CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/03/16 12:32:25
| Available memory: 1.248 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.c0]
	Reading '../ctraj.c0' 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,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6]
    DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6, 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 chin]
    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 chin]
    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, 67 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (1 total):
 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 204603 of 204603)
  Coordinate processing will occur on 204603 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*](43)
	Reference mask: [:1,2&!@H*](43)
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,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6]
	:1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (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 chin]
	 [: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 chin]
	 [:2@O4'](1) [:2@C1'](1) [:2@N9](1) [:2@C4](1)
----- ctraj.c0 (1-204603, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 204603 frames and processed 204603 frames.
TIME: Avg. throughput= 143527.7711 frames / second.

ACTION OUTPUT:

DATASETS (14 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 204603
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 204603
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 204603
	COM "COM" (double, distance), size is 204603
	g1 "g1" (double, torsion(gamma)), size is 204603
	d1 "d1" (double, torsion(delta)), size is 204603
	e1 "e1" (double, torsion(epsilon)), size is 204603
	z1 "z1" (double, torsion(zeta)), size is 204603
	c1 "c1" (double, torsion(chin)), size is 204603
	a2 "a2" (double, torsion(alpha)), size is 204603
	b2 "b2" (double, torsion(beta)), size is 204603
	g2 "g2" (double, torsion(gamma)), size is 204603
	d2 "d2" (double, torsion(delta)), size is 204603
	c2 "c2" (double, torsion(chin)), size is 204603

RUN TIMING:
TIME:		Init               : 0.0001 s (  0.00%)
TIME:		Trajectory Process : 1.4255 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 1.4256 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_g1-hist.dat name gamma_1 norm]
	Hist: dihed_g1-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, 67 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (1 total):
 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 204603 of 204603)
  Coordinate processing will occur on 204603 frames.

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

BEGIN TRAJECTORY PROCESSING:
----- ctraj.c0 (1-204603, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 204603 frames and processed 204603 frames.
TIME: Avg. throughput= 1015142.5694 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: 204603 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 204603
  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: 204603 data points in each dimension.
	Hist: Allocating histogram, total bins = 100
	Warning: Frame 644 Coordinates out of bounds (-1)
	Warning: Frame 1376 Coordinates out of bounds (-1)
	Warning: Frame 2385 Coordinates out of bounds (-1)
	Warning: Frame 2531 Coordinates out of bounds (-1)
	Warning: Frame 3420 Coordinates out of bounds (-1)
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	Warning: Frame 100221 Coordinates out of bounds (-1)
	Warning: Frame 100222 Coordinates out of bounds (-1)
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	Warning: Frame 100870 Coordinates out of bounds (-1)
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	Warning: Frame 105372 Coordinates out of bounds (-1)
	Warning: Frame 105467 Coordinates out of bounds (-1)
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	Warning: Frame 106250 Coordinates out of bounds (-1)
	Warning: Frame 106307 Coordinates out of bounds (-1)
	Warning: Frame 106469 Coordinates out of bounds (-1)
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	Warning: Frame 106825 Coordinates out of bounds (-1)
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	Warning: Frame 107161 Coordinates out of bounds (-1)
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	Warning: Frame 107599 Coordinates out of bounds (-1)
	Warning: Frame 107603 Coordinates out of bounds (-1)
	Warning: Frame 107607 Coordinates out of bounds (-1)
	Warning: Frame 107615 Coordinates out of bounds (-1)
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	Warning: Frame 108223 Coordinates out of bounds (-1)
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	Warning: Frame 108725 Coordinates out of bounds (-1)
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	Warning: Frame 108833 Coordinates out of bounds (-1)
	Warning: Frame 109260 Coordinates out of bounds (-1)
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	Warning: Frame 109356 Coordinates out of bounds (-1)
	Warning: Frame 109555 Coordinates out of bounds (-1)
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	Warning: Frame 110022 Coordinates out of bounds (-1)
	Warning: Frame 110100 Coordinates out of bounds (-1)
	Warning: Frame 110357 Coordinates out of bounds (-1)
	Warning: Frame 110729 Coordinates out of bounds (-1)
	Warning: Frame 110927 Coordinates out of bounds (-1)
	Warning: Frame 110973 Coordinates out of bounds (-1)
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	Warning: Frame 111855 Coordinates out of bounds (-1)
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	Warning: Frame 111989 Coordinates out of bounds (-1)
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	Warning: Frame 115188 Coordinates out of bounds (-1)
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	Warning: Frame 115578 Coordinates out of bounds (-1)
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	Warning: Frame 115666 Coordinates out of bounds (-1)
	Warning: Frame 115715 Coordinates out of bounds (-1)
	Warning: Frame 115878 Coordinates out of bounds (-1)
	Warning: Frame 115974 Coordinates out of bounds (-1)
	Warning: Frame 116009 Coordinates out of bounds (-1)
	Warning: Frame 116356 Coordinates out of bounds (-1)
	Warning: Frame 116697 Coordinates out of bounds (-1)
	Warning: Frame 116914 Coordinates out of bounds (-1)
	Warning: Frame 116928 Coordinates out of bounds (-1)
	Warning: Frame 116966 Coordinates out of bounds (-1)
	Warning: Frame 117192 Coordinates out of bounds (-1)
	Warning: Frame 117234 Coordinates out of bounds (-1)
	Warning: Frame 117235 Coordinates out of bounds (-1)
	Warning: Frame 117318 Coordinates out of bounds (-1)
	Warning: Frame 117682 Coordinates out of bounds (-1)
	Warning: Frame 117699 Coordinates out of bounds (-1)
	Warning: Frame 117700 Coordinates out of bounds (-1)
	Warning: Frame 117702 Coordinates out of bounds (-1)
	Warning: Frame 117709 Coordinates out of bounds (-1)
	Warning: Frame 117810 Coordinates out of bounds (-1)
	Warning: Frame 117811 Coordinates out of bounds (-1)
	Warning: Frame 117812 Coordinates out of bounds (-1)
	Warning: Frame 117875 Coordinates out of bounds (-1)
	Warning: Frame 118465 Coordinates out of bounds (-1)
	Warning: Frame 118564 Coordinates out of bounds (-1)
	Warning: Frame 118569 Coordinates out of bounds (-1)
	Warning: Frame 118585 Coordinates out of bounds (-1)
	Warning: Frame 118705 Coordinates out of bounds (-1)
	Warning: Frame 118862 Coordinates out of bounds (-1)
	Warning: Frame 118872 Coordinates out of bounds (-1)
	Warning: Frame 118874 Coordinates out of bounds (-1)
	Warning: Frame 118875 Coordinates out of bounds (-1)
	Warning: Frame 118919 Coordinates out of bounds (-1)
	Warning: Frame 119143 Coordinates out of bounds (-1)
	Warning: Frame 119154 Coordinates out of bounds (-1)
	Warning: Frame 119161 Coordinates out of bounds (-1)
	Warning: Frame 119163 Coordinates out of bounds (-1)
	Warning: Frame 119194 Coordinates out of bounds (-1)
	Warning: Frame 119195 Coordinates out of bounds (-1)
	Warning: Frame 119200 Coordinates out of bounds (-1)
	Warning: Frame 119202 Coordinates out of bounds (-1)
	Warning: Frame 119442 Coordinates out of bounds (-1)
	Warning: Frame 119526 Coordinates out of bounds (-1)
	Warning: Frame 120013 Coordinates out of bounds (-1)
	Warning: Frame 120066 Coordinates out of bounds (-1)
	Warning: Frame 120176 Coordinates out of bounds (-1)
	Warning: Frame 120180 Coordinates out of bounds (-1)
	Warning: Frame 120228 Coordinates out of bounds (-1)
	Warning: Frame 120392 Coordinates out of bounds (-1)
	Warning: Frame 120817 Coordinates out of bounds (-1)
	Warning: Frame 120966 Coordinates out of bounds (-1)
	Warning: Frame 120975 Coordinates out of bounds (-1)
	Warning: Frame 121111 Coordinates out of bounds (-1)
	Warning: Frame 121112 Coordinates out of bounds (-1)
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	Warning: Frame 121555 Coordinates out of bounds (-1)
	Warning: Frame 121592 Coordinates out of bounds (-1)
	Warning: Frame 121631 Coordinates out of bounds (-1)
	Warning: Frame 121643 Coordinates out of bounds (-1)
	Warning: Frame 121941 Coordinates out of bounds (-1)
	Warning: Frame 121986 Coordinates out of bounds (-1)
	Warning: Frame 122044 Coordinates out of bounds (-1)
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	Warning: Frame 122200 Coordinates out of bounds (-1)
	Warning: Frame 122564 Coordinates out of bounds (-1)
	Warning: Frame 122583 Coordinates out of bounds (-1)
	Warning: Frame 122639 Coordinates out of bounds (-1)
	Warning: Frame 122653 Coordinates out of bounds (-1)
	Warning: Frame 122669 Coordinates out of bounds (-1)
	Warning: Frame 122889 Coordinates out of bounds (-1)
	Warning: Frame 122890 Coordinates out of bounds (-1)
	Warning: Frame 123065 Coordinates out of bounds (-1)
	Warning: Frame 123123 Coordinates out of bounds (-1)
	Warning: Frame 123135 Coordinates out of bounds (-1)
	Warning: Frame 123136 Coordinates out of bounds (-1)
	Warning: Frame 123517 Coordinates out of bounds (-1)
	Warning: Frame 123803 Coordinates out of bounds (-1)
	Warning: Frame 123945 Coordinates out of bounds (-1)
	Warning: Frame 124174 Coordinates out of bounds (-1)
	Warning: Frame 124183 Coordinates out of bounds (-1)
	Warning: Frame 124186 Coordinates out of bounds (-1)
	Warning: Frame 124191 Coordinates out of bounds (-1)
	Warning: Frame 124440 Coordinates out of bounds (-1)
	Warning: Frame 124566 Coordinates out of bounds (-1)
	Warning: Frame 124622 Coordinates out of bounds (-1)
	Warning: Frame 124737 Coordinates out of bounds (-1)
	Warning: Frame 124944 Coordinates out of bounds (-1)
	Warning: Frame 125024 Coordinates out of bounds (-1)
	Warning: Frame 125025 Coordinates out of bounds (-1)
	Warning: Frame 125150 Coordinates out of bounds (-1)
	Warning: Frame 125268 Coordinates out of bounds (-1)
	Warning: Frame 125370 Coordinates out of bounds (-1)
	Warning: Frame 125371 Coordinates out of bounds (-1)
	Warning: Frame 125385 Coordinates out of bounds (-1)
	Warning: Frame 125518 Coordinates out of bounds (-1)
	Warning: Frame 125519 Coordinates out of bounds (-1)
	Warning: Frame 125535 Coordinates out of bounds (-1)
	Warning: Frame 125556 Coordinates out of bounds (-1)
	Warning: Frame 125847 Coordinates out of bounds (-1)
	Warning: Frame 128385 Coordinates out of bounds (-1)
	Warning: Frame 130403 Coordinates out of bounds (-1)
	Warning: Frame 132303 Coordinates out of bounds (-1)
	Warning: Frame 133240 Coordinates out of bounds (-1)
	Warning: Frame 135547 Coordinates out of bounds (-1)
	Warning: Frame 136215 Coordinates out of bounds (-1)
	Warning: Frame 137498 Coordinates out of bounds (-1)
	Warning: Frame 141456 Coordinates out of bounds (-1)
	Warning: Frame 141457 Coordinates out of bounds (-1)
	Warning: Frame 141458 Coordinates out of bounds (-1)
	Warning: Frame 141545 Coordinates out of bounds (-1)
	Warning: Frame 141562 Coordinates out of bounds (-1)
	Warning: Frame 141576 Coordinates out of bounds (-1)
	Warning: Frame 141577 Coordinates out of bounds (-1)
	Warning: Frame 142693 Coordinates out of bounds (-1)
	Warning: Frame 143775 Coordinates out of bounds (-1)
	Warning: Frame 143789 Coordinates out of bounds (-1)
	Warning: Frame 146355 Coordinates out of bounds (-1)
	Warning: Frame 146358 Coordinates out of bounds (-1)
	Warning: Frame 147337 Coordinates out of bounds (-1)
	Warning: Frame 151153 Coordinates out of bounds (-1)
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	Warning: Frame 153618 Coordinates out of bounds (-1)
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	Warning: Frame 155271 Coordinates out of bounds (-1)
	Warning: Frame 158100 Coordinates out of bounds (-1)
	Warning: Frame 158101 Coordinates out of bounds (-1)
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	Warning: Frame 160832 Coordinates out of bounds (-1)
	Warning: Frame 161876 Coordinates out of bounds (-1)
	Warning: Frame 163605 Coordinates out of bounds (-1)
	Warning: Frame 163763 Coordinates out of bounds (-1)
	Warning: Frame 163770 Coordinates out of bounds (-1)
	Warning: Frame 164144 Coordinates out of bounds (-1)
	Warning: Frame 165003 Coordinates out of bounds (-1)
	Warning: Frame 165004 Coordinates out of bounds (-1)
	Warning: Frame 165006 Coordinates out of bounds (-1)
	Warning: Frame 165009 Coordinates out of bounds (-1)
	Warning: Frame 165010 Coordinates out of bounds (-1)
	Warning: Frame 165663 Coordinates out of bounds (-1)
	Warning: Frame 168140 Coordinates out of bounds (-1)
	Warning: Frame 168142 Coordinates out of bounds (-1)
	Warning: Frame 169924 Coordinates out of bounds (-1)
	Warning: Frame 169928 Coordinates out of bounds (-1)
	Warning: Frame 171373 Coordinates out of bounds (-1)
	Warning: Frame 171375 Coordinates out of bounds (-1)
	Warning: Frame 172917 Coordinates out of bounds (-1)
	Warning: Frame 172918 Coordinates out of bounds (-1)
	Warning: Frame 172919 Coordinates out of bounds (-1)
	Warning: Frame 172921 Coordinates out of bounds (-1)
	Warning: Frame 173730 Coordinates out of bounds (-1)
	Warning: Frame 173731 Coordinates out of bounds (-1)
	Warning: Frame 175947 Coordinates out of bounds (-1)
	Warning: Frame 176127 Coordinates out of bounds (-1)
	Warning: Frame 176128 Coordinates out of bounds (-1)
	Warning: Frame 176821 Coordinates out of bounds (-1)
	Warning: Frame 179337 Coordinates out of bounds (-1)
	Warning: Frame 179338 Coordinates out of bounds (-1)
	Warning: Frame 179339 Coordinates out of bounds (-1)
	Warning: Frame 180106 Coordinates out of bounds (-1)
	Warning: Frame 181994 Coordinates out of bounds (-1)
	Warning: Frame 184270 Coordinates out of bounds (-1)
	Warning: Frame 186141 Coordinates out of bounds (-1)
	Warning: Frame 186550 Coordinates out of bounds (-1)
	Warning: Frame 188402 Coordinates out of bounds (-1)
	Warning: Frame 189871 Coordinates out of bounds (-1)
	Warning: Frame 189872 Coordinates out of bounds (-1)
	Warning: Frame 190843 Coordinates out of bounds (-1)
	Warning: Frame 190844 Coordinates out of bounds (-1)
	Warning: Frame 191075 Coordinates out of bounds (-1)
	Warning: Frame 191079 Coordinates out of bounds (-1)
	Warning: Frame 191088 Coordinates out of bounds (-1)
	Warning: Frame 192206 Coordinates out of bounds (-1)
	Warning: Frame 192414 Coordinates out of bounds (-1)
	Warning: Frame 192416 Coordinates out of bounds (-1)
	Warning: Frame 196818 Coordinates out of bounds (-1)
	Warning: Frame 198765 Coordinates out of bounds (-1)
	Warning: Frame 200108 Coordinates out of bounds (-1)
	Warning: Frame 200109 Coordinates out of bounds (-1)
	Warning: Frame 200901 Coordinates out of bounds (-1)
	Warning: Frame 202221 Coordinates out of bounds (-1)
	Warning: Frame 203331 Coordinates out of bounds (-1)
	Warning: Frame 203332 Coordinates out of bounds (-1)
	Warning: Frame 203333 Coordinates out of bounds (-1)
	Warning: Frame 203334 Coordinates out of bounds (-1)
	Warning: Frame 203335 Coordinates out of bounds (-1)
	Warning: Frame 203726 Coordinates out of bounds (-1)
	Warning: Frame 203727 Coordinates out of bounds (-1)
	Warning: Frame 203956 Coordinates out of bounds (-1)
	Warning: Frame 203957 Coordinates out of bounds (-1)
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 204011
  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: 204603 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 204603
  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: 204603 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 204603
  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: 204603 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 204603
  6: [hist g1,-180,180,1 out dihed_g1-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: 204603 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 204603
  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: 204603 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 204603
  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: 204603 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 204603
  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: 204603 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 204603
  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: 204603 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 204603
  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: 204603 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 204603
  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: 204603 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 204603
  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: 204603 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 204603
  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: 204603 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 204603
  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: 204603 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 204603

TIME: Analyses took 0.0346 seconds.

DATASETS (36 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 204603
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 204603
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 204603
	COM "COM" (double, distance), size is 204603
	g1 "g1" (double, torsion(gamma)), size is 204603
	d1 "d1" (double, torsion(delta)), size is 204603
	e1 "e1" (double, torsion(epsilon)), size is 204603
	z1 "z1" (double, torsion(zeta)), size is 204603
	c1 "c1" (double, torsion(chin)), size is 204603
	a2 "a2" (double, torsion(alpha)), size is 204603
	b2 "b2" (double, torsion(beta)), size is 204603
	g2 "g2" (double, torsion(gamma)), size is 204603
	d2 "d2" (double, torsion(delta)), size is 204603
	c2 "c2" (double, torsion(chin)), size is 204603
	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 (16 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_g1-hist.dat (Standard Data File):  gamma_1
  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_a2-hist.dat (Standard Data File):  alpha_2
  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 (  0.03%)
TIME:		Trajectory Process : 0.2016 s ( 70.87%)
TIME:		Action Post        : 0.0000 s (  0.00%)
TIME:		Analysis           : 0.0346 s ( 12.17%)
TIME:		Data File Write    : 0.0481 s ( 16.92%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.2844 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 1.7203 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.