CPPTRAJ: Trajectory Analysis. V16.00b OpenMP
    ___  ___  ___  ___
     | \/ | \/ | \/ | 
    _|_/\_|_/\_|_/\_|_

| Date/time: 06/03/16 10:42:52
| Available memory: 2.429 GB

INPUT: Reading input from 'pt-analysis1.in'
  [parm ../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr]
	Reading '../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
  [trajin ../ctraj.c1]
	Reading '../ctraj.c1' as Amber NetCDF
  [reference ../../../A-form.pdb [a-form]]
	Reading '../../../A-form.pdb' as PDB
	Setting active reference for distance-based masks: 'A-form.pdb'
  [rmsd rms_2_aform :1,2&!@H= ref [a-form] mass]
    RMSD: (:1,2&!@H*), reference is "[a-form]:1" (:1,2&!@H*), mass-weighted.
	Best-fit RMSD will be calculated, coords will be rotated and translated.
  [distance dist_sugar_ox :1@O2' :2@O4']
    DISTANCE: :1@O2' to :2@O4', center of mass.
  [distance dist_N3-O5p :1@N3 :1@O5']
    DISTANCE: :1@N3 to :1@O5', center of mass.
  [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9]
    DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9, center of mass.
  [dihedral g1 :1@O5' :1@C5' :1@C4' :1@C3' type gamma]
    DIHEDRAL: [:1@O5']-[:1@C5']-[:1@C4']-[:1@C3']
              Output range is -180 to 180 degrees.
  [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta]
    DIHEDRAL: [:1@C5']-[:1@C4']-[:1@C3']-[:1@O3']
              Output range is -180 to 180 degrees.
  [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon]
    DIHEDRAL: [:1@C4']-[:1@C3']-[:1@O3']-[:2@P]
              Output range is -180 to 180 degrees.
  [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta]
    DIHEDRAL: [:1@C3']-[:1@O3']-[:2@P]-[:2@O5']
              Output range is -180 to 180 degrees.
  [dihedral c1 :1@O4' :1@C1' :1@N9 :1@C4 type chi]
    DIHEDRAL: [:1@O4']-[:1@C1']-[:1@N9]-[:1@C4]
              Output range is -180 to 180 degrees.
  [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha]
    DIHEDRAL: [:1@O3']-[:2@P]-[:2@O5']-[:2@C5']
              Output range is -180 to 180 degrees.
  [dihedral b2 :2@P :2@O5' :2@C5' :2@C4' type beta]
    DIHEDRAL: [:2@P]-[:2@O5']-[:2@C5']-[:2@C4']
              Output range is -180 to 180 degrees.
  [dihedral g2 :2@O5' :2@C5' :2@C4' :2@C3' type gamma]
    DIHEDRAL: [:2@O5']-[:2@C5']-[:2@C4']-[:2@C3']
              Output range is -180 to 180 degrees.
  [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta]
    DIHEDRAL: [:2@C5']-[:2@C4']-[:2@C3']-[:2@O3']
              Output range is -180 to 180 degrees.
  [dihedral c2 :2@O4' :2@C1' :2@N9 :2@C4 type chi]
    DIHEDRAL: [:2@O4']-[:2@C1']-[:2@N9]-[:2@C4]
              Output range is -180 to 180 degrees.
  [run]
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES (1 total):
 0: noWAt.topo.hmr, 65 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (1 total):
 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 169803 of 169803)
  Coordinate processing will occur on 169803 frames.

REFERENCE FRAMES (1 total):
    0: [a-form]:1
	Active reference frame for distance-based masks is '[a-form]:1'

BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'noWAt.topo.hmr' (14 actions):
  0: [rmsd rms_2_aform :1,2&!@H= ref [a-form] mass]
	Target mask: [:1,2&!@H*](41)
	Reference mask: [:1,2&!@H*](41)
Warning: Coordinates are being rotated and box coordinates are present.
Warning: Unit cell vectors are NOT rotated; imaging will not be possible
Warning:  after the RMS-fit is performed.
  1: [distance dist_sugar_ox :1@O2' :2@O4']
	:1@O2' (1 atoms) to :2@O4' (1 atoms), imaged.
  2: [distance dist_N3-O5p :1@N3 :1@O5']
	:1@N3 (1 atoms) to :1@O5' (1 atoms), imaged.
  3: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9]
	:1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms), imaged.
  4: [dihedral g1 :1@O5' :1@C5' :1@C4' :1@C3' type gamma]
	 [:1@O5'](1) [:1@C5'](1) [:1@C4'](1) [:1@C3'](1)
  5: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta]
	 [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1)
  6: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon]
	 [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1)
  7: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta]
	 [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1)
  8: [dihedral c1 :1@O4' :1@C1' :1@N9 :1@C4 type chi]
	 [:1@O4'](1) [:1@C1'](1) [:1@N9](1) [:1@C4](1)
  9: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha]
	 [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1)
  10: [dihedral b2 :2@P :2@O5' :2@C5' :2@C4' type beta]
	 [:2@P](1) [:2@O5'](1) [:2@C5'](1) [:2@C4'](1)
  11: [dihedral g2 :2@O5' :2@C5' :2@C4' :2@C3' type gamma]
	 [:2@O5'](1) [:2@C5'](1) [:2@C4'](1) [:2@C3'](1)
  12: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta]
	 [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1)
  13: [dihedral c2 :2@O4' :2@C1' :2@N9 :2@C4 type chi]
	 [:2@O4'](1) [:2@C1'](1) [:2@N9](1) [:2@C4](1)
----- ctraj.c1 (1-169803, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 169803 frames and processed 169803 frames.
TIME: Avg. throughput= 154345.8777 frames / second.

ACTION OUTPUT:

DATASETS (14 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 169803
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 169803
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 169803
	COM "COM" (double, distance), size is 169803
	g1 "g1" (double, torsion(gamma)), size is 169803
	d1 "d1" (double, torsion(delta)), size is 169803
	e1 "e1" (double, torsion(epsilon)), size is 169803
	z1 "z1" (double, torsion(zeta)), size is 169803
	c1 "c1" (double, torsion(chin)), size is 169803
	a2 "a2" (double, torsion(alpha)), size is 169803
	b2 "b2" (double, torsion(beta)), size is 169803
	g2 "g2" (double, torsion(gamma)), size is 169803
	d2 "d2" (double, torsion(delta)), size is 169803
	c2 "c2" (double, torsion(chin)), size is 169803

RUN TIMING:
TIME:		Init               : 0.0001 s (  0.01%)
TIME:		Trajectory Process : 1.1001 s ( 99.99%)
TIME:		Action Post        : 0.0000 s (  0.00%)
TIME:		Analysis           : 0.0000 s (  0.00%)
TIME:		Data File Write    : 0.0000 s (  0.00%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 1.1003 s
---------- RUN END ---------------------------------------------------
  [avg rms_2_aform out avg-rmsd-all.dat]
    AVERAGE: Calculating average of 1 data sets.
	Data set base name 'AVERAGE_00016'
	Output to to 'avg-rmsd-all.dat'
  [hist rms_2_aform,0,5,0.1 out rmsd-hist.dat name RMSD norm]
	Hist: rmsd-hist.dat: Set up for 1 dimensions using the following datasets:
	[ rms_2_aform ]
	norm: Sum over bins will be normalized to 1.0.
  [hist COM,0,10,0.1 out COM-hist.dat name CoM norm]
	Hist: COM-hist.dat: Set up for 1 dimensions using the following datasets:
	[ COM ]
	norm: Sum over bins will be normalized to 1.0.
  [hist dist_sugar_ox,0,10,0.1 out distO2O4-hist.dat norm]
	Hist: distO2O4-hist.dat: Set up for 1 dimensions using the following datasets:
	[ dist_sugar_ox ]
	norm: Sum over bins will be normalized to 1.0.
  [hist dist_N3-O5p,0,10,0.1 out distN3-O5p-hist.dat norm]
	Hist: distN3-O5p-hist.dat: Set up for 1 dimensions using the following datasets:
	[ dist_N3-O5p ]
	norm: Sum over bins will be normalized to 1.0.
  [hist rms_2_aform,0,5,0.1 dist_sugar_ox,0,10,0.1 out 2dhist_rms-dist.gnu norm]
	Hist: 2dhist_rms-dist.gnu: Set up for 2 dimensions using the following datasets:
	[ rms_2_aform dist_sugar_ox ]
	norm: Sum over bins will be normalized to 1.0.
  [hist g1,-180,180,1 out dihed_a2-hist.dat name gamma_1 norm]
	Hist: dihed_a2-hist.dat: Set up for 1 dimensions using the following datasets:
	[ g1 ]
	norm: Sum over bins will be normalized to 1.0.
  [hist d1,-180,180,1 out dihed_d1-hist.dat name delta_1 norm]
	Hist: dihed_d1-hist.dat: Set up for 1 dimensions using the following datasets:
	[ d1 ]
	norm: Sum over bins will be normalized to 1.0.
  [hist e1,-180,180,1 out dihed_e1-hist.dat name epsilon_1 norm]
	Hist: dihed_e1-hist.dat: Set up for 1 dimensions using the following datasets:
	[ e1 ]
	norm: Sum over bins will be normalized to 1.0.
  [hist z1,-180,180,1 out dihed_z1-hist.dat name zeta_1 norm]
	Hist: dihed_z1-hist.dat: Set up for 1 dimensions using the following datasets:
	[ z1 ]
	norm: Sum over bins will be normalized to 1.0.
  [hist c1,-180,180,1 out dihed_c1-hist.dat name chi_1 norm]
	Hist: dihed_c1-hist.dat: Set up for 1 dimensions using the following datasets:
	[ c1 ]
	norm: Sum over bins will be normalized to 1.0.
  [hist a2,-180,180,1 out dihed_a2-hist.dat name alpha_2 norm]
	Hist: dihed_a2-hist.dat: Set up for 1 dimensions using the following datasets:
	[ a2 ]
	norm: Sum over bins will be normalized to 1.0.
  [hist b2,-180,180,1 out dihed_b2-hist.dat name beta_2 norm]
	Hist: dihed_b2-hist.dat: Set up for 1 dimensions using the following datasets:
	[ b2 ]
	norm: Sum over bins will be normalized to 1.0.
  [hist g2,-180,180,1 out dihed_g2-hist.dat name gamma_2 norm]
	Hist: dihed_g2-hist.dat: Set up for 1 dimensions using the following datasets:
	[ g2 ]
	norm: Sum over bins will be normalized to 1.0.
  [hist d2,-180,180,1 out dihed_d2-hist.dat name delta_2 norm]
	Hist: dihed_d2-hist.dat: Set up for 1 dimensions using the following datasets:
	[ d2 ]
	norm: Sum over bins will be normalized to 1.0.
  [hist c2,-180,180,1 out dihed_c2-hist.dat name chi_2 norm]
	Hist: dihed_c2-hist.dat: Set up for 1 dimensions using the following datasets:
	[ c2 ]
	norm: Sum over bins will be normalized to 1.0.
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES (1 total):
 0: noWAt.topo.hmr, 65 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (1 total):
 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 169803 of 169803)
  Coordinate processing will occur on 169803 frames.

REFERENCE FRAMES (1 total):
    0: [a-form]:1
	Active reference frame for distance-based masks is '[a-form]:1'

BEGIN TRAJECTORY PROCESSING:
----- ctraj.c1 (1-169803, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 169803 frames and processed 169803 frames.
TIME: Avg. throughput= 580926.2497 frames / second.

ACTION OUTPUT:

ANALYSIS: Performing 16 analyses:
  0: [avg rms_2_aform out avg-rmsd-all.dat]
	1: rms_2_aform
  1: [hist rms_2_aform,0,5,0.1 out rmsd-hist.dat name RMSD norm]
		Calculating bins from min=0 max=5 step=0.1.
	Dim rms_2_aform: 0.000000->5.000000, step 0.100000, 50 bins.
	Hist: 169803 data points in each dimension.
	Hist: Allocating histogram, total bins = 50
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 169803
  2: [hist COM,0,10,0.1 out COM-hist.dat name CoM norm]
		Calculating bins from min=0 max=10 step=0.1.
	Dim COM: 0.000000->10.000000, step 0.100000, 100 bins.
	Hist: 169803 data points in each dimension.
	Hist: Allocating histogram, total bins = 100
	Warning: Frame 938 Coordinates out of bounds (-1)
	Warning: Frame 1439 Coordinates out of bounds (-1)
	Warning: Frame 1819 Coordinates out of bounds (-1)
	Warning: Frame 2150 Coordinates out of bounds (-1)
	Warning: Frame 2919 Coordinates out of bounds (-1)
	Warning: Frame 6127 Coordinates out of bounds (-1)
	Warning: Frame 13481 Coordinates out of bounds (-1)
	Warning: Frame 13930 Coordinates out of bounds (-1)
	Warning: Frame 16935 Coordinates out of bounds (-1)
	Warning: Frame 18758 Coordinates out of bounds (-1)
	Warning: Frame 24005 Coordinates out of bounds (-1)
	Warning: Frame 24683 Coordinates out of bounds (-1)
	Warning: Frame 24996 Coordinates out of bounds (-1)
	Warning: Frame 26137 Coordinates out of bounds (-1)
	Warning: Frame 26138 Coordinates out of bounds (-1)
	Warning: Frame 28048 Coordinates out of bounds (-1)
	Warning: Frame 28424 Coordinates out of bounds (-1)
	Warning: Frame 28946 Coordinates out of bounds (-1)
	Warning: Frame 30475 Coordinates out of bounds (-1)
	Warning: Frame 31636 Coordinates out of bounds (-1)
	Warning: Frame 33695 Coordinates out of bounds (-1)
	Warning: Frame 33696 Coordinates out of bounds (-1)
	Warning: Frame 35394 Coordinates out of bounds (-1)
	Warning: Frame 36915 Coordinates out of bounds (-1)
	Warning: Frame 36925 Coordinates out of bounds (-1)
	Warning: Frame 38354 Coordinates out of bounds (-1)
	Warning: Frame 40574 Coordinates out of bounds (-1)
	Warning: Frame 41645 Coordinates out of bounds (-1)
	Warning: Frame 43576 Coordinates out of bounds (-1)
	Warning: Frame 44623 Coordinates out of bounds (-1)
	Warning: Frame 45156 Coordinates out of bounds (-1)
	Warning: Frame 45157 Coordinates out of bounds (-1)
	Warning: Frame 49676 Coordinates out of bounds (-1)
	Warning: Frame 51207 Coordinates out of bounds (-1)
	Warning: Frame 51212 Coordinates out of bounds (-1)
	Warning: Frame 51214 Coordinates out of bounds (-1)
	Warning: Frame 53354 Coordinates out of bounds (-1)
	Warning: Frame 54301 Coordinates out of bounds (-1)
	Warning: Frame 55038 Coordinates out of bounds (-1)
	Warning: Frame 57932 Coordinates out of bounds (-1)
	Warning: Frame 57933 Coordinates out of bounds (-1)
	Warning: Frame 59296 Coordinates out of bounds (-1)
	Warning: Frame 59770 Coordinates out of bounds (-1)
	Warning: Frame 59777 Coordinates out of bounds (-1)
	Warning: Frame 59929 Coordinates out of bounds (-1)
	Warning: Frame 60433 Coordinates out of bounds (-1)
	Warning: Frame 62129 Coordinates out of bounds (-1)
	Warning: Frame 62499 Coordinates out of bounds (-1)
	Warning: Frame 63566 Coordinates out of bounds (-1)
	Warning: Frame 66928 Coordinates out of bounds (-1)
	Warning: Frame 68797 Coordinates out of bounds (-1)
	Warning: Frame 68820 Coordinates out of bounds (-1)
	Warning: Frame 68939 Coordinates out of bounds (-1)
	Warning: Frame 69012 Coordinates out of bounds (-1)
	Warning: Frame 69766 Coordinates out of bounds (-1)
	Warning: Frame 69802 Coordinates out of bounds (-1)
	Warning: Frame 69803 Coordinates out of bounds (-1)
	Warning: Frame 69915 Coordinates out of bounds (-1)
	Warning: Frame 69960 Coordinates out of bounds (-1)
	Warning: Frame 69974 Coordinates out of bounds (-1)
	Warning: Frame 70260 Coordinates out of bounds (-1)
	Warning: Frame 70396 Coordinates out of bounds (-1)
	Warning: Frame 70581 Coordinates out of bounds (-1)
	Warning: Frame 70897 Coordinates out of bounds (-1)
	Warning: Frame 71081 Coordinates out of bounds (-1)
	Warning: Frame 71242 Coordinates out of bounds (-1)
	Warning: Frame 71291 Coordinates out of bounds (-1)
	Warning: Frame 71298 Coordinates out of bounds (-1)
	Warning: Frame 71861 Coordinates out of bounds (-1)
	Warning: Frame 73499 Coordinates out of bounds (-1)
	Warning: Frame 73501 Coordinates out of bounds (-1)
	Warning: Frame 73505 Coordinates out of bounds (-1)
	Warning: Frame 73697 Coordinates out of bounds (-1)
	Warning: Frame 73818 Coordinates out of bounds (-1)
	Warning: Frame 74058 Coordinates out of bounds (-1)
	Warning: Frame 74104 Coordinates out of bounds (-1)
	Warning: Frame 74668 Coordinates out of bounds (-1)
	Warning: Frame 74675 Coordinates out of bounds (-1)
	Warning: Frame 74802 Coordinates out of bounds (-1)
	Warning: Frame 74803 Coordinates out of bounds (-1)
	Warning: Frame 75626 Coordinates out of bounds (-1)
	Warning: Frame 75628 Coordinates out of bounds (-1)
	Warning: Frame 75629 Coordinates out of bounds (-1)
	Warning: Frame 75630 Coordinates out of bounds (-1)
	Warning: Frame 75690 Coordinates out of bounds (-1)
	Warning: Frame 75796 Coordinates out of bounds (-1)
	Warning: Frame 76185 Coordinates out of bounds (-1)
	Warning: Frame 76206 Coordinates out of bounds (-1)
	Warning: Frame 76366 Coordinates out of bounds (-1)
	Warning: Frame 76379 Coordinates out of bounds (-1)
	Warning: Frame 76511 Coordinates out of bounds (-1)
	Warning: Frame 77223 Coordinates out of bounds (-1)
	Warning: Frame 77494 Coordinates out of bounds (-1)
	Warning: Frame 77553 Coordinates out of bounds (-1)
	Warning: Frame 77885 Coordinates out of bounds (-1)
	Warning: Frame 78017 Coordinates out of bounds (-1)
	Warning: Frame 78188 Coordinates out of bounds (-1)
	Warning: Frame 78311 Coordinates out of bounds (-1)
	Warning: Frame 78435 Coordinates out of bounds (-1)
	Warning: Frame 78529 Coordinates out of bounds (-1)
	Warning: Frame 78536 Coordinates out of bounds (-1)
	Warning: Frame 79067 Coordinates out of bounds (-1)
	Warning: Frame 79445 Coordinates out of bounds (-1)
	Warning: Frame 80005 Coordinates out of bounds (-1)
	Warning: Frame 80981 Coordinates out of bounds (-1)
	Warning: Frame 80982 Coordinates out of bounds (-1)
	Warning: Frame 81490 Coordinates out of bounds (-1)
	Warning: Frame 82249 Coordinates out of bounds (-1)
	Warning: Frame 82453 Coordinates out of bounds (-1)
	Warning: Frame 83609 Coordinates out of bounds (-1)
	Warning: Frame 83826 Coordinates out of bounds (-1)
	Warning: Frame 84312 Coordinates out of bounds (-1)
	Warning: Frame 84391 Coordinates out of bounds (-1)
	Warning: Frame 84428 Coordinates out of bounds (-1)
	Warning: Frame 84481 Coordinates out of bounds (-1)
	Warning: Frame 84483 Coordinates out of bounds (-1)
	Warning: Frame 84486 Coordinates out of bounds (-1)
	Warning: Frame 84878 Coordinates out of bounds (-1)
	Warning: Frame 85653 Coordinates out of bounds (-1)
	Warning: Frame 85827 Coordinates out of bounds (-1)
	Warning: Frame 86082 Coordinates out of bounds (-1)
	Warning: Frame 86378 Coordinates out of bounds (-1)
	Warning: Frame 86380 Coordinates out of bounds (-1)
	Warning: Frame 86382 Coordinates out of bounds (-1)
	Warning: Frame 86813 Coordinates out of bounds (-1)
	Warning: Frame 86814 Coordinates out of bounds (-1)
	Warning: Frame 86816 Coordinates out of bounds (-1)
	Warning: Frame 87607 Coordinates out of bounds (-1)
	Warning: Frame 87885 Coordinates out of bounds (-1)
	Warning: Frame 88586 Coordinates out of bounds (-1)
	Warning: Frame 88904 Coordinates out of bounds (-1)
	Warning: Frame 88905 Coordinates out of bounds (-1)
	Warning: Frame 88906 Coordinates out of bounds (-1)
	Warning: Frame 88958 Coordinates out of bounds (-1)
	Warning: Frame 89063 Coordinates out of bounds (-1)
	Warning: Frame 89462 Coordinates out of bounds (-1)
	Warning: Frame 89873 Coordinates out of bounds (-1)
	Warning: Frame 90068 Coordinates out of bounds (-1)
	Warning: Frame 90779 Coordinates out of bounds (-1)
	Warning: Frame 90892 Coordinates out of bounds (-1)
	Warning: Frame 91115 Coordinates out of bounds (-1)
	Warning: Frame 91332 Coordinates out of bounds (-1)
	Warning: Frame 91619 Coordinates out of bounds (-1)
	Warning: Frame 91942 Coordinates out of bounds (-1)
	Warning: Frame 92006 Coordinates out of bounds (-1)
	Warning: Frame 92009 Coordinates out of bounds (-1)
	Warning: Frame 92297 Coordinates out of bounds (-1)
	Warning: Frame 92298 Coordinates out of bounds (-1)
	Warning: Frame 92479 Coordinates out of bounds (-1)
	Warning: Frame 93029 Coordinates out of bounds (-1)
	Warning: Frame 93112 Coordinates out of bounds (-1)
	Warning: Frame 93267 Coordinates out of bounds (-1)
	Warning: Frame 93268 Coordinates out of bounds (-1)
	Warning: Frame 93324 Coordinates out of bounds (-1)
	Warning: Frame 93425 Coordinates out of bounds (-1)
	Warning: Frame 93536 Coordinates out of bounds (-1)
	Warning: Frame 93550 Coordinates out of bounds (-1)
	Warning: Frame 93557 Coordinates out of bounds (-1)
	Warning: Frame 93610 Coordinates out of bounds (-1)
	Warning: Frame 94039 Coordinates out of bounds (-1)
	Warning: Frame 94146 Coordinates out of bounds (-1)
	Warning: Frame 94267 Coordinates out of bounds (-1)
	Warning: Frame 95083 Coordinates out of bounds (-1)
	Warning: Frame 95914 Coordinates out of bounds (-1)
	Warning: Frame 96119 Coordinates out of bounds (-1)
	Warning: Frame 96241 Coordinates out of bounds (-1)
	Warning: Frame 97491 Coordinates out of bounds (-1)
	Warning: Frame 97492 Coordinates out of bounds (-1)
	Warning: Frame 97612 Coordinates out of bounds (-1)
	Warning: Frame 97614 Coordinates out of bounds (-1)
	Warning: Frame 98023 Coordinates out of bounds (-1)
	Warning: Frame 99421 Coordinates out of bounds (-1)
	Warning: Frame 99790 Coordinates out of bounds (-1)
	Warning: Frame 99791 Coordinates out of bounds (-1)
	Warning: Frame 100137 Coordinates out of bounds (-1)
	Warning: Frame 100673 Coordinates out of bounds (-1)
	Warning: Frame 100679 Coordinates out of bounds (-1)
	Warning: Frame 100849 Coordinates out of bounds (-1)
	Warning: Frame 100850 Coordinates out of bounds (-1)
	Warning: Frame 101087 Coordinates out of bounds (-1)
	Warning: Frame 101092 Coordinates out of bounds (-1)
	Warning: Frame 101170 Coordinates out of bounds (-1)
	Warning: Frame 101241 Coordinates out of bounds (-1)
	Warning: Frame 101609 Coordinates out of bounds (-1)
	Warning: Frame 102032 Coordinates out of bounds (-1)
	Warning: Frame 102636 Coordinates out of bounds (-1)
	Warning: Frame 103058 Coordinates out of bounds (-1)
	Warning: Frame 104249 Coordinates out of bounds (-1)
	Warning: Frame 104375 Coordinates out of bounds (-1)
	Warning: Frame 106260 Coordinates out of bounds (-1)
	Warning: Frame 108098 Coordinates out of bounds (-1)
	Warning: Frame 108554 Coordinates out of bounds (-1)
	Warning: Frame 108776 Coordinates out of bounds (-1)
	Warning: Frame 109628 Coordinates out of bounds (-1)
	Warning: Frame 110716 Coordinates out of bounds (-1)
	Warning: Frame 111740 Coordinates out of bounds (-1)
	Warning: Frame 112258 Coordinates out of bounds (-1)
	Warning: Frame 112862 Coordinates out of bounds (-1)
	Warning: Frame 113308 Coordinates out of bounds (-1)
	Warning: Frame 113562 Coordinates out of bounds (-1)
	Warning: Frame 114438 Coordinates out of bounds (-1)
	Warning: Frame 115536 Coordinates out of bounds (-1)
	Warning: Frame 117805 Coordinates out of bounds (-1)
	Warning: Frame 119345 Coordinates out of bounds (-1)
	Warning: Frame 122594 Coordinates out of bounds (-1)
	Warning: Frame 123762 Coordinates out of bounds (-1)
	Warning: Frame 124013 Coordinates out of bounds (-1)
	Warning: Frame 124564 Coordinates out of bounds (-1)
	Warning: Frame 125982 Coordinates out of bounds (-1)
	Warning: Frame 127228 Coordinates out of bounds (-1)
	Warning: Frame 127229 Coordinates out of bounds (-1)
	Warning: Frame 128050 Coordinates out of bounds (-1)
	Warning: Frame 128060 Coordinates out of bounds (-1)
	Warning: Frame 130141 Coordinates out of bounds (-1)
	Warning: Frame 130970 Coordinates out of bounds (-1)
	Warning: Frame 130973 Coordinates out of bounds (-1)
	Warning: Frame 132732 Coordinates out of bounds (-1)
	Warning: Frame 133826 Coordinates out of bounds (-1)
	Warning: Frame 133827 Coordinates out of bounds (-1)
	Warning: Frame 134923 Coordinates out of bounds (-1)
	Warning: Frame 136332 Coordinates out of bounds (-1)
	Warning: Frame 136441 Coordinates out of bounds (-1)
	Warning: Frame 136503 Coordinates out of bounds (-1)
	Warning: Frame 136861 Coordinates out of bounds (-1)
	Warning: Frame 137296 Coordinates out of bounds (-1)
	Warning: Frame 137462 Coordinates out of bounds (-1)
	Warning: Frame 139953 Coordinates out of bounds (-1)
	Warning: Frame 141705 Coordinates out of bounds (-1)
	Warning: Frame 142957 Coordinates out of bounds (-1)
	Warning: Frame 149454 Coordinates out of bounds (-1)
	Warning: Frame 149455 Coordinates out of bounds (-1)
	Warning: Frame 150495 Coordinates out of bounds (-1)
	Warning: Frame 152052 Coordinates out of bounds (-1)
	Warning: Frame 152061 Coordinates out of bounds (-1)
	Warning: Frame 152062 Coordinates out of bounds (-1)
	Warning: Frame 152657 Coordinates out of bounds (-1)
	Warning: Frame 153256 Coordinates out of bounds (-1)
	Warning: Frame 153258 Coordinates out of bounds (-1)
	Warning: Frame 153259 Coordinates out of bounds (-1)
	Warning: Frame 154168 Coordinates out of bounds (-1)
	Warning: Frame 154461 Coordinates out of bounds (-1)
	Warning: Frame 154462 Coordinates out of bounds (-1)
	Warning: Frame 154483 Coordinates out of bounds (-1)
	Warning: Frame 154493 Coordinates out of bounds (-1)
	Warning: Frame 154494 Coordinates out of bounds (-1)
	Warning: Frame 154508 Coordinates out of bounds (-1)
	Warning: Frame 155242 Coordinates out of bounds (-1)
	Warning: Frame 155573 Coordinates out of bounds (-1)
	Warning: Frame 156629 Coordinates out of bounds (-1)
	Warning: Frame 156630 Coordinates out of bounds (-1)
	Warning: Frame 156735 Coordinates out of bounds (-1)
	Warning: Frame 159509 Coordinates out of bounds (-1)
	Warning: Frame 161981 Coordinates out of bounds (-1)
	Warning: Frame 166758 Coordinates out of bounds (-1)
	Warning: Frame 168522 Coordinates out of bounds (-1)
	Warning: Frame 168621 Coordinates out of bounds (-1)
	Warning: Frame 168622 Coordinates out of bounds (-1)
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 169546
  3: [hist dist_sugar_ox,0,10,0.1 out distO2O4-hist.dat norm]
		Calculating bins from min=0 max=10 step=0.1.
	Dim dist_sugar_ox: 0.000000->10.000000, step 0.100000, 100 bins.
	Hist: 169803 data points in each dimension.
	Hist: Allocating histogram, total bins = 100
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 169803
  4: [hist dist_N3-O5p,0,10,0.1 out distN3-O5p-hist.dat norm]
		Calculating bins from min=0 max=10 step=0.1.
	Dim dist_N3-O5p: 0.000000->10.000000, step 0.100000, 100 bins.
	Hist: 169803 data points in each dimension.
	Hist: Allocating histogram, total bins = 100
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 169803
  5: [hist rms_2_aform,0,5,0.1 dist_sugar_ox,0,10,0.1 out 2dhist_rms-dist.gnu norm]
		Calculating bins from min=0 max=5 step=0.1.
	Dim rms_2_aform: 0.000000->5.000000, step 0.100000, 50 bins.
		Calculating bins from min=0 max=10 step=0.1.
	Dim dist_sugar_ox: 0.000000->10.000000, step 0.100000, 100 bins.
	Hist: 169803 data points in each dimension.
	Hist: Allocating histogram, total bins = 5000
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 169803
  6: [hist g1,-180,180,1 out dihed_a2-hist.dat name gamma_1 norm]
		Calculating bins from min=-180 max=180 step=1.
	Dim g1: -180.000000->180.000000, step 1.000000, 360 bins.
	Hist: 169803 data points in each dimension.
	Hist: Allocating histogram, total bins = 360
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 169803
  7: [hist d1,-180,180,1 out dihed_d1-hist.dat name delta_1 norm]
		Calculating bins from min=-180 max=180 step=1.
	Dim d1: -180.000000->180.000000, step 1.000000, 360 bins.
	Hist: 169803 data points in each dimension.
	Hist: Allocating histogram, total bins = 360
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 169803
  8: [hist e1,-180,180,1 out dihed_e1-hist.dat name epsilon_1 norm]
		Calculating bins from min=-180 max=180 step=1.
	Dim e1: -180.000000->180.000000, step 1.000000, 360 bins.
	Hist: 169803 data points in each dimension.
	Hist: Allocating histogram, total bins = 360
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 169803
  9: [hist z1,-180,180,1 out dihed_z1-hist.dat name zeta_1 norm]
		Calculating bins from min=-180 max=180 step=1.
	Dim z1: -180.000000->180.000000, step 1.000000, 360 bins.
	Hist: 169803 data points in each dimension.
	Hist: Allocating histogram, total bins = 360
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 169803
  10: [hist c1,-180,180,1 out dihed_c1-hist.dat name chi_1 norm]
		Calculating bins from min=-180 max=180 step=1.
	Dim c1: -180.000000->180.000000, step 1.000000, 360 bins.
	Hist: 169803 data points in each dimension.
	Hist: Allocating histogram, total bins = 360
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 169803
  11: [hist a2,-180,180,1 out dihed_a2-hist.dat name alpha_2 norm]
		Calculating bins from min=-180 max=180 step=1.
	Dim a2: -180.000000->180.000000, step 1.000000, 360 bins.
	Hist: 169803 data points in each dimension.
	Hist: Allocating histogram, total bins = 360
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 169803
  12: [hist b2,-180,180,1 out dihed_b2-hist.dat name beta_2 norm]
		Calculating bins from min=-180 max=180 step=1.
	Dim b2: -180.000000->180.000000, step 1.000000, 360 bins.
	Hist: 169803 data points in each dimension.
	Hist: Allocating histogram, total bins = 360
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 169803
  13: [hist g2,-180,180,1 out dihed_g2-hist.dat name gamma_2 norm]
		Calculating bins from min=-180 max=180 step=1.
	Dim g2: -180.000000->180.000000, step 1.000000, 360 bins.
	Hist: 169803 data points in each dimension.
	Hist: Allocating histogram, total bins = 360
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 169803
  14: [hist d2,-180,180,1 out dihed_d2-hist.dat name delta_2 norm]
		Calculating bins from min=-180 max=180 step=1.
	Dim d2: -180.000000->180.000000, step 1.000000, 360 bins.
	Hist: 169803 data points in each dimension.
	Hist: Allocating histogram, total bins = 360
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 169803
  15: [hist c2,-180,180,1 out dihed_c2-hist.dat name chi_2 norm]
		Calculating bins from min=-180 max=180 step=1.
	Dim c2: -180.000000->180.000000, step 1.000000, 360 bins.
	Hist: 169803 data points in each dimension.
	Hist: Allocating histogram, total bins = 360
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 169803

TIME: Analyses took 0.0530 seconds.

DATASETS (36 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 169803
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 169803
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 169803
	COM "COM" (double, distance), size is 169803
	g1 "g1" (double, torsion(gamma)), size is 169803
	d1 "d1" (double, torsion(delta)), size is 169803
	e1 "e1" (double, torsion(epsilon)), size is 169803
	z1 "z1" (double, torsion(zeta)), size is 169803
	c1 "c1" (double, torsion(chin)), size is 169803
	a2 "a2" (double, torsion(alpha)), size is 169803
	b2 "b2" (double, torsion(beta)), size is 169803
	g2 "g2" (double, torsion(gamma)), size is 169803
	d2 "d2" (double, torsion(delta)), size is 169803
	c2 "c2" (double, torsion(chin)), size is 169803
	AVERAGE_00016[avg] "AVERAGE_00016[avg]" (double), size is 1
	AVERAGE_00016[sd] "AVERAGE_00016[sd]" (double), size is 1
	AVERAGE_00016[ymin] "AVERAGE_00016[ymin]" (double), size is 1
	AVERAGE_00016[ymax] "AVERAGE_00016[ymax]" (double), size is 1
	AVERAGE_00016[yminidx] "AVERAGE_00016[yminidx]" (integer), size is 1
	AVERAGE_00016[ymaxidx] "AVERAGE_00016[ymaxidx]" (integer), size is 1
	AVERAGE_00016[names] "AVERAGE_00016[names]" (string), size is 1
	RMSD "RMSD" (double), size is 50
	CoM "CoM" (double), size is 100
	Hist_00025 "Hist_00025" (double), size is 100
	Hist_00026 "Hist_00026" (double), size is 100
	Hist_00027 "Hist_00027" (double matrix), size is 5000
	gamma_1 "gamma_1" (double), size is 360
	delta_1 "delta_1" (double), size is 360
	epsilon_1 "epsilon_1" (double), size is 360
	zeta_1 "zeta_1" (double), size is 360
	chi_1 "chi_1" (double), size is 360
	alpha_2 "alpha_2" (double), size is 360
	beta_2 "beta_2" (double), size is 360
	gamma_2 "gamma_2" (double), size is 360
	delta_2 "delta_2" (double), size is 360
	chi_2 "chi_2" (double), size is 360

DATAFILES (15 total):
  avg-rmsd-all.dat (Standard Data File):  AVERAGE_00016[avg] AVERAGE_00016[sd] AVERAGE_00016[ymin] AVERAGE_00016[ymax] AVERAGE_00016[yminidx] AVERAGE_00016[ymaxidx] AVERAGE_00016[names]
  rmsd-hist.dat (Standard Data File):  RMSD
  COM-hist.dat (Standard Data File):  CoM
  distO2O4-hist.dat (Standard Data File):  Hist_00025
  distN3-O5p-hist.dat (Standard Data File):  Hist_00026
  2dhist_rms-dist.gnu (Gnuplot File):  Hist_00027
  dihed_a2-hist.dat (Standard Data File):  gamma_1 alpha_2
  dihed_d1-hist.dat (Standard Data File):  delta_1
  dihed_e1-hist.dat (Standard Data File):  epsilon_1
  dihed_z1-hist.dat (Standard Data File):  zeta_1
  dihed_c1-hist.dat (Standard Data File):  chi_1
  dihed_b2-hist.dat (Standard Data File):  beta_2
  dihed_g2-hist.dat (Standard Data File):  gamma_2
  dihed_d2-hist.dat (Standard Data File):  delta_2
  dihed_c2-hist.dat (Standard Data File):  chi_2

RUN TIMING:
TIME:		Init               : 0.0001 s (  0.04%)
TIME:		Trajectory Process : 0.2923 s ( 78.49%)
TIME:		Action Post        : 0.0000 s (  0.00%)
TIME:		Analysis           : 0.0530 s ( 14.23%)
TIME:		Data File Write    : 0.0269 s (  7.23%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.3724 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 1.4874 seconds.
--------------------------------------------------------------------------------
To cite CPPTRAJ use:
Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
  Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
  Theory Comput., 2013, 9 (7), pp 3084-3095.