51 2 C002 has 30 10 10 10.91 3 C003 has 2610 870 870 0.00 4 C004 has 819 273 273 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1185 395 395 0.00 9 C009 has 1194 398 398 0.00 Total of12145 atoms and 4041 groups and 4036 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3325 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.014" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1096" Evaluating: 1096-13 Parameter: NUMWAT <- "1083" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1083" Comparing "1075" and "1083". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.014" Parameter: BOX -> "35.014" Parameter: BOX -> "35.014" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.01400 B = 35.01400 C = 35.01400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6234 2 1 -1 -2 -1 13.8258 3 1 -1 -1 -1 2.1166 4 1 -1 0 -1 0.5333 5 1 0 -1 -1 4.4663 6 1 0 0 -1 5.6761 7 1 -1 -1 0 2.7800 8 1 -1 0 0 5.9012 9 1 0 -1 0 2.6390 10 1 0 1 0 2.6390 11 1 0 0 1 5.6761 12 1 0 1 1 4.4663 13 1 2 1 1 9.6234 14 1 1 2 1 13.8258 15 1 1 1 1 2.1166 16 1 1 0 1 0.5333 17 1 1 1 0 2.7800 18 1 1 0 0 5.9012 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3249 atoms have been selected out of 3325 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.50 2 C002 has 30 10 10 10.91 3 C003 has 2610 870 870 0.00 4 C004 has 819 273 273 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1185 395 395 0.00 9 C009 has 1194 398 398 0.00 Total of12145 atoms and 4041 groups and 4036 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3325 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.012" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1096" Evaluating: 1096-13 Parameter: NUMWAT <- "1083" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1083" Comparing "1075" and "1083". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.012" Parameter: BOX -> "35.012" Parameter: BOX -> "35.012" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.01200 B = 35.01200 C = 35.01200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6210 2 1 -1 -2 -1 13.8228 3 1 -1 -1 -1 2.1146 4 1 -1 0 -1 0.5348 5 1 0 -1 -1 4.4668 6 1 0 0 -1 5.6744 7 1 -1 -1 0 2.7788 8 1 -1 0 0 5.9005 9 1 0 -1 0 2.6382 10 1 0 1 0 2.6382 11 1 0 0 1 5.6744 12 1 0 1 1 4.4668 13 1 2 1 1 9.6210 14 1 1 2 1 13.8228 15 1 1 1 1 2.1146 16 1 1 0 1 0.5348 17 1 1 1 0 2.7788 18 1 1 0 0 5.9005 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3249 atoms have been selected out of 3325 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.50 2 C002 has 30 10 10 10.91 3 C003 has 2610 870 870 0.00 4 C004 has 819 273 273 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1185 395 395 0.00 9 C009 has 1194 398 398 0.00 Total of12145 atoms and 4041 groups and 4036 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3325 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.01" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1096" Evaluating: 1096-13 Parameter: NUMWAT <- "1083" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1083" Comparing "1075" and "1083". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.01" Parameter: BOX -> "35.01" Parameter: BOX -> "35.01" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.01000 B = 35.01000 C = 35.01000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6185 2 1 -1 -2 -1 13.8199 3 1 -1 -1 -1 2.1127 4 1 -1 0 -1 0.5364 5 1 0 -1 -1 4.4673 6 1 0 0 -1 5.6728 7 1 -1 -1 0 2.7776 8 1 -1 0 0 5.8997 9 1 0 -1 0 2.6374 10 1 0 1 0 2.6374 11 1 0 0 1 5.6728 12 1 0 1 1 4.4673 13 1 2 1 1 9.6185 14 1 1 2 1 13.8199 15 1 1 1 1 2.1127 16 1 1 0 1 0.5364 17 1 1 1 0 2.7776 18 1 1 0 0 5.8997 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3249 atoms have been selected out of 3325 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.50 2 C002 has 30 10 10 10.90 3 C003 has 2610 870 870 0.00 4 C004 has 819 273 273 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1185 395 395 0.00 9 C009 has 1194 398 398 0.00 Total of12145 atoms and 4041 groups and 4036 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3325 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.008" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1096" Evaluating: 1096-13 Parameter: NUMWAT <- "1083" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1083" Comparing "1075" and "1083". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.008" Parameter: BOX -> "35.008" Parameter: BOX -> "35.008" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.00800 B = 35.00800 C = 35.00800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6161 2 1 -1 -2 -1 13.8169 3 1 -1 -1 -1 2.1107 4 1 -1 0 -1 0.5379 5 1 0 -1 -1 4.4679 6 1 0 0 -1 5.6711 7 1 -1 -1 0 2.7764 8 1 -1 0 0 5.8990 9 1 0 -1 0 2.6367 10 1 0 1 0 2.6367 11 1 0 0 1 5.6711 12 1 0 1 1 4.4679 13 1 2 1 1 9.6161 14 1 1 2 1 13.8169 15 1 1 1 1 2.1107 16 1 1 0 1 0.5379 17 1 1 1 0 2.7764 18 1 1 0 0 5.8990 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3249 atoms have been selected out of 3325 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.49 2 C002 has 30 10 10 10.90 3 C003 has 2610 870 870 0.00 4 C004 has 819 273 273 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1185 395 395 0.00 9 C009 has 1194 398 398 0.00 Total of12145 atoms and 4041 groups and 4036 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3325 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.006" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1096" Evaluating: 1096-13 Parameter: NUMWAT <- "1083" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1083" Comparing "1075" and "1083". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.006" Parameter: BOX -> "35.006" Parameter: BOX -> "35.006" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.00600 B = 35.00600 C = 35.00600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6136 2 1 -1 -2 -1 13.8139 3 1 -1 -1 -1 2.1087 4 1 -1 0 -1 0.5395 5 1 0 -1 -1 4.4684 6 1 0 0 -1 5.6695 7 1 -1 -1 0 2.7752 8 1 -1 0 0 5.8983 9 1 0 -1 0 2.6359 10 1 0 1 0 2.6359 11 1 0 0 1 5.6695 12 1 0 1 1 4.4684 13 1 2 1 1 9.6136 14 1 1 2 1 13.8139 15 1 1 1 1 2.1087 16 1 1 0 1 0.5395 17 1 1 1 0 2.7752 18 1 1 0 0 5.8983 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3249 atoms have been selected out of 3325 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.49 2 C002 has 30 10 10 10.90 3 C003 has 2610 870 870 0.00 4 C004 has 819 273 273 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1185 395 395 0.00 9 C009 has 1194 398 398 0.00 Total of12145 atoms and 4041 groups and 4036 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3325 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.004" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1096" Evaluating: 1096-13 Parameter: NUMWAT <- "1083" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1083" Comparing "1075" and "1083". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.004" Parameter: BOX -> "35.004" Parameter: BOX -> "35.004" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.00400 B = 35.00400 C = 35.00400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6112 2 1 -1 -2 -1 13.8110 3 1 -1 -1 -1 2.1067 4 1 -1 0 -1 0.5410 5 1 0 -1 -1 4.4689 6 1 0 0 -1 5.6678 7 1 -1 -1 0 2.7740 8 1 -1 0 0 5.8976 9 1 0 -1 0 2.6352 10 1 0 1 0 2.6352 11 1 0 0 1 5.6678 12 1 0 1 1 4.4689 13 1 2 1 1 9.6112 14 1 1 2 1 13.8110 15 1 1 1 1 2.1067 16 1 1 0 1 0.5410 17 1 1 1 0 2.7740 18 1 1 0 0 5.8976 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3249 atoms have been selected out of 3325 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.49 2 C002 has 30 10 10 10.89 3 C003 has 2613 871 871 0.00 4 C004 has 819 273 273 0.00 5 C005 has 834 278 278 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1185 395 395 0.00 9 C009 has 1194 398 398 0.00 Total of12148 atoms and 4042 groups and 4037 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3325 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> join wat renumber THE RESIDUE IDENTIFIERS HAVE BEEN RENUMBERED PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 1096 Number of atoms = 3325 Number of groups = 1101 Number of bonds = 3319 Number of angles = 1205 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1099 Number of HB donors = 2174 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> crystal free CHARMM> incr box by -@boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "35.002" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1096" Evaluating: 1096-13 Parameter: NUMWAT <- "1083" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1083" Comparing "1075" and "1083". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35.002" Parameter: BOX -> "35.002" Parameter: BOX -> "35.002" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.00200 B = 35.00200 C = 35.00200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 9.6087 2 1 -1 -2 -1 13.8080 3 1 -1 -1 -1 2.1047 4 1 -1 0 -1 0.5426 5 1 0 -1 -1 4.4695 6 1 0 0 -1 5.6662 7 1 -1 -1 0 2.7728 8 1 -1 0 0 5.8968 9 1 0 -1 0 2.6344 10 1 0 1 0 2.6344 11 1 0 0 1 5.6662 12 1 0 1 1 4.4695 13 1 2 1 1 9.6087 14 1 1 2 1 13.8080 15 1 1 1 1 2.1047 16 1 1 0 1 0.5426 17 1 1 1 0 2.7728 18 1 1 0 0 5.8968 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations have been processed. CHARMM> CHARMM> coordinate copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> image byres select segid wat end SELRPN> 3249 atoms have been selected out of 3325 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 815 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.48 2 C002 has 30 10 10 10.89 3 C003 has 2613 871 871 0.00 4 C004 has 819 273 273 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1158 386 386 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1197 399 399 0.00 Total of12148 atoms and 4042 groups and 4037 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3325 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 = 1095 Number of atoms = 3322 Number of groups = 1100 Number of bonds = 3316 Number of angles = 1204 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1098 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 = 3322 Number of groups = 1100 Number of bonds = 3316 Number of angles = 1204 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1098 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 <- "35" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1095" Evaluating: 1095-13 Parameter: NUMWAT <- "1082" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1082" Comparing "1075" and "1082". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "35" Parameter: BOX -> "35" Parameter: BOX -> "35" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 35.00000 B = 35.00000 C = 35.00000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8344 2 1 -1 -2 -1 13.8051 3 1 -1 -1 -1 2.1027 4 1 -1 0 -1 0.5441 5 1 0 -1 -1 4.4700 6 1 0 0 -1 5.6645 7 1 -1 -1 0 2.7717 8 1 -1 0 0 4.9039 9 1 0 -1 0 2.6337 10 1 0 1 0 2.6337 11 1 0 0 1 5.6645 12 1 0 1 1 4.4700 13 1 2 1 1 8.8344 14 1 1 2 1 13.8051 15 1 1 1 1 2.1027 16 1 1 0 1 0.5441 17 1 1 1 0 2.7717 18 1 1 0 0 4.9039 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3322 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.48 2 C002 has 30 10 10 10.89 3 C003 has 2610 870 870 0.00 4 C004 has 819 273 273 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1194 398 398 0.00 Total of12136 atoms and 4038 groups and 4033 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3322 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3322 Number of groups = 1100 Number of bonds = 3316 Number of angles = 1204 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1098 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 = 3322 Number of groups = 1100 Number of bonds = 3316 Number of angles = 1204 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1098 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 <- "34.998" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1095" Evaluating: 1095-13 Parameter: NUMWAT <- "1082" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1082" Comparing "1075" and "1082". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.998" Parameter: BOX -> "34.998" Parameter: BOX -> "34.998" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.99800 B = 34.99800 C = 34.99800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8322 2 1 -1 -2 -1 13.8021 3 1 -1 -1 -1 2.1008 4 1 -1 0 -1 0.5457 5 1 0 -1 -1 4.4706 6 1 0 0 -1 5.6629 7 1 -1 -1 0 2.7705 8 1 -1 0 0 4.9035 9 1 0 -1 0 2.6329 10 1 0 1 0 2.6329 11 1 0 0 1 5.6629 12 1 0 1 1 4.4706 13 1 2 1 1 8.8322 14 1 1 2 1 13.8021 15 1 1 1 1 2.1008 16 1 1 0 1 0.5457 17 1 1 1 0 2.7705 18 1 1 0 0 4.9035 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3322 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.48 2 C002 has 30 10 10 10.89 3 C003 has 2610 870 870 0.00 4 C004 has 822 274 274 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1194 398 398 0.00 Total of12139 atoms and 4039 groups and 4034 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3322 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3322 Number of groups = 1100 Number of bonds = 3316 Number of angles = 1204 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1098 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 = 3322 Number of groups = 1100 Number of bonds = 3316 Number of angles = 1204 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1098 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 <- "34.996" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1095" Evaluating: 1095-13 Parameter: NUMWAT <- "1082" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1082" Comparing "1075" and "1082". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.996" Parameter: BOX -> "34.996" Parameter: BOX -> "34.996" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.99600 B = 34.99600 C = 34.99600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8301 2 1 -1 -2 -1 13.7991 3 1 -1 -1 -1 2.0988 4 1 -1 0 -1 0.5473 5 1 0 -1 -1 4.4711 6 1 0 0 -1 5.6612 7 1 -1 -1 0 2.7693 8 1 -1 0 0 4.9032 9 1 0 -1 0 2.6321 10 1 0 1 0 2.6321 11 1 0 0 1 5.6612 12 1 0 1 1 4.4711 13 1 2 1 1 8.8301 14 1 1 2 1 13.7991 15 1 1 1 1 2.0988 16 1 1 0 1 0.5473 17 1 1 1 0 2.7693 18 1 1 0 0 4.9032 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3322 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.48 2 C002 has 30 10 10 10.88 3 C003 has 2610 870 870 0.00 4 C004 has 822 274 274 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1194 398 398 0.00 Total of12139 atoms and 4039 groups and 4034 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3322 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3322 Number of groups = 1100 Number of bonds = 3316 Number of angles = 1204 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1098 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 = 3322 Number of groups = 1100 Number of bonds = 3316 Number of angles = 1204 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1098 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 <- "34.994" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1095" Evaluating: 1095-13 Parameter: NUMWAT <- "1082" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1082" Comparing "1075" and "1082". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.994" Parameter: BOX -> "34.994" Parameter: BOX -> "34.994" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.99400 B = 34.99400 C = 34.99400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8279 2 1 -1 -2 -1 13.7962 3 1 -1 -1 -1 2.0968 4 1 -1 0 -1 0.5488 5 1 0 -1 -1 4.4717 6 1 0 0 -1 5.6596 7 1 -1 -1 0 2.7681 8 1 -1 0 0 4.9029 9 1 0 -1 0 2.6314 10 1 0 1 0 2.6314 11 1 0 0 1 5.6596 12 1 0 1 1 4.4717 13 1 2 1 1 8.8279 14 1 1 2 1 13.7962 15 1 1 1 1 2.0968 16 1 1 0 1 0.5488 17 1 1 1 0 2.7681 18 1 1 0 0 4.9029 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3322 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.47 2 C002 has 30 10 10 10.88 3 C003 has 2610 870 870 0.00 4 C004 has 822 274 274 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1194 398 398 0.00 Total of12139 atoms and 4039 groups and 4034 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3322 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3322 Number of groups = 1100 Number of bonds = 3316 Number of angles = 1204 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1098 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 = 3322 Number of groups = 1100 Number of bonds = 3316 Number of angles = 1204 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1098 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 <- "34.992" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1095" Evaluating: 1095-13 Parameter: NUMWAT <- "1082" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1082" Comparing "1075" and "1082". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.992" Parameter: BOX -> "34.992" Parameter: BOX -> "34.992" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.99200 B = 34.99200 C = 34.99200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8257 2 1 -1 -2 -1 13.7932 3 1 -1 -1 -1 2.0948 4 1 -1 0 -1 0.5504 5 1 0 -1 -1 4.4722 6 1 0 0 -1 5.6579 7 1 -1 -1 0 2.7669 8 1 -1 0 0 4.9026 9 1 0 -1 0 2.6306 10 1 0 1 0 2.6306 11 1 0 0 1 5.6579 12 1 0 1 1 4.4722 13 1 2 1 1 8.8257 14 1 1 2 1 13.7932 15 1 1 1 1 2.0948 16 1 1 0 1 0.5504 17 1 1 1 0 2.7669 18 1 1 0 0 4.9026 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3322 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.47 2 C002 has 30 10 10 10.88 3 C003 has 2610 870 870 0.00 4 C004 has 822 274 274 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1194 398 398 0.00 Total of12139 atoms and 4039 groups and 4034 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3322 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3322 Number of groups = 1100 Number of bonds = 3316 Number of angles = 1204 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1098 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 = 3322 Number of groups = 1100 Number of bonds = 3316 Number of angles = 1204 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1098 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 <- "34.99" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1095" Evaluating: 1095-13 Parameter: NUMWAT <- "1082" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1082" Comparing "1075" and "1082". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.99" Parameter: BOX -> "34.99" Parameter: BOX -> "34.99" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.99000 B = 34.99000 C = 34.99000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8236 2 1 -1 -2 -1 13.7903 3 1 -1 -1 -1 2.0928 4 1 -1 0 -1 0.5520 5 1 0 -1 -1 4.4728 6 1 0 0 -1 5.6563 7 1 -1 -1 0 2.7657 8 1 -1 0 0 4.9023 9 1 0 -1 0 2.6299 10 1 0 1 0 2.6299 11 1 0 0 1 5.6563 12 1 0 1 1 4.4728 13 1 2 1 1 8.8236 14 1 1 2 1 13.7903 15 1 1 1 1 2.0928 16 1 1 0 1 0.5520 17 1 1 1 0 2.7657 18 1 1 0 0 4.9023 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3322 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.47 2 C002 has 30 10 10 10.87 3 C003 has 2610 870 870 0.00 4 C004 has 822 274 274 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1197 399 399 0.00 Total of12142 atoms and 4040 groups and 4035 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3322 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3322 Number of groups = 1100 Number of bonds = 3316 Number of angles = 1204 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1098 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 = 3322 Number of groups = 1100 Number of bonds = 3316 Number of angles = 1204 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1098 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 <- "34.988" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1095" Evaluating: 1095-13 Parameter: NUMWAT <- "1082" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1082" Comparing "1075" and "1082". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.988" Parameter: BOX -> "34.988" Parameter: BOX -> "34.988" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.98800 B = 34.98800 C = 34.98800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8214 2 1 -1 -2 -1 13.7873 3 1 -1 -1 -1 2.0909 4 1 -1 0 -1 0.5536 5 1 0 -1 -1 4.4733 6 1 0 0 -1 5.6546 7 1 -1 -1 0 2.7645 8 1 -1 0 0 4.9019 9 1 0 -1 0 2.6292 10 1 0 1 0 2.6292 11 1 0 0 1 5.6546 12 1 0 1 1 4.4733 13 1 2 1 1 8.8214 14 1 1 2 1 13.7873 15 1 1 1 1 2.0909 16 1 1 0 1 0.5536 17 1 1 1 0 2.7645 18 1 1 0 0 4.9019 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3322 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.46 2 C002 has 30 10 10 10.87 3 C003 has 2610 870 870 0.00 4 C004 has 822 274 274 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1197 399 399 0.00 Total of12142 atoms and 4040 groups and 4035 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3322 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3322 Number of groups = 1100 Number of bonds = 3316 Number of angles = 1204 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1098 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 = 3322 Number of groups = 1100 Number of bonds = 3316 Number of angles = 1204 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1098 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 <- "34.986" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1095" Evaluating: 1095-13 Parameter: NUMWAT <- "1082" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1082" Comparing "1075" and "1082". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.986" Parameter: BOX -> "34.986" Parameter: BOX -> "34.986" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.98600 B = 34.98600 C = 34.98600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8193 2 1 -1 -2 -1 13.7844 3 1 -1 -1 -1 2.0889 4 1 -1 0 -1 0.5552 5 1 0 -1 -1 4.4712 6 1 0 0 -1 5.6530 7 1 -1 -1 0 2.7633 8 1 -1 0 0 4.9016 9 1 0 -1 0 2.6284 10 1 0 1 0 2.6284 11 1 0 0 1 5.6530 12 1 0 1 1 4.4712 13 1 2 1 1 8.8193 14 1 1 2 1 13.7844 15 1 1 1 1 2.0889 16 1 1 0 1 0.5552 17 1 1 1 0 2.7633 18 1 1 0 0 4.9016 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3322 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.46 2 C002 has 30 10 10 10.87 3 C003 has 2610 870 870 0.00 4 C004 has 822 274 274 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1197 399 399 0.00 Total of12142 atoms and 4040 groups and 4035 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3322 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3322 Number of groups = 1100 Number of bonds = 3316 Number of angles = 1204 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1098 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 = 3322 Number of groups = 1100 Number of bonds = 3316 Number of angles = 1204 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1098 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 <- "34.984" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1095" Evaluating: 1095-13 Parameter: NUMWAT <- "1082" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1082" Comparing "1075" and "1082". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.984" Parameter: BOX -> "34.984" Parameter: BOX -> "34.984" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.98400 B = 34.98400 C = 34.98400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8171 2 1 -1 -2 -1 13.7814 3 1 -1 -1 -1 2.0869 4 1 -1 0 -1 0.5568 5 1 0 -1 -1 4.4691 6 1 0 0 -1 5.6513 7 1 -1 -1 0 2.7622 8 1 -1 0 0 4.9013 9 1 0 -1 0 2.6277 10 1 0 1 0 2.6277 11 1 0 0 1 5.6513 12 1 0 1 1 4.4691 13 1 2 1 1 8.8171 14 1 1 2 1 13.7814 15 1 1 1 1 2.0869 16 1 1 0 1 0.5568 17 1 1 1 0 2.7622 18 1 1 0 0 4.9013 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3322 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.46 2 C002 has 30 10 10 10.86 3 C003 has 2610 870 870 0.00 4 C004 has 822 274 274 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1197 399 399 0.00 Total of12142 atoms and 4040 groups and 4035 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3322 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3322 Number of groups = 1100 Number of bonds = 3316 Number of angles = 1204 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1098 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 = 3322 Number of groups = 1100 Number of bonds = 3316 Number of angles = 1204 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1098 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 <- "34.982" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1095" Evaluating: 1095-13 Parameter: NUMWAT <- "1082" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1082" Comparing "1075" and "1082". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.982" Parameter: BOX -> "34.982" Parameter: BOX -> "34.982" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.98200 B = 34.98200 C = 34.98200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8150 2 1 -1 -2 -1 13.7784 3 1 -1 -1 -1 2.0849 4 1 -1 0 -1 0.5584 5 1 0 -1 -1 4.4670 6 1 0 0 -1 5.6497 7 1 -1 -1 0 2.7610 8 1 -1 0 0 4.9010 9 1 0 -1 0 2.6269 10 1 0 1 0 2.6269 11 1 0 0 1 5.6497 12 1 0 1 1 4.4670 13 1 2 1 1 8.8150 14 1 1 2 1 13.7784 15 1 1 1 1 2.0849 16 1 1 0 1 0.5584 17 1 1 1 0 2.7610 18 1 1 0 0 4.9010 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3322 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.45 2 C002 has 30 10 10 10.86 3 C003 has 2610 870 870 0.00 4 C004 has 822 274 274 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1197 399 399 0.00 Total of12142 atoms and 4040 groups and 4035 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3322 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3322 Number of groups = 1100 Number of bonds = 3316 Number of angles = 1204 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1098 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 = 3322 Number of groups = 1100 Number of bonds = 3316 Number of angles = 1204 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1098 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 <- "34.98" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1095" Evaluating: 1095-13 Parameter: NUMWAT <- "1082" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1082" Comparing "1075" and "1082". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.98" Parameter: BOX -> "34.98" Parameter: BOX -> "34.98" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.98000 B = 34.98000 C = 34.98000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8128 2 1 -1 -2 -1 13.7755 3 1 -1 -1 -1 2.0829 4 1 -1 0 -1 0.5600 5 1 0 -1 -1 4.4648 6 1 0 0 -1 5.6480 7 1 -1 -1 0 2.7598 8 1 -1 0 0 4.9007 9 1 0 -1 0 2.6262 10 1 0 1 0 2.6262 11 1 0 0 1 5.6480 12 1 0 1 1 4.4648 13 1 2 1 1 8.8128 14 1 1 2 1 13.7755 15 1 1 1 1 2.0829 16 1 1 0 1 0.5600 17 1 1 1 0 2.7598 18 1 1 0 0 4.9007 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3322 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.45 2 C002 has 30 10 10 10.86 3 C003 has 2610 870 870 0.00 4 C004 has 822 274 274 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1197 399 399 0.00 Total of12142 atoms and 4040 groups and 4035 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3322 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3322 Number of groups = 1100 Number of bonds = 3316 Number of angles = 1204 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1098 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 = 3322 Number of groups = 1100 Number of bonds = 3316 Number of angles = 1204 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1098 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 <- "34.978" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1095" Evaluating: 1095-13 Parameter: NUMWAT <- "1082" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1082" Comparing "1075" and "1082". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.978" Parameter: BOX -> "34.978" Parameter: BOX -> "34.978" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.97800 B = 34.97800 C = 34.97800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8107 2 1 -1 -2 -1 13.7725 3 1 -1 -1 -1 2.0809 4 1 -1 0 -1 0.5617 5 1 0 -1 -1 4.4627 6 1 0 0 -1 5.6464 7 1 -1 -1 0 2.7586 8 1 -1 0 0 4.9003 9 1 0 -1 0 2.6254 10 1 0 1 0 2.6254 11 1 0 0 1 5.6464 12 1 0 1 1 4.4627 13 1 2 1 1 8.8107 14 1 1 2 1 13.7725 15 1 1 1 1 2.0809 16 1 1 0 1 0.5617 17 1 1 1 0 2.7586 18 1 1 0 0 4.9003 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3322 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.45 2 C002 has 30 10 10 10.85 3 C003 has 2610 870 870 0.00 4 C004 has 822 274 274 0.00 5 C005 has 837 279 279 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1197 399 399 0.00 Total of12142 atoms and 4040 groups and 4035 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3322 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3322 Number of groups = 1100 Number of bonds = 3316 Number of angles = 1204 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1098 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 = 3322 Number of groups = 1100 Number of bonds = 3316 Number of angles = 1204 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1098 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 <- "34.976" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1095" Evaluating: 1095-13 Parameter: NUMWAT <- "1082" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1082" Comparing "1075" and "1082". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.976" Parameter: BOX -> "34.976" Parameter: BOX -> "34.976" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.97600 B = 34.97600 C = 34.97600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8085 2 1 -1 -2 -1 13.7696 3 1 -1 -1 -1 2.0790 4 1 -1 0 -1 0.5633 5 1 0 -1 -1 4.4606 6 1 0 0 -1 5.6448 7 1 -1 -1 0 2.7574 8 1 -1 0 0 4.9000 9 1 0 -1 0 2.6247 10 1 0 1 0 2.6247 11 1 0 0 1 5.6448 12 1 0 1 1 4.4606 13 1 2 1 1 8.8085 14 1 1 2 1 13.7696 15 1 1 1 1 2.0790 16 1 1 0 1 0.5633 17 1 1 1 0 2.7574 18 1 1 0 0 4.9000 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3322 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 146 OPERATED ON BY TRANSFORMATION C010 RESIDUE 153 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 204 68 68 5.44 2 C002 has 30 10 10 10.85 3 C003 has 2610 870 870 0.00 4 C004 has 822 274 274 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1182 394 394 0.00 9 C009 has 1203 401 401 0.00 Total of12151 atoms and 4043 groups and 4038 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3322 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 = 1093 Number of atoms = 3316 Number of groups = 1098 Number of bonds = 3310 Number of angles = 1202 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1096 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 = 3316 Number of groups = 1098 Number of bonds = 3310 Number of angles = 1202 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1096 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 <- "34.974" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1093" Evaluating: 1093-13 Parameter: NUMWAT <- "1080" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1080" Comparing "1075" and "1080". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.974" Parameter: BOX -> "34.974" Parameter: BOX -> "34.974" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.97400 B = 34.97400 C = 34.97400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8064 2 1 -1 -2 -1 13.7666 3 1 -1 -1 -1 2.0770 4 1 -1 0 -1 0.5649 5 1 0 -1 -1 4.4584 6 1 0 0 -1 5.6431 7 1 -1 -1 0 2.7563 8 1 -1 0 0 4.8997 9 1 0 -1 0 2.6240 10 1 0 1 0 2.6240 11 1 0 0 1 5.6431 12 1 0 1 1 4.4584 13 1 2 1 1 8.8064 14 1 1 2 1 13.7666 15 1 1 1 1 2.0770 16 1 1 0 1 0.5649 17 1 1 1 0 2.7563 18 1 1 0 0 4.8997 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3316 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 204 68 68 5.44 2 C002 has 30 10 10 10.85 3 C003 has 2607 869 869 0.00 4 C004 has 825 275 275 0.00 5 C005 has 840 280 280 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1176 392 392 0.00 9 C009 has 1197 399 399 0.00 Total of12127 atoms and 4035 groups and 4030 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3316 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3316 Number of groups = 1098 Number of bonds = 3310 Number of angles = 1202 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1096 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 = 3316 Number of groups = 1098 Number of bonds = 3310 Number of angles = 1202 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1096 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 <- "34.972" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1093" Evaluating: 1093-13 Parameter: NUMWAT <- "1080" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1080" Comparing "1075" and "1080". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.972" Parameter: BOX -> "34.972" Parameter: BOX -> "34.972" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.97200 B = 34.97200 C = 34.97200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8042 2 1 -1 -2 -1 13.7637 3 1 -1 -1 -1 2.0750 4 1 -1 0 -1 0.5665 5 1 0 -1 -1 4.4563 6 1 0 0 -1 5.6415 7 1 -1 -1 0 2.7551 8 1 -1 0 0 4.8994 9 1 0 -1 0 2.6232 10 1 0 1 0 2.6232 11 1 0 0 1 5.6415 12 1 0 1 1 4.4563 13 1 2 1 1 8.8042 14 1 1 2 1 13.7637 15 1 1 1 1 2.0750 16 1 1 0 1 0.5665 17 1 1 1 0 2.7551 18 1 1 0 0 4.8994 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3316 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 204 68 68 5.44 2 C002 has 30 10 10 10.85 3 C003 has 2607 869 869 0.00 4 C004 has 825 275 275 0.00 5 C005 has 840 280 280 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1176 392 392 0.00 9 C009 has 1197 399 399 0.00 Total of12127 atoms and 4035 groups and 4030 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3316 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3316 Number of groups = 1098 Number of bonds = 3310 Number of angles = 1202 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1096 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 = 3316 Number of groups = 1098 Number of bonds = 3310 Number of angles = 1202 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1096 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 <- "34.97" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1093" Evaluating: 1093-13 Parameter: NUMWAT <- "1080" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1080" Comparing "1075" and "1080". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.97" Parameter: BOX -> "34.97" Parameter: BOX -> "34.97" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.97000 B = 34.97000 C = 34.97000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.8021 2 1 -1 -2 -1 13.7607 3 1 -1 -1 -1 2.0730 4 1 -1 0 -1 0.5682 5 1 0 -1 -1 4.4542 6 1 0 0 -1 5.6398 7 1 -1 -1 0 2.7539 8 1 -1 0 0 4.8991 9 1 0 -1 0 2.6225 10 1 0 1 0 2.6225 11 1 0 0 1 5.6398 12 1 0 1 1 4.4542 13 1 2 1 1 8.8021 14 1 1 2 1 13.7607 15 1 1 1 1 2.0730 16 1 1 0 1 0.5682 17 1 1 1 0 2.7539 18 1 1 0 0 4.8991 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3316 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 204 68 68 5.44 2 C002 has 30 10 10 10.84 3 C003 has 2607 869 869 0.00 4 C004 has 825 275 275 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1176 392 392 0.00 9 C009 has 1197 399 399 0.00 Total of12130 atoms and 4036 groups and 4031 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3316 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3316 Number of groups = 1098 Number of bonds = 3310 Number of angles = 1202 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1096 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 = 3316 Number of groups = 1098 Number of bonds = 3310 Number of angles = 1202 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1096 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 <- "34.968" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1093" Evaluating: 1093-13 Parameter: NUMWAT <- "1080" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1080" Comparing "1075" and "1080". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.968" Parameter: BOX -> "34.968" Parameter: BOX -> "34.968" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.96800 B = 34.96800 C = 34.96800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7999 2 1 -1 -2 -1 13.7578 3 1 -1 -1 -1 2.0710 4 1 -1 0 -1 0.5698 5 1 0 -1 -1 4.4520 6 1 0 0 -1 5.6382 7 1 -1 -1 0 2.7528 8 1 -1 0 0 4.8988 9 1 0 -1 0 2.6217 10 1 0 1 0 2.6217 11 1 0 0 1 5.6382 12 1 0 1 1 4.4520 13 1 2 1 1 8.7999 14 1 1 2 1 13.7578 15 1 1 1 1 2.0710 16 1 1 0 1 0.5698 17 1 1 1 0 2.7528 18 1 1 0 0 4.8988 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3316 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.43 2 C002 has 30 10 10 10.84 3 C003 has 2607 869 869 0.00 4 C004 has 825 275 275 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1176 392 392 0.00 9 C009 has 1197 399 399 0.00 Total of12133 atoms and 4037 groups and 4032 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3316 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3316 Number of groups = 1098 Number of bonds = 3310 Number of angles = 1202 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1096 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 = 3316 Number of groups = 1098 Number of bonds = 3310 Number of angles = 1202 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1096 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 <- "34.966" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1093" Evaluating: 1093-13 Parameter: NUMWAT <- "1080" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1080" Comparing "1075" and "1080". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.966" Parameter: BOX -> "34.966" Parameter: BOX -> "34.966" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.96600 B = 34.96600 C = 34.96600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7978 2 1 -1 -2 -1 13.7548 3 1 -1 -1 -1 2.0691 4 1 -1 0 -1 0.5715 5 1 0 -1 -1 4.4499 6 1 0 0 -1 5.6365 7 1 -1 -1 0 2.7516 8 1 -1 0 0 4.8985 9 1 0 -1 0 2.6210 10 1 0 1 0 2.6210 11 1 0 0 1 5.6365 12 1 0 1 1 4.4499 13 1 2 1 1 8.7978 14 1 1 2 1 13.7548 15 1 1 1 1 2.0691 16 1 1 0 1 0.5715 17 1 1 1 0 2.7516 18 1 1 0 0 4.8985 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3316 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.43 2 C002 has 30 10 10 10.84 3 C003 has 2607 869 869 0.00 4 C004 has 825 275 275 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1176 392 392 0.00 9 C009 has 1197 399 399 0.00 Total of12136 atoms and 4038 groups and 4033 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3316 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3316 Number of groups = 1098 Number of bonds = 3310 Number of angles = 1202 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1096 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 = 3316 Number of groups = 1098 Number of bonds = 3310 Number of angles = 1202 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1096 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 <- "34.964" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1093" Evaluating: 1093-13 Parameter: NUMWAT <- "1080" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1080" Comparing "1075" and "1080". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.964" Parameter: BOX -> "34.964" Parameter: BOX -> "34.964" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.96400 B = 34.96400 C = 34.96400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7956 2 1 -1 -2 -1 13.7518 3 1 -1 -1 -1 2.0671 4 1 -1 0 -1 0.5731 5 1 0 -1 -1 4.4478 6 1 0 0 -1 5.6349 7 1 -1 -1 0 2.7504 8 1 -1 0 0 4.8982 9 1 0 -1 0 2.6203 10 1 0 1 0 2.6203 11 1 0 0 1 5.6349 12 1 0 1 1 4.4478 13 1 2 1 1 8.7956 14 1 1 2 1 13.7518 15 1 1 1 1 2.0671 16 1 1 0 1 0.5731 17 1 1 1 0 2.7504 18 1 1 0 0 4.8982 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3316 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.43 2 C002 has 30 10 10 10.83 3 C003 has 2607 869 869 0.00 4 C004 has 825 275 275 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1184 393 393 0.00 9 C009 has 1197 399 399 0.00 Total of12144 atoms and 4039 groups and 4034 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3316 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3316 Number of groups = 1098 Number of bonds = 3310 Number of angles = 1202 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1096 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 = 3316 Number of groups = 1098 Number of bonds = 3310 Number of angles = 1202 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1096 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 <- "34.962" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1093" Evaluating: 1093-13 Parameter: NUMWAT <- "1080" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1080" Comparing "1075" and "1080". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.962" Parameter: BOX -> "34.962" Parameter: BOX -> "34.962" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.96200 B = 34.96200 C = 34.96200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7935 2 1 -1 -2 -1 13.7489 3 1 -1 -1 -1 2.0651 4 1 -1 0 -1 0.5748 5 1 0 -1 -1 4.4456 6 1 0 0 -1 5.6332 7 1 -1 -1 0 2.7493 8 1 -1 0 0 4.8978 9 1 0 -1 0 2.6196 10 1 0 1 0 2.6196 11 1 0 0 1 5.6332 12 1 0 1 1 4.4456 13 1 2 1 1 8.7935 14 1 1 2 1 13.7489 15 1 1 1 1 2.0651 16 1 1 0 1 0.5748 17 1 1 1 0 2.7493 18 1 1 0 0 4.8978 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3316 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.42 2 C002 has 30 10 10 10.83 3 C003 has 2607 869 869 0.00 4 C004 has 825 275 275 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1184 393 393 0.00 9 C009 has 1197 399 399 0.00 Total of12144 atoms and 4039 groups and 4034 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3316 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3316 Number of groups = 1098 Number of bonds = 3310 Number of angles = 1202 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1096 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 = 3316 Number of groups = 1098 Number of bonds = 3310 Number of angles = 1202 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1096 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 <- "34.96" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1093" Evaluating: 1093-13 Parameter: NUMWAT <- "1080" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1080" Comparing "1075" and "1080". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.96" Parameter: BOX -> "34.96" Parameter: BOX -> "34.96" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.96000 B = 34.96000 C = 34.96000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7913 2 1 -1 -2 -1 13.7459 3 1 -1 -1 -1 2.0631 4 1 -1 0 -1 0.5764 5 1 0 -1 -1 4.4435 6 1 0 0 -1 5.6316 7 1 -1 -1 0 2.7481 8 1 -1 0 0 4.8975 9 1 0 -1 0 2.6188 10 1 0 1 0 2.6188 11 1 0 0 1 5.6316 12 1 0 1 1 4.4435 13 1 2 1 1 8.7913 14 1 1 2 1 13.7459 15 1 1 1 1 2.0631 16 1 1 0 1 0.5764 17 1 1 1 0 2.7481 18 1 1 0 0 4.8975 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3316 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.42 2 C002 has 30 10 10 10.83 3 C003 has 2607 869 869 0.00 4 C004 has 825 275 275 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1184 393 393 0.00 9 C009 has 1197 399 399 0.00 Total of12144 atoms and 4039 groups and 4034 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3316 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3316 Number of groups = 1098 Number of bonds = 3310 Number of angles = 1202 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1096 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 = 3316 Number of groups = 1098 Number of bonds = 3310 Number of angles = 1202 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1096 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 <- "34.958" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1093" Evaluating: 1093-13 Parameter: NUMWAT <- "1080" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1080" Comparing "1075" and "1080". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.958" Parameter: BOX -> "34.958" Parameter: BOX -> "34.958" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.95800 B = 34.95800 C = 34.95800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7892 2 1 -1 -2 -1 13.7430 3 1 -1 -1 -1 2.0611 4 1 -1 0 -1 0.5781 5 1 0 -1 -1 4.4414 6 1 0 0 -1 5.6299 7 1 -1 -1 0 2.7469 8 1 -1 0 0 4.8972 9 1 0 -1 0 2.6181 10 1 0 1 0 2.6181 11 1 0 0 1 5.6299 12 1 0 1 1 4.4414 13 1 2 1 1 8.7892 14 1 1 2 1 13.7430 15 1 1 1 1 2.0611 16 1 1 0 1 0.5781 17 1 1 1 0 2.7469 18 1 1 0 0 4.8972 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3316 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.42 2 C002 has 30 10 10 10.82 3 C003 has 2607 869 869 0.00 4 C004 has 825 275 275 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1184 393 393 0.00 9 C009 has 1197 399 399 0.00 Total of12144 atoms and 4039 groups and 4034 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3316 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3316 Number of groups = 1098 Number of bonds = 3310 Number of angles = 1202 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1096 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 = 3316 Number of groups = 1098 Number of bonds = 3310 Number of angles = 1202 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1096 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 <- "34.956" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1093" Evaluating: 1093-13 Parameter: NUMWAT <- "1080" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1080" Comparing "1075" and "1080". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.956" Parameter: BOX -> "34.956" Parameter: BOX -> "34.956" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.95600 B = 34.95600 C = 34.95600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7870 2 1 -1 -2 -1 13.7400 3 1 -1 -1 -1 2.0592 4 1 -1 0 -1 0.5798 5 1 0 -1 -1 4.4392 6 1 0 0 -1 5.6283 7 1 -1 -1 0 2.7458 8 1 -1 0 0 4.8969 9 1 0 -1 0 2.6174 10 1 0 1 0 2.6174 11 1 0 0 1 5.6283 12 1 0 1 1 4.4392 13 1 2 1 1 8.7870 14 1 1 2 1 13.7400 15 1 1 1 1 2.0592 16 1 1 0 1 0.5798 17 1 1 1 0 2.7458 18 1 1 0 0 4.8969 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3316 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 C007 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.41 2 C002 has 30 10 10 10.82 3 C003 has 2604 868 868 0.00 4 C004 has 825 275 275 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1161 387 387 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1181 392 392 0.00 9 C009 has 1194 398 398 0.00 Total of12138 atoms and 4037 groups and 4032 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3316 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 = 3313 Number of groups = 1097 Number of bonds = 3307 Number of angles = 1201 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1095 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 = 3313 Number of groups = 1097 Number of bonds = 3307 Number of angles = 1201 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1095 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 <- "34.954" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1092" Evaluating: 1092-13 Parameter: NUMWAT <- "1079" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1079" Comparing "1075" and "1079". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.954" Parameter: BOX -> "34.954" Parameter: BOX -> "34.954" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.95400 B = 34.95400 C = 34.95400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7849 2 1 -1 -2 -1 13.7371 3 1 -1 -1 -1 2.0572 4 1 -1 0 -1 0.5814 5 1 0 -1 -1 4.4371 6 1 0 0 -1 5.6266 7 1 -1 -1 0 2.7446 8 1 -1 0 0 4.8966 9 1 0 -1 0 2.6166 10 1 0 1 0 2.6166 11 1 0 0 1 5.6266 12 1 0 1 1 4.4371 13 1 2 1 1 8.7849 14 1 1 2 1 13.7371 15 1 1 1 1 2.0572 16 1 1 0 1 0.5814 17 1 1 1 0 2.7446 18 1 1 0 0 4.8966 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3313 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.41 2 C002 has 30 10 10 10.82 3 C003 has 2604 868 868 0.00 4 C004 has 825 275 275 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1158 386 386 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1181 392 392 0.00 9 C009 has 1194 398 398 0.00 Total of12132 atoms and 4035 groups and 4030 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3313 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3313 Number of groups = 1097 Number of bonds = 3307 Number of angles = 1201 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1095 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 = 3313 Number of groups = 1097 Number of bonds = 3307 Number of angles = 1201 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1095 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 <- "34.952" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1092" Evaluating: 1092-13 Parameter: NUMWAT <- "1079" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1079" Comparing "1075" and "1079". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.952" Parameter: BOX -> "34.952" Parameter: BOX -> "34.952" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.95200 B = 34.95200 C = 34.95200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7827 2 1 -1 -2 -1 13.7341 3 1 -1 -1 -1 2.0552 4 1 -1 0 -1 0.5831 5 1 0 -1 -1 4.4350 6 1 0 0 -1 5.6250 7 1 -1 -1 0 2.7434 8 1 -1 0 0 4.8963 9 1 0 -1 0 2.6159 10 1 0 1 0 2.6159 11 1 0 0 1 5.6250 12 1 0 1 1 4.4350 13 1 2 1 1 8.7827 14 1 1 2 1 13.7341 15 1 1 1 1 2.0552 16 1 1 0 1 0.5831 17 1 1 1 0 2.7434 18 1 1 0 0 4.8963 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3313 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.41 2 C002 has 30 10 10 10.81 3 C003 has 2604 868 868 0.00 4 C004 has 825 275 275 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1158 386 386 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1181 392 392 0.00 9 C009 has 1194 398 398 0.00 Total of12132 atoms and 4035 groups and 4030 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3313 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3313 Number of groups = 1097 Number of bonds = 3307 Number of angles = 1201 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1095 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 = 3313 Number of groups = 1097 Number of bonds = 3307 Number of angles = 1201 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1095 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 <- "34.95" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1092" Evaluating: 1092-13 Parameter: NUMWAT <- "1079" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1079" Comparing "1075" and "1079". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.95" Parameter: BOX -> "34.95" Parameter: BOX -> "34.95" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.95000 B = 34.95000 C = 34.95000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7806 2 1 -1 -2 -1 13.7312 3 1 -1 -1 -1 2.0532 4 1 -1 0 -1 0.5848 5 1 0 -1 -1 4.4328 6 1 0 0 -1 5.6234 7 1 -1 -1 0 2.7423 8 1 -1 0 0 4.8960 9 1 0 -1 0 2.6152 10 1 0 1 0 2.6152 11 1 0 0 1 5.6234 12 1 0 1 1 4.4328 13 1 2 1 1 8.7806 14 1 1 2 1 13.7312 15 1 1 1 1 2.0532 16 1 1 0 1 0.5848 17 1 1 1 0 2.7423 18 1 1 0 0 4.8960 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3313 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.40 2 C002 has 30 10 10 10.81 3 C003 has 2604 868 868 0.00 4 C004 has 825 275 275 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1158 386 386 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1181 392 392 0.00 9 C009 has 1194 398 398 0.00 Total of12132 atoms and 4035 groups and 4030 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3313 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3313 Number of groups = 1097 Number of bonds = 3307 Number of angles = 1201 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1095 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 = 3313 Number of groups = 1097 Number of bonds = 3307 Number of angles = 1201 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1095 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 <- "34.948" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1092" Evaluating: 1092-13 Parameter: NUMWAT <- "1079" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1079" Comparing "1075" and "1079". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.948" Parameter: BOX -> "34.948" Parameter: BOX -> "34.948" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.94800 B = 34.94800 C = 34.94800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7785 2 1 -1 -2 -1 13.7282 3 1 -1 -1 -1 2.0512 4 1 -1 0 -1 0.5865 5 1 0 -1 -1 4.4307 6 1 0 0 -1 5.6217 7 1 -1 -1 0 2.7411 8 1 -1 0 0 4.8957 9 1 0 -1 0 2.6145 10 1 0 1 0 2.6145 11 1 0 0 1 5.6217 12 1 0 1 1 4.4307 13 1 2 1 1 8.7785 14 1 1 2 1 13.7282 15 1 1 1 1 2.0512 16 1 1 0 1 0.5865 17 1 1 1 0 2.7411 18 1 1 0 0 4.8957 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3313 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.40 2 C002 has 30 10 10 10.81 3 C003 has 2604 868 868 0.00 4 C004 has 825 275 275 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1158 386 386 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1181 392 392 0.00 9 C009 has 1194 398 398 0.00 Total of12132 atoms and 4035 groups and 4030 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3313 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3313 Number of groups = 1097 Number of bonds = 3307 Number of angles = 1201 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1095 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 = 3313 Number of groups = 1097 Number of bonds = 3307 Number of angles = 1201 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1095 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 <- "34.946" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1092" Evaluating: 1092-13 Parameter: NUMWAT <- "1079" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1079" Comparing "1075" and "1079". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.946" Parameter: BOX -> "34.946" Parameter: BOX -> "34.946" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.94600 B = 34.94600 C = 34.94600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7763 2 1 -1 -2 -1 13.7253 3 1 -1 -1 -1 2.0493 4 1 -1 0 -1 0.5882 5 1 0 -1 -1 4.4286 6 1 0 0 -1 5.6201 7 1 -1 -1 0 2.7400 8 1 -1 0 0 4.8954 9 1 0 -1 0 2.6138 10 1 0 1 0 2.6138 11 1 0 0 1 5.6201 12 1 0 1 1 4.4286 13 1 2 1 1 8.7763 14 1 1 2 1 13.7253 15 1 1 1 1 2.0493 16 1 1 0 1 0.5882 17 1 1 1 0 2.7400 18 1 1 0 0 4.8954 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3313 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.40 2 C002 has 30 10 10 10.81 3 C003 has 2604 868 868 0.00 4 C004 has 825 275 275 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1158 386 386 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1181 392 392 0.00 9 C009 has 1194 398 398 0.00 Total of12132 atoms and 4035 groups and 4030 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3313 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3313 Number of groups = 1097 Number of bonds = 3307 Number of angles = 1201 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1095 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 = 3313 Number of groups = 1097 Number of bonds = 3307 Number of angles = 1201 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1095 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 <- "34.944" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1092" Evaluating: 1092-13 Parameter: NUMWAT <- "1079" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1079" Comparing "1075" and "1079". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.944" Parameter: BOX -> "34.944" Parameter: BOX -> "34.944" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.94400 B = 34.94400 C = 34.94400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7742 2 1 -1 -2 -1 13.7223 3 1 -1 -1 -1 2.0473 4 1 -1 0 -1 0.5899 5 1 0 -1 -1 4.4265 6 1 0 0 -1 5.6184 7 1 -1 -1 0 2.7388 8 1 -1 0 0 4.8951 9 1 0 -1 0 2.6130 10 1 0 1 0 2.6130 11 1 0 0 1 5.6184 12 1 0 1 1 4.4265 13 1 2 1 1 8.7742 14 1 1 2 1 13.7223 15 1 1 1 1 2.0473 16 1 1 0 1 0.5899 17 1 1 1 0 2.7388 18 1 1 0 0 4.8951 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3313 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.40 2 C002 has 30 10 10 10.80 3 C003 has 2604 868 868 0.00 4 C004 has 825 275 275 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1158 386 386 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1181 392 392 0.00 9 C009 has 1194 398 398 0.00 Total of12132 atoms and 4035 groups and 4030 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3313 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3313 Number of groups = 1097 Number of bonds = 3307 Number of angles = 1201 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1095 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 = 3313 Number of groups = 1097 Number of bonds = 3307 Number of angles = 1201 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1095 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 <- "34.942" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1092" Evaluating: 1092-13 Parameter: NUMWAT <- "1079" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1079" Comparing "1075" and "1079". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.942" Parameter: BOX -> "34.942" Parameter: BOX -> "34.942" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.94200 B = 34.94200 C = 34.94200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7720 2 1 -1 -2 -1 13.7193 3 1 -1 -1 -1 2.0453 4 1 -1 0 -1 0.5916 5 1 0 -1 -1 4.4243 6 1 0 0 -1 5.6168 7 1 -1 -1 0 2.7377 8 1 -1 0 0 4.8948 9 1 0 -1 0 2.6123 10 1 0 1 0 2.6123 11 1 0 0 1 5.6168 12 1 0 1 1 4.4243 13 1 2 1 1 8.7720 14 1 1 2 1 13.7193 15 1 1 1 1 2.0453 16 1 1 0 1 0.5916 17 1 1 1 0 2.7377 18 1 1 0 0 4.8948 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3313 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.39 2 C002 has 30 10 10 10.80 3 C003 has 2604 868 868 0.00 4 C004 has 825 275 275 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1158 386 386 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1181 392 392 0.00 9 C009 has 1194 398 398 0.00 Total of12132 atoms and 4035 groups and 4030 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3313 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3313 Number of groups = 1097 Number of bonds = 3307 Number of angles = 1201 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1095 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 = 3313 Number of groups = 1097 Number of bonds = 3307 Number of angles = 1201 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1095 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 <- "34.94" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1092" Evaluating: 1092-13 Parameter: NUMWAT <- "1079" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1079" Comparing "1075" and "1079". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.94" Parameter: BOX -> "34.94" Parameter: BOX -> "34.94" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.94000 B = 34.94000 C = 34.94000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7699 2 1 -1 -2 -1 13.7164 3 1 -1 -1 -1 2.0433 4 1 -1 0 -1 0.5933 5 1 0 -1 -1 4.4222 6 1 0 0 -1 5.6151 7 1 -1 -1 0 2.7365 8 1 -1 0 0 4.8945 9 1 0 -1 0 2.6116 10 1 0 1 0 2.6116 11 1 0 0 1 5.6151 12 1 0 1 1 4.4222 13 1 2 1 1 8.7699 14 1 1 2 1 13.7164 15 1 1 1 1 2.0433 16 1 1 0 1 0.5933 17 1 1 1 0 2.7365 18 1 1 0 0 4.8945 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3313 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 491 OPERATED ON BY TRANSFORMATION C011 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.39 2 C002 has 30 10 10 10.80 3 C003 has 2607 869 869 0.00 4 C004 has 825 275 275 0.00 5 C005 has 846 282 282 0.00 6 C006 has 1158 386 386 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1181 392 392 0.00 9 C009 has 1191 397 397 0.00 Total of12132 atoms and 4035 groups and 4030 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3313 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 <- "34.938" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1091" Evaluating: 1091-13 Parameter: NUMWAT <- "1078" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1078" Comparing "1075" and "1078". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.938" Parameter: BOX -> "34.938" Parameter: BOX -> "34.938" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.93800 B = 34.93800 C = 34.93800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7678 2 1 -1 -2 -1 13.7134 3 1 -1 -1 -1 2.0413 4 1 -1 0 -1 0.5950 5 1 0 -1 -1 4.4201 6 1 0 0 -1 5.6135 7 1 -1 -1 0 2.7354 8 1 -1 0 0 4.8942 9 1 0 -1 0 2.6109 10 1 0 1 0 2.6109 11 1 0 0 1 5.6135 12 1 0 1 1 4.4201 13 1 2 1 1 8.7678 14 1 1 2 1 13.7134 15 1 1 1 1 2.0413 16 1 1 0 1 0.5950 17 1 1 1 0 2.7354 18 1 1 0 0 4.8942 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3310 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.39 2 C002 has 30 10 10 10.79 3 C003 has 2604 868 868 0.00 4 C004 has 825 275 275 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1181 392 392 0.00 9 C009 has 1191 397 397 0.00 Total of12120 atoms and 4031 groups and 4026 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3310 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 <- "34.936" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1091" Evaluating: 1091-13 Parameter: NUMWAT <- "1078" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1078" Comparing "1075" and "1078". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.936" Parameter: BOX -> "34.936" Parameter: BOX -> "34.936" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.93600 B = 34.93600 C = 34.93600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7656 2 1 -1 -2 -1 13.7105 3 1 -1 -1 -1 2.0394 4 1 -1 0 -1 0.5967 5 1 0 -1 -1 4.4179 6 1 0 0 -1 5.6119 7 1 -1 -1 0 2.7342 8 1 -1 0 0 4.8939 9 1 0 -1 0 2.6102 10 1 0 1 0 2.6102 11 1 0 0 1 5.6119 12 1 0 1 1 4.4179 13 1 2 1 1 8.7656 14 1 1 2 1 13.7105 15 1 1 1 1 2.0394 16 1 1 0 1 0.5967 17 1 1 1 0 2.7342 18 1 1 0 0 4.8939 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3310 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.38 2 C002 has 30 10 10 10.79 3 C003 has 2604 868 868 0.00 4 C004 has 825 275 275 0.00 5 C005 has 843 281 281 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1181 392 392 0.00 9 C009 has 1191 397 397 0.00 Total of12120 atoms and 4031 groups and 4026 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3310 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 <- "34.934" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1091" Evaluating: 1091-13 Parameter: NUMWAT <- "1078" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1078" Comparing "1075" and "1078". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.934" Parameter: BOX -> "34.934" Parameter: BOX -> "34.934" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.93400 B = 34.93400 C = 34.93400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7635 2 1 -1 -2 -1 13.7075 3 1 -1 -1 -1 2.0374 4 1 -1 0 -1 0.5984 5 1 0 -1 -1 4.4158 6 1 0 0 -1 5.6102 7 1 -1 -1 0 2.7331 8 1 -1 0 0 4.8936 9 1 0 -1 0 2.6095 10 1 0 1 0 2.6095 11 1 0 0 1 5.6102 12 1 0 1 1 4.4158 13 1 2 1 1 8.7635 14 1 1 2 1 13.7075 15 1 1 1 1 2.0374 16 1 1 0 1 0.5984 17 1 1 1 0 2.7331 18 1 1 0 0 4.8936 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3310 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.38 2 C002 has 30 10 10 10.79 3 C003 has 2604 868 868 0.00 4 C004 has 825 275 275 0.00 5 C005 has 846 282 282 0.00 6 C006 has 1155 385 385 0.00 7 C007 has 774 258 258 0.00 8 C008 has 1181 392 392 0.00 9 C009 has 1191 397 397 0.00 Total of12123 atoms and 4032 groups and 4027 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3310 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 <- "34.932" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1091" Evaluating: 1091-13 Parameter: NUMWAT <- "1078" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1078" Comparing "1075" and "1078". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.932" Parameter: BOX -> "34.932" Parameter: BOX -> "34.932" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.93200 B = 34.93200 C = 34.93200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7613 2 1 -1 -2 -1 13.7046 3 1 -1 -1 -1 2.0354 4 1 -1 0 -1 0.6001 5 1 0 -1 -1 4.4137 6 1 0 0 -1 5.6086 7 1 -1 -1 0 2.7319 8 1 -1 0 0 4.8933 9 1 0 -1 0 2.6088 10 1 0 1 0 2.6088 11 1 0 0 1 5.6086 12 1 0 1 1 4.4137 13 1 2 1 1 8.7613 14 1 1 2 1 13.7046 15 1 1 1 1 2.0354 16 1 1 0 1 0.6001 17 1 1 1 0 2.7319 18 1 1 0 0 4.8933 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3310 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.38 2 C002 has 30 10 10 10.78 3 C003 has 2604 868 868 0.00 4 C004 has 825 275 275 0.00 5 C005 has 846 282 282 0.00 6 C006 has 1158 386 386 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1181 392 392 0.00 9 C009 has 1194 398 398 0.00 Total of12132 atoms and 4035 groups and 4030 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3310 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 <- "34.93" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1091" Evaluating: 1091-13 Parameter: NUMWAT <- "1078" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1078" Comparing "1075" and "1078". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.93" Parameter: BOX -> "34.93" Parameter: BOX -> "34.93" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.93000 B = 34.93000 C = 34.93000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7592 2 1 -1 -2 -1 13.7016 3 1 -1 -1 -1 2.0334 4 1 -1 0 -1 0.6018 5 1 0 -1 -1 4.4116 6 1 0 0 -1 5.6069 7 1 -1 -1 0 2.7308 8 1 -1 0 0 4.8930 9 1 0 -1 0 2.6081 10 1 0 1 0 2.6081 11 1 0 0 1 5.6069 12 1 0 1 1 4.4116 13 1 2 1 1 8.7592 14 1 1 2 1 13.7016 15 1 1 1 1 2.0334 16 1 1 0 1 0.6018 17 1 1 1 0 2.7308 18 1 1 0 0 4.8930 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3310 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.37 2 C002 has 30 10 10 10.78 3 C003 has 2604 868 868 0.00 4 C004 has 825 275 275 0.00 5 C005 has 846 282 282 0.00 6 C006 has 1158 386 386 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1181 392 392 0.00 9 C009 has 1194 398 398 0.00 Total of12132 atoms and 4035 groups and 4030 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3310 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 <- "34.928" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1091" Evaluating: 1091-13 Parameter: NUMWAT <- "1078" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1078" Comparing "1075" and "1078". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.928" Parameter: BOX -> "34.928" Parameter: BOX -> "34.928" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.92800 B = 34.92800 C = 34.92800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7571 2 1 -1 -2 -1 13.6987 3 1 -1 -1 -1 2.0314 4 1 -1 0 -1 0.6036 5 1 0 -1 -1 4.4094 6 1 0 0 -1 5.6053 7 1 -1 -1 0 2.7297 8 1 -1 0 0 4.8927 9 1 0 -1 0 2.6073 10 1 0 1 0 2.6073 11 1 0 0 1 5.6053 12 1 0 1 1 4.4094 13 1 2 1 1 8.7571 14 1 1 2 1 13.6987 15 1 1 1 1 2.0314 16 1 1 0 1 0.6036 17 1 1 1 0 2.7297 18 1 1 0 0 4.8927 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3310 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.37 2 C002 has 30 10 10 10.78 3 C003 has 2604 868 868 0.00 4 C004 has 825 275 275 0.00 5 C005 has 846 282 282 0.00 6 C006 has 1158 386 386 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1181 392 392 0.00 9 C009 has 1194 398 398 0.00 Total of12132 atoms and 4035 groups and 4030 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3310 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 <- "34.926" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1091" Evaluating: 1091-13 Parameter: NUMWAT <- "1078" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1078" Comparing "1075" and "1078". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.926" Parameter: BOX -> "34.926" Parameter: BOX -> "34.926" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.92600 B = 34.92600 C = 34.92600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7549 2 1 -1 -2 -1 13.6957 3 1 -1 -1 -1 2.0294 4 1 -1 0 -1 0.6053 5 1 0 -1 -1 4.4073 6 1 0 0 -1 5.6036 7 1 -1 -1 0 2.7285 8 1 -1 0 0 4.8924 9 1 0 -1 0 2.6066 10 1 0 1 0 2.6066 11 1 0 0 1 5.6036 12 1 0 1 1 4.4073 13 1 2 1 1 8.7549 14 1 1 2 1 13.6957 15 1 1 1 1 2.0294 16 1 1 0 1 0.6053 17 1 1 1 0 2.7285 18 1 1 0 0 4.8924 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3310 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.37 2 C002 has 30 10 10 10.77 3 C003 has 2604 868 868 0.00 4 C004 has 825 275 275 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1158 386 386 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1181 392 392 0.00 9 C009 has 1194 398 398 0.00 Total of12135 atoms and 4036 groups and 4031 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3310 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 <- "34.924" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1091" Evaluating: 1091-13 Parameter: NUMWAT <- "1078" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1078" Comparing "1075" and "1078". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.924" Parameter: BOX -> "34.924" Parameter: BOX -> "34.924" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.92400 B = 34.92400 C = 34.92400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7528 2 1 -1 -2 -1 13.6928 3 1 -1 -1 -1 2.0275 4 1 -1 0 -1 0.6070 5 1 0 -1 -1 4.4052 6 1 0 0 -1 5.6020 7 1 -1 -1 0 2.7274 8 1 -1 0 0 4.8921 9 1 0 -1 0 2.6059 10 1 0 1 0 2.6059 11 1 0 0 1 5.6020 12 1 0 1 1 4.4052 13 1 2 1 1 8.7528 14 1 1 2 1 13.6928 15 1 1 1 1 2.0275 16 1 1 0 1 0.6070 17 1 1 1 0 2.7274 18 1 1 0 0 4.8921 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3310 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.36 2 C002 has 33 11 11 10.77 3 C003 has 2604 868 868 0.00 4 C004 has 825 275 275 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1158 386 386 0.00 7 C007 has 777 259 259 0.00 8 C008 has 1181 392 392 0.00 9 C009 has 1194 398 398 0.00 Total of12138 atoms and 4037 groups and 4032 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3310 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 <- "34.922" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1091" Evaluating: 1091-13 Parameter: NUMWAT <- "1078" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1078" Comparing "1075" and "1078". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.922" Parameter: BOX -> "34.922" Parameter: BOX -> "34.922" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.92200 B = 34.92200 C = 34.92200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7507 2 1 -1 -2 -1 13.6898 3 1 -1 -1 -1 2.0255 4 1 -1 0 -1 0.6088 5 1 0 -1 -1 4.4030 6 1 0 0 -1 5.6004 7 1 -1 -1 0 2.7262 8 1 -1 0 0 4.8918 9 1 0 -1 0 2.6052 10 1 0 1 0 2.6052 11 1 0 0 1 5.6004 12 1 0 1 1 4.4030 13 1 2 1 1 8.7507 14 1 1 2 1 13.6898 15 1 1 1 1 2.0255 16 1 1 0 1 0.6088 17 1 1 1 0 2.7262 18 1 1 0 0 4.8918 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3310 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.36 2 C002 has 33 11 11 10.77 3 C003 has 2604 868 868 0.00 4 C004 has 825 275 275 0.00 5 C005 has 849 283 283 0.00 6 C006 has 1158 386 386 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1181 392 392 0.00 9 C009 has 1194 398 398 0.00 Total of12141 atoms and 4038 groups and 4033 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3310 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 <- "34.92" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1091" Evaluating: 1091-13 Parameter: NUMWAT <- "1078" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1078" Comparing "1075" and "1078". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.92" Parameter: BOX -> "34.92" Parameter: BOX -> "34.92" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.92000 B = 34.92000 C = 34.92000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7485 2 1 -1 -2 -1 13.6869 3 1 -1 -1 -1 2.0235 4 1 -1 0 -1 0.6105 5 1 0 -1 -1 4.4009 6 1 0 0 -1 5.5987 7 1 -1 -1 0 2.7251 8 1 -1 0 0 4.8915 9 1 0 -1 0 2.6045 10 1 0 1 0 2.6045 11 1 0 0 1 5.5987 12 1 0 1 1 4.4009 13 1 2 1 1 8.7485 14 1 1 2 1 13.6869 15 1 1 1 1 2.0235 16 1 1 0 1 0.6105 17 1 1 1 0 2.7251 18 1 1 0 0 4.8915 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3310 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.36 2 C002 has 33 11 11 10.77 3 C003 has 2604 868 868 0.00 4 C004 has 825 275 275 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1158 386 386 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1184 393 393 0.00 9 C009 has 1194 398 398 0.00 Total of12147 atoms and 4040 groups and 4035 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3310 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 <- "34.918" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1091" Evaluating: 1091-13 Parameter: NUMWAT <- "1078" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1078" Comparing "1075" and "1078". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.918" Parameter: BOX -> "34.918" Parameter: BOX -> "34.918" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.91800 B = 34.91800 C = 34.91800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7464 2 1 -1 -2 -1 13.6839 3 1 -1 -1 -1 2.0215 4 1 -1 0 -1 0.6123 5 1 0 -1 -1 4.3988 6 1 0 0 -1 5.5971 7 1 -1 -1 0 2.7240 8 1 -1 0 0 4.8912 9 1 0 -1 0 2.6038 10 1 0 1 0 2.6038 11 1 0 0 1 5.5971 12 1 0 1 1 4.3988 13 1 2 1 1 8.7464 14 1 1 2 1 13.6839 15 1 1 1 1 2.0215 16 1 1 0 1 0.6123 17 1 1 1 0 2.7240 18 1 1 0 0 4.8912 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3310 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.36 2 C002 has 33 11 11 10.76 3 C003 has 2604 868 868 0.00 4 C004 has 825 275 275 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1161 387 387 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1184 393 393 0.00 9 C009 has 1194 398 398 0.00 Total of12150 atoms and 4041 groups and 4036 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3310 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 <- "34.916" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1091" Evaluating: 1091-13 Parameter: NUMWAT <- "1078" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1078" Comparing "1075" and "1078". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.916" Parameter: BOX -> "34.916" Parameter: BOX -> "34.916" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.91600 B = 34.91600 C = 34.91600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7443 2 1 -1 -2 -1 13.6810 3 1 -1 -1 -1 2.0195 4 1 -1 0 -1 0.6140 5 1 0 -1 -1 4.3967 6 1 0 0 -1 5.5954 7 1 -1 -1 0 2.7228 8 1 -1 0 0 4.8909 9 1 0 -1 0 2.6031 10 1 0 1 0 2.6031 11 1 0 0 1 5.5954 12 1 0 1 1 4.3967 13 1 2 1 1 8.7443 14 1 1 2 1 13.6810 15 1 1 1 1 2.0195 16 1 1 0 1 0.6140 17 1 1 1 0 2.7228 18 1 1 0 0 4.8909 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3310 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.35 2 C002 has 33 11 11 10.76 3 C003 has 2604 868 868 0.00 4 C004 has 825 275 275 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1161 387 387 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1184 393 393 0.00 9 C009 has 1194 398 398 0.00 Total of12150 atoms and 4041 groups and 4036 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3310 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 <- "34.914" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1091" Evaluating: 1091-13 Parameter: NUMWAT <- "1078" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1078" Comparing "1075" and "1078". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.914" Parameter: BOX -> "34.914" Parameter: BOX -> "34.914" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.91400 B = 34.91400 C = 34.91400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7421 2 1 -1 -2 -1 13.6780 3 1 -1 -1 -1 2.0176 4 1 -1 0 -1 0.6158 5 1 0 -1 -1 4.3945 6 1 0 0 -1 5.5938 7 1 -1 -1 0 2.7217 8 1 -1 0 0 4.8906 9 1 0 -1 0 2.6024 10 1 0 1 0 2.6024 11 1 0 0 1 5.5938 12 1 0 1 1 4.3945 13 1 2 1 1 8.7421 14 1 1 2 1 13.6780 15 1 1 1 1 2.0176 16 1 1 0 1 0.6158 17 1 1 1 0 2.7217 18 1 1 0 0 4.8906 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3310 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.35 2 C002 has 33 11 11 10.76 3 C003 has 2604 868 868 0.00 4 C004 has 825 275 275 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1161 387 387 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1184 393 393 0.00 9 C009 has 1194 398 398 0.00 Total of12150 atoms and 4041 groups and 4036 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3310 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 <- "34.912" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1091" Evaluating: 1091-13 Parameter: NUMWAT <- "1078" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1078" Comparing "1075" and "1078". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.912" Parameter: BOX -> "34.912" Parameter: BOX -> "34.912" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.91200 B = 34.91200 C = 34.91200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7400 2 1 -1 -2 -1 13.6751 3 1 -1 -1 -1 2.0156 4 1 -1 0 -1 0.6175 5 1 0 -1 -1 4.3924 6 1 0 0 -1 5.5922 7 1 -1 -1 0 2.7206 8 1 -1 0 0 4.8904 9 1 0 -1 0 2.6017 10 1 0 1 0 2.6017 11 1 0 0 1 5.5922 12 1 0 1 1 4.3924 13 1 2 1 1 8.7400 14 1 1 2 1 13.6751 15 1 1 1 1 2.0156 16 1 1 0 1 0.6175 17 1 1 1 0 2.7206 18 1 1 0 0 4.8904 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3310 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.35 2 C002 has 33 11 11 10.75 3 C003 has 2604 868 868 0.00 4 C004 has 825 275 275 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1161 387 387 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1184 393 393 0.00 9 C009 has 1197 399 399 0.00 Total of12153 atoms and 4042 groups and 4037 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3310 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 = 3310 Number of groups = 1096 Number of bonds = 3304 Number of angles = 1200 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1094 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 <- "34.91" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1091" Evaluating: 1091-13 Parameter: NUMWAT <- "1078" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1078" Comparing "1075" and "1078". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.91" Parameter: BOX -> "34.91" Parameter: BOX -> "34.91" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.91000 B = 34.91000 C = 34.91000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7379 2 1 -1 -2 -1 13.6721 3 1 -1 -1 -1 2.0136 4 1 -1 0 -1 0.6193 5 1 0 -1 -1 4.3903 6 1 0 0 -1 5.5905 7 1 -1 -1 0 2.7195 8 1 -1 0 0 4.8901 9 1 0 -1 0 2.6010 10 1 0 1 0 2.6010 11 1 0 0 1 5.5905 12 1 0 1 1 4.3903 13 1 2 1 1 8.7379 14 1 1 2 1 13.6721 15 1 1 1 1 2.0136 16 1 1 0 1 0.6193 17 1 1 1 0 2.7195 18 1 1 0 0 4.8901 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3310 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 C009 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.34 2 C002 has 33 11 11 10.75 3 C003 has 2601 867 867 0.00 4 C004 has 828 276 276 0.00 5 C005 has 852 284 284 0.00 6 C006 has 1161 387 387 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1184 393 393 0.00 9 C009 has 1194 398 398 0.00 Total of12150 atoms and 4041 groups and 4036 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3310 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 <- "34.908" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1090" Evaluating: 1090-13 Parameter: NUMWAT <- "1077" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1077" Comparing "1075" and "1077". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.908" Parameter: BOX -> "34.908" Parameter: BOX -> "34.908" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.90800 B = 34.90800 C = 34.90800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7358 2 1 -1 -2 -1 13.6692 3 1 -1 -1 -1 2.0116 4 1 -1 0 -1 0.6210 5 1 0 -1 -1 4.3881 6 1 0 0 -1 5.5889 7 1 -1 -1 0 2.7183 8 1 -1 0 0 4.8898 9 1 0 -1 0 2.6003 10 1 0 1 0 2.6003 11 1 0 0 1 5.5889 12 1 0 1 1 4.3881 13 1 2 1 1 8.7358 14 1 1 2 1 13.6692 15 1 1 1 1 2.0116 16 1 1 0 1 0.6210 17 1 1 1 0 2.7183 18 1 1 0 0 4.8898 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3307 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.34 2 C002 has 33 11 11 10.75 3 C003 has 2601 867 867 0.00 4 C004 has 825 275 275 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1161 387 387 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1184 393 393 0.00 9 C009 has 1194 398 398 0.00 Total of12147 atoms and 4040 groups and 4035 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3307 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 <- "34.906" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1090" Evaluating: 1090-13 Parameter: NUMWAT <- "1077" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1077" Comparing "1075" and "1077". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.906" Parameter: BOX -> "34.906" Parameter: BOX -> "34.906" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.90600 B = 34.90600 C = 34.90600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7336 2 1 -1 -2 -1 13.6662 3 1 -1 -1 -1 2.0096 4 1 -1 0 -1 0.6228 5 1 0 -1 -1 4.3860 6 1 0 0 -1 5.5872 7 1 -1 -1 0 2.7172 8 1 -1 0 0 4.8895 9 1 0 -1 0 2.5996 10 1 0 1 0 2.5996 11 1 0 0 1 5.5872 12 1 0 1 1 4.3860 13 1 2 1 1 8.7336 14 1 1 2 1 13.6662 15 1 1 1 1 2.0096 16 1 1 0 1 0.6228 17 1 1 1 0 2.7172 18 1 1 0 0 4.8895 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3307 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.34 2 C002 has 33 11 11 10.74 3 C003 has 2601 867 867 0.00 4 C004 has 825 275 275 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1161 387 387 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1184 393 393 0.00 9 C009 has 1194 398 398 0.00 Total of12147 atoms and 4040 groups and 4035 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3307 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 <- "34.904" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1090" Evaluating: 1090-13 Parameter: NUMWAT <- "1077" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1077" Comparing "1075" and "1077". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.904" Parameter: BOX -> "34.904" Parameter: BOX -> "34.904" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.90400 B = 34.90400 C = 34.90400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7315 2 1 -1 -2 -1 13.6633 3 1 -1 -1 -1 2.0077 4 1 -1 0 -1 0.6246 5 1 0 -1 -1 4.3839 6 1 0 0 -1 5.5856 7 1 -1 -1 0 2.7161 8 1 -1 0 0 4.8892 9 1 0 -1 0 2.5990 10 1 0 1 0 2.5990 11 1 0 0 1 5.5856 12 1 0 1 1 4.3839 13 1 2 1 1 8.7315 14 1 1 2 1 13.6633 15 1 1 1 1 2.0077 16 1 1 0 1 0.6246 17 1 1 1 0 2.7161 18 1 1 0 0 4.8892 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3307 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.33 2 C002 has 33 11 11 10.74 3 C003 has 2604 868 868 0.00 4 C004 has 825 275 275 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1161 387 387 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1184 393 393 0.00 9 C009 has 1194 398 398 0.00 Total of12150 atoms and 4041 groups and 4036 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3307 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 <- "34.902" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1090" Evaluating: 1090-13 Parameter: NUMWAT <- "1077" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1077" Comparing "1075" and "1077". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.902" Parameter: BOX -> "34.902" Parameter: BOX -> "34.902" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.90200 B = 34.90200 C = 34.90200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7294 2 1 -1 -2 -1 13.6603 3 1 -1 -1 -1 2.0057 4 1 -1 0 -1 0.6264 5 1 0 -1 -1 4.3818 6 1 0 0 -1 5.5840 7 1 -1 -1 0 2.7150 8 1 -1 0 0 4.8889 9 1 0 -1 0 2.5983 10 1 0 1 0 2.5983 11 1 0 0 1 5.5840 12 1 0 1 1 4.3818 13 1 2 1 1 8.7294 14 1 1 2 1 13.6603 15 1 1 1 1 2.0057 16 1 1 0 1 0.6264 17 1 1 1 0 2.7150 18 1 1 0 0 4.8889 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3307 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.33 2 C002 has 33 11 11 10.74 3 C003 has 2604 868 868 0.00 4 C004 has 825 275 275 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1161 387 387 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1184 393 393 0.00 9 C009 has 1194 398 398 0.00 Total of12150 atoms and 4041 groups and 4036 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3307 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 <- "34.9" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1090" Evaluating: 1090-13 Parameter: NUMWAT <- "1077" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1077" Comparing "1075" and "1077". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.9" Parameter: BOX -> "34.9" Parameter: BOX -> "34.9" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.90000 B = 34.90000 C = 34.90000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7273 2 1 -1 -2 -1 13.6574 3 1 -1 -1 -1 2.0037 4 1 -1 0 -1 0.6281 5 1 0 -1 -1 4.3796 6 1 0 0 -1 5.5823 7 1 -1 -1 0 2.7138 8 1 -1 0 0 4.8886 9 1 0 -1 0 2.5976 10 1 0 1 0 2.5976 11 1 0 0 1 5.5823 12 1 0 1 1 4.3796 13 1 2 1 1 8.7273 14 1 1 2 1 13.6574 15 1 1 1 1 2.0037 16 1 1 0 1 0.6281 17 1 1 1 0 2.7138 18 1 1 0 0 4.8886 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3307 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.33 2 C002 has 33 11 11 10.73 3 C003 has 2607 869 869 0.00 4 C004 has 825 275 275 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1161 387 387 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1184 393 393 0.00 9 C009 has 1194 398 398 0.00 Total of12153 atoms and 4042 groups and 4037 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3307 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 <- "34.898" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1090" Evaluating: 1090-13 Parameter: NUMWAT <- "1077" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1077" Comparing "1075" and "1077". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.898" Parameter: BOX -> "34.898" Parameter: BOX -> "34.898" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.89800 B = 34.89800 C = 34.89800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7251 2 1 -1 -2 -1 13.6544 3 1 -1 -1 -1 2.0017 4 1 -1 0 -1 0.6299 5 1 0 -1 -1 4.3775 6 1 0 0 -1 5.5807 7 1 -1 -1 0 2.7127 8 1 -1 0 0 4.8884 9 1 0 -1 0 2.5969 10 1 0 1 0 2.5969 11 1 0 0 1 5.5807 12 1 0 1 1 4.3775 13 1 2 1 1 8.7251 14 1 1 2 1 13.6544 15 1 1 1 1 2.0017 16 1 1 0 1 0.6299 17 1 1 1 0 2.7127 18 1 1 0 0 4.8884 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3307 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.32 2 C002 has 33 11 11 10.73 3 C003 has 2607 869 869 0.00 4 C004 has 825 275 275 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1161 387 387 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1184 393 393 0.00 9 C009 has 1194 398 398 0.00 Total of12153 atoms and 4042 groups and 4037 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3307 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 <- "34.896" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1090" Evaluating: 1090-13 Parameter: NUMWAT <- "1077" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1077" Comparing "1075" and "1077". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.896" Parameter: BOX -> "34.896" Parameter: BOX -> "34.896" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.89600 B = 34.89600 C = 34.89600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7230 2 1 -1 -2 -1 13.6514 3 1 -1 -1 -1 1.9997 4 1 -1 0 -1 0.6317 5 1 0 -1 -1 4.3754 6 1 0 0 -1 5.5790 7 1 -1 -1 0 2.7116 8 1 -1 0 0 4.8881 9 1 0 -1 0 2.5962 10 1 0 1 0 2.5962 11 1 0 0 1 5.5790 12 1 0 1 1 4.3754 13 1 2 1 1 8.7230 14 1 1 2 1 13.6514 15 1 1 1 1 1.9997 16 1 1 0 1 0.6317 17 1 1 1 0 2.7116 18 1 1 0 0 4.8881 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3307 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.32 2 C002 has 33 11 11 10.73 3 C003 has 2607 869 869 0.00 4 C004 has 825 275 275 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1161 387 387 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1184 393 393 0.00 9 C009 has 1194 398 398 0.00 Total of12153 atoms and 4042 groups and 4037 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3307 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 <- "34.894" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1090" Evaluating: 1090-13 Parameter: NUMWAT <- "1077" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1077" Comparing "1075" and "1077". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.894" Parameter: BOX -> "34.894" Parameter: BOX -> "34.894" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.89400 B = 34.89400 C = 34.89400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7209 2 1 -1 -2 -1 13.6485 3 1 -1 -1 -1 1.9978 4 1 -1 0 -1 0.6335 5 1 0 -1 -1 4.3733 6 1 0 0 -1 5.5774 7 1 -1 -1 0 2.7105 8 1 -1 0 0 4.8878 9 1 0 -1 0 2.5955 10 1 0 1 0 2.5955 11 1 0 0 1 5.5774 12 1 0 1 1 4.3733 13 1 2 1 1 8.7209 14 1 1 2 1 13.6485 15 1 1 1 1 1.9978 16 1 1 0 1 0.6335 17 1 1 1 0 2.7105 18 1 1 0 0 4.8878 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3307 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.32 2 C002 has 33 11 11 10.73 3 C003 has 2607 869 869 0.00 4 C004 has 825 275 275 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1161 387 387 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1184 393 393 0.00 9 C009 has 1194 398 398 0.00 Total of12153 atoms and 4042 groups and 4037 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3307 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 <- "34.892" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1090" Evaluating: 1090-13 Parameter: NUMWAT <- "1077" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1077" Comparing "1075" and "1077". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.892" Parameter: BOX -> "34.892" Parameter: BOX -> "34.892" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.89200 B = 34.89200 C = 34.89200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7188 2 1 -1 -2 -1 13.6455 3 1 -1 -1 -1 1.9958 4 1 -1 0 -1 0.6353 5 1 0 -1 -1 4.3711 6 1 0 0 -1 5.5758 7 1 -1 -1 0 2.7094 8 1 -1 0 0 4.8875 9 1 0 -1 0 2.5948 10 1 0 1 0 2.5948 11 1 0 0 1 5.5758 12 1 0 1 1 4.3711 13 1 2 1 1 8.7188 14 1 1 2 1 13.6455 15 1 1 1 1 1.9958 16 1 1 0 1 0.6353 17 1 1 1 0 2.7094 18 1 1 0 0 4.8875 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3307 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.32 2 C002 has 33 11 11 10.72 3 C003 has 2607 869 869 0.00 4 C004 has 825 275 275 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1161 387 387 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1184 393 393 0.00 9 C009 has 1194 398 398 0.00 Total of12153 atoms and 4042 groups and 4037 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3307 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 <- "34.89" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1090" Evaluating: 1090-13 Parameter: NUMWAT <- "1077" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1077" Comparing "1075" and "1077". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.89" Parameter: BOX -> "34.89" Parameter: BOX -> "34.89" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.89000 B = 34.89000 C = 34.89000 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7166 2 1 -1 -2 -1 13.6426 3 1 -1 -1 -1 1.9938 4 1 -1 0 -1 0.6371 5 1 0 -1 -1 4.3690 6 1 0 0 -1 5.5741 7 1 -1 -1 0 2.7083 8 1 -1 0 0 4.8872 9 1 0 -1 0 2.5942 10 1 0 1 0 2.5942 11 1 0 0 1 5.5741 12 1 0 1 1 4.3690 13 1 2 1 1 8.7166 14 1 1 2 1 13.6426 15 1 1 1 1 1.9938 16 1 1 0 1 0.6371 17 1 1 1 0 2.7083 18 1 1 0 0 4.8872 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3307 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.31 2 C002 has 33 11 11 10.72 3 C003 has 2607 869 869 0.00 4 C004 has 825 275 275 0.00 5 C005 has 855 285 285 0.00 6 C006 has 1161 387 387 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1184 393 393 0.00 9 C009 has 1194 398 398 0.00 Total of12153 atoms and 4042 groups and 4037 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3307 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 <- "34.888" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1090" Evaluating: 1090-13 Parameter: NUMWAT <- "1077" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1077" Comparing "1075" and "1077". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.888" Parameter: BOX -> "34.888" Parameter: BOX -> "34.888" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.88800 B = 34.88800 C = 34.88800 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7145 2 1 -1 -2 -1 13.6396 3 1 -1 -1 -1 1.9918 4 1 -1 0 -1 0.6389 5 1 0 -1 -1 4.3669 6 1 0 0 -1 5.5725 7 1 -1 -1 0 2.7071 8 1 -1 0 0 4.8869 9 1 0 -1 0 2.5935 10 1 0 1 0 2.5935 11 1 0 0 1 5.5725 12 1 0 1 1 4.3669 13 1 2 1 1 8.7145 14 1 1 2 1 13.6396 15 1 1 1 1 1.9918 16 1 1 0 1 0.6389 17 1 1 1 0 2.7071 18 1 1 0 0 4.8869 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3307 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.31 2 C002 has 33 11 11 10.72 3 C003 has 2607 869 869 0.00 4 C004 has 825 275 275 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1161 387 387 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1184 393 393 0.00 9 C009 has 1194 398 398 0.00 Total of12156 atoms and 4043 groups and 4038 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3307 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 <- "34.886" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1090" Evaluating: 1090-13 Parameter: NUMWAT <- "1077" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1077" Comparing "1075" and "1077". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.886" Parameter: BOX -> "34.886" Parameter: BOX -> "34.886" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.88600 B = 34.88600 C = 34.88600 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7124 2 1 -1 -2 -1 13.6367 3 1 -1 -1 -1 1.9899 4 1 -1 0 -1 0.6407 5 1 0 -1 -1 4.3648 6 1 0 0 -1 5.5709 7 1 -1 -1 0 2.7060 8 1 -1 0 0 4.8867 9 1 0 -1 0 2.5928 10 1 0 1 0 2.5928 11 1 0 0 1 5.5709 12 1 0 1 1 4.3648 13 1 2 1 1 8.7124 14 1 1 2 1 13.6367 15 1 1 1 1 1.9899 16 1 1 0 1 0.6407 17 1 1 1 0 2.7060 18 1 1 0 0 4.8867 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3307 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.31 2 C002 has 36 12 12 10.71 3 C003 has 2607 869 869 0.00 4 C004 has 825 275 275 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1161 387 387 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1184 393 393 0.00 9 C009 has 1194 398 398 0.00 Total of12159 atoms and 4044 groups and 4039 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3307 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 <- "34.884" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1090" Evaluating: 1090-13 Parameter: NUMWAT <- "1077" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1077" Comparing "1075" and "1077". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.884" Parameter: BOX -> "34.884" Parameter: BOX -> "34.884" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.88400 B = 34.88400 C = 34.88400 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7103 2 1 -1 -2 -1 13.6337 3 1 -1 -1 -1 1.9879 4 1 -1 0 -1 0.6425 5 1 0 -1 -1 4.3626 6 1 0 0 -1 5.5692 7 1 -1 -1 0 2.7049 8 1 -1 0 0 4.8864 9 1 0 -1 0 2.5921 10 1 0 1 0 2.5921 11 1 0 0 1 5.5692 12 1 0 1 1 4.3626 13 1 2 1 1 8.7103 14 1 1 2 1 13.6337 15 1 1 1 1 1.9879 16 1 1 0 1 0.6425 17 1 1 1 0 2.7049 18 1 1 0 0 4.8864 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3307 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbfrq 0 ihbfrq 0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 207 69 69 5.30 2 C002 has 36 12 12 10.71 3 C003 has 2607 869 869 0.00 4 C004 has 825 275 275 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1164 388 388 0.00 7 C007 has 780 260 260 0.00 8 C008 has 1184 393 393 0.00 9 C009 has 1194 398 398 0.00 Total of12162 atoms and 4045 groups and 4040 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE COMPARISON SET. CHARMM> coordinate dist weigh comp CHARMM> CHARMM> delete atom select .byres. (atom WAT * O .and. (property wcomp .gt. 0.001 )) end SELRPN> 0 atoms have been selected out of 3307 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 = 3307 Number of groups = 1095 Number of bonds = 3301 Number of angles = 1199 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1093 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 <- "34.882" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1090" Evaluating: 1090-13 Parameter: NUMWAT <- "1077" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1077" Comparing "1075" and "1077". IF test evaluated as true. Performing command CHARMM> CHARMM> CHARMM> set angle = 109.4712206344907 Parameter: ANGLE <- "109.4712206344907" CHARMM> CHARMM> crystal define octahedral @box @box @box @angle @angle @angle Parameter: BOX -> "34.882" Parameter: BOX -> "34.882" Parameter: BOX -> "34.882" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.88200 B = 34.88200 C = 34.88200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> crystal build cutoff 14.0 XBUILD> Building all transformations with a minimum atom-atom contact distance of less than 14.00 Angstroms. Range of Grid Search for Transformation 1 : Lattice Vector A -3 TO 3 Lattice Vector B -3 TO 3 Lattice Vector C -3 TO 3 The number of transformations generated = 18 Number Symop A B C Distance 1 1 -2 -1 -1 8.7082 2 1 -1 -2 -1 13.6308 3 1 -1 -1 -1 1.9859 4 1 -1 0 -1 0.6443 5 1 0 -1 -1 4.3605 6 1 0 0 -1 5.5676 7 1 -1 -1 0 2.7038 8 1 -1 0 0 4.8861 9 1 0 -1 0 2.5914 10 1 0 1 0 2.5914 11 1 0 0 1 5.5676 12 1 0 1 1 4.3605 13 1 2 1 1 8.7082 14 1 1 2 1 13.6308 15 1 1 1 1 1.9859 16 1 1 0 1 0.6443 17 1 1 1 0 2.7038 18 1 1 0 0 4.8861 THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 18 Transformations 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 3307 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 52 OPERATED ON BY TRANSFORMATION C015 RESIDUE 846 OPERATED ON BY TRANSFORMATION C018 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 210 70 70 5.12 2 C002 has 39 13 13 10.71 3 C003 has 2610 870 870 0.00 4 C004 has 828 276 276 0.00 5 C005 has 858 286 286 0.00 6 C006 has 1161 387 387 0.00 7 C007 has 783 261 261 0.00 8 C008 has 1178 391 391 0.00 9 C009 has 1194 398 398 0.00 Total of12168 atoms and 4047 groups and 4042 residues were included CHARMM> CHARMM> coordinate diff comp SELECTED COORDINATES DIFFERENCED TO THE 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 3307 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 = 1088 Number of atoms = 3301 Number of groups = 1093 Number of bonds = 3295 Number of angles = 1197 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1091 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 = 3301 Number of groups = 1093 Number of bonds = 3295 Number of angles = 1197 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1091 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 <- "34.88" CHARMM> CHARMM> ! CHARMM> ! fudge factor for waters CHARMM> ! CHARMM> calc numwat ?NRES - 13 RDCMND substituted energy or value "?NRES" to "1088" Evaluating: 1088-13 Parameter: NUMWAT <- "1075" CHARMM> if @waters .lt. @numwat goto loop2 Parameter: WATERS -> "1075" Parameter: NUMWAT -> "1075" Comparing "1075" and "1075". IF test evaluated as false. Skipping command CHARMM> incr box by @boxincr Parameter: BOXINCR -> "0.002" Parameter: BOX <- "34.882" CHARMM> CHARMM> CHARMM> CHARMM> crystal define octa @box @box @box @angle @angle @angle Parameter: BOX -> "34.882" Parameter: BOX -> "34.882" Parameter: BOX -> "34.882" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Parameter: ANGLE -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 34.88200 B = 34.88200 C = 34.88200 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 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 1.9859 2 1 -1 0 -1 0.6443 3 1 0 -1 -1 4.3605 4 1 0 0 -1 5.5676 5 1 -1 -1 0 2.7038 6 1 -1 0 0 4.8861 7 1 0 -1 0 2.5914 8 1 0 1 0 2.5914 9 1 0 0 1 5.5676 10 1 0 1 1 4.3605 11 1 1 1 1 1.9859 12 1 1 0 1 0.6443 13 1 1 1 0 2.7038 14 1 1 0 0 4.8861 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 3301 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 150 50 50 0.00 2 C002 has 15 5 5 0.00 3 C003 has 21 7 7 0.00 4 C004 has 15 5 5 0.00 5 C005 has 9 3 3 0.00 6 C006 has 21 7 7 0.00 7 C007 has 15 5 5 0.00 Total of 3547 atoms and 1175 groups and 1170 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 3301 ***** LEVEL 0 WARNING FROM ***** ***** No atoms selected for deletion. Nothing done. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL 0 WARNING FROM ***** ***** PSF modified with image centering active: Now off. ****************************************** BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 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 = 3301 Number of groups = 1093 Number of bonds = 3295 Number of angles = 1197 Number of dihedrals = 184 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 1091 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 -> "AA" Parameter: FFNAME -> "C36" VOPEN> Attempting to open::aa_c36.psf:: OPNLGU> Unit 1 opened for WRITE access to /uufs/chpc.utah.edu/common/home/u0181375/aa-charmm/aa_c36.psf CHARMM> write psf unit 1 card RDTITL> * AA "Initial ApA model" RDTITL> * 34.882 34.882 34.882 109.471 109.471 109.471 RDTITL> * 3 NA+ IONS + 1075 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 -> "AA" Parameter: FFNAME -> "C36" VOPEN> Attempting to open::aa_c36.cor:: OPNLGU> Unit 1 opened for WRITE access to /uufs/chpc.utah.edu/common/home/u0181375/aa-charmm/aa_c36.cor CHARMM> coor write unit 1 card select all end RDTITL> * AA "Initial ApA model" RDTITL> * 34.882 34.882 34.882 109.471 109.471 109.471 RDTITL> * 3 NA+ IONS + 1075 WATERS RDTITL> * SELRPN> 3301 atoms have been selected out of 3301 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 -> "AA" Parameter: FFNAME -> "C36" VOPEN> Attempting to open::aa_c36.pdb:: OPNLGU> Unit 1 opened for WRITE access to /uufs/chpc.utah.edu/common/home/u0181375/aa-charmm/aa_c36.pdb CHARMM> coor write unit 1 pdb select all end RDTITL> * AA "Initial ApA model" RDTITL> * 34.882 34.882 34.882 109.471 109.471 109.471 RDTITL> * 3 NA+ IONS + 1075 WATERS RDTITL> * Write CHARMM-pdb format SELRPN> 3301 atoms have been selected out of 3301 CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" $$$$$$ New timer profile $$$$$ Total time 16.19 Other: 0.00 NORMAL TERMINATION BY END OF FILE MOST SEVERE WARNING WAS AT LEVEL 0 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 16.19 SECONDS CPU TIME: 16.18 SECONDS