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

| Date/time: 06/02/16 18:07:45
| Available memory: 3.863 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.c2]
	Reading '../ctraj.c2' 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,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2]
    DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2, 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@N1 :2@C2 type chi]
    DIHEDRAL: [:2@O4']-[:2@C1']-[:2@N1]-[:2@C2]
              Output range is -180 to 180 degrees.
  [run]
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES (1 total):
 0: noWAt.topo.hmr, 64 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (1 total):
 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 18792 of 18792)
  Coordinate processing will occur on 18792 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*](40)
	Reference mask: [:1,2&!@H*](40)
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,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2]
	:1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 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@N1 :2@C2 type chi]
	 [:2@O4'](1) [:2@C1'](1) [:2@N1](1) [:2@C2](1)
----- ctraj.c2 (1-18792, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 18792 frames and processed 18792 frames.
TIME: Avg. throughput= 87552.8802 frames / second.

ACTION OUTPUT:

DATASETS (14 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 18792
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 18792
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 18792
	COM "COM" (double, distance), size is 18792
	g1 "g1" (double, torsion(gamma)), size is 18792
	d1 "d1" (double, torsion(delta)), size is 18792
	e1 "e1" (double, torsion(epsilon)), size is 18792
	z1 "z1" (double, torsion(zeta)), size is 18792
	c1 "c1" (double, torsion(chin)), size is 18792
	a2 "a2" (double, torsion(alpha)), size is 18792
	b2 "b2" (double, torsion(beta)), size is 18792
	g2 "g2" (double, torsion(gamma)), size is 18792
	d2 "d2" (double, torsion(delta)), size is 18792
	c2 "c2" (double, torsion(chin)), size is 18792

RUN TIMING:
TIME:		Init               : 0.0000 s (  0.02%)
TIME:		Trajectory Process : 0.2146 s ( 99.95%)
TIME:		Action Post        : 0.0000 s (  0.00%)
TIME:		Analysis           : 0.0000 s (  0.00%)
TIME:		Data File Write    : 0.0000 s (  0.02%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.2147 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, 64 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (1 total):
 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 18792 of 18792)
  Coordinate processing will occur on 18792 frames.

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

BEGIN TRAJECTORY PROCESSING:
----- ctraj.c2 (1-18792, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 18792 frames and processed 18792 frames.
TIME: Avg. throughput= 246643.3043 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: 18792 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 18792
  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: 18792 data points in each dimension.
	Hist: Allocating histogram, total bins = 100
	Warning: Frame 21 Coordinates out of bounds (-1)
	Warning: Frame 57 Coordinates out of bounds (-1)
	Warning: Frame 95 Coordinates out of bounds (-1)
	Warning: Frame 285 Coordinates out of bounds (-1)
	Warning: Frame 290 Coordinates out of bounds (-1)
	Warning: Frame 293 Coordinates out of bounds (-1)
	Warning: Frame 406 Coordinates out of bounds (-1)
	Warning: Frame 527 Coordinates out of bounds (-1)
	Warning: Frame 528 Coordinates out of bounds (-1)
	Warning: Frame 529 Coordinates out of bounds (-1)
	Warning: Frame 534 Coordinates out of bounds (-1)
	Warning: Frame 924 Coordinates out of bounds (-1)
	Warning: Frame 990 Coordinates out of bounds (-1)
	Warning: Frame 1013 Coordinates out of bounds (-1)
	Warning: Frame 1427 Coordinates out of bounds (-1)
	Warning: Frame 1447 Coordinates out of bounds (-1)
	Warning: Frame 1448 Coordinates out of bounds (-1)
	Warning: Frame 1449 Coordinates out of bounds (-1)
	Warning: Frame 1572 Coordinates out of bounds (-1)
	Warning: Frame 1716 Coordinates out of bounds (-1)
	Warning: Frame 2076 Coordinates out of bounds (-1)
	Warning: Frame 2261 Coordinates out of bounds (-1)
	Warning: Frame 2571 Coordinates out of bounds (-1)
	Warning: Frame 2672 Coordinates out of bounds (-1)
	Warning: Frame 2681 Coordinates out of bounds (-1)
	Warning: Frame 2841 Coordinates out of bounds (-1)
	Warning: Frame 2842 Coordinates out of bounds (-1)
	Warning: Frame 2856 Coordinates out of bounds (-1)
	Warning: Frame 2858 Coordinates out of bounds (-1)
	Warning: Frame 2859 Coordinates out of bounds (-1)
	Warning: Frame 2925 Coordinates out of bounds (-1)
	Warning: Frame 3038 Coordinates out of bounds (-1)
	Warning: Frame 3039 Coordinates out of bounds (-1)
	Warning: Frame 3084 Coordinates out of bounds (-1)
	Warning: Frame 3176 Coordinates out of bounds (-1)
	Warning: Frame 3177 Coordinates out of bounds (-1)
	Warning: Frame 3178 Coordinates out of bounds (-1)
	Warning: Frame 3179 Coordinates out of bounds (-1)
	Warning: Frame 3180 Coordinates out of bounds (-1)
	Warning: Frame 3181 Coordinates out of bounds (-1)
	Warning: Frame 3182 Coordinates out of bounds (-1)
	Warning: Frame 3303 Coordinates out of bounds (-1)
	Warning: Frame 3497 Coordinates out of bounds (-1)
	Warning: Frame 3517 Coordinates out of bounds (-1)
	Warning: Frame 3522 Coordinates out of bounds (-1)
	Warning: Frame 3584 Coordinates out of bounds (-1)
	Warning: Frame 3640 Coordinates out of bounds (-1)
	Warning: Frame 3641 Coordinates out of bounds (-1)
	Warning: Frame 3682 Coordinates out of bounds (-1)
	Warning: Frame 3689 Coordinates out of bounds (-1)
	Warning: Frame 3739 Coordinates out of bounds (-1)
	Warning: Frame 4093 Coordinates out of bounds (-1)
	Warning: Frame 4372 Coordinates out of bounds (-1)
	Warning: Frame 4373 Coordinates out of bounds (-1)
	Warning: Frame 4607 Coordinates out of bounds (-1)
	Warning: Frame 4608 Coordinates out of bounds (-1)
	Warning: Frame 4692 Coordinates out of bounds (-1)
	Warning: Frame 4693 Coordinates out of bounds (-1)
	Warning: Frame 4777 Coordinates out of bounds (-1)
	Warning: Frame 4810 Coordinates out of bounds (-1)
	Warning: Frame 4960 Coordinates out of bounds (-1)
	Warning: Frame 4961 Coordinates out of bounds (-1)
	Warning: Frame 4987 Coordinates out of bounds (-1)
	Warning: Frame 5061 Coordinates out of bounds (-1)
	Warning: Frame 5249 Coordinates out of bounds (-1)
	Warning: Frame 5399 Coordinates out of bounds (-1)
	Warning: Frame 5407 Coordinates out of bounds (-1)
	Warning: Frame 5754 Coordinates out of bounds (-1)
	Warning: Frame 5756 Coordinates out of bounds (-1)
	Warning: Frame 6064 Coordinates out of bounds (-1)
	Warning: Frame 6099 Coordinates out of bounds (-1)
	Warning: Frame 6100 Coordinates out of bounds (-1)
	Warning: Frame 6217 Coordinates out of bounds (-1)
	Warning: Frame 6283 Coordinates out of bounds (-1)
	Warning: Frame 6383 Coordinates out of bounds (-1)
	Warning: Frame 6389 Coordinates out of bounds (-1)
	Warning: Frame 6390 Coordinates out of bounds (-1)
	Warning: Frame 6542 Coordinates out of bounds (-1)
	Warning: Frame 6682 Coordinates out of bounds (-1)
	Warning: Frame 6713 Coordinates out of bounds (-1)
	Warning: Frame 6776 Coordinates out of bounds (-1)
	Warning: Frame 6804 Coordinates out of bounds (-1)
	Warning: Frame 6807 Coordinates out of bounds (-1)
	Warning: Frame 6817 Coordinates out of bounds (-1)
	Warning: Frame 6916 Coordinates out of bounds (-1)
	Warning: Frame 7009 Coordinates out of bounds (-1)
	Warning: Frame 7013 Coordinates out of bounds (-1)
	Warning: Frame 7194 Coordinates out of bounds (-1)
	Warning: Frame 7242 Coordinates out of bounds (-1)
	Warning: Frame 7243 Coordinates out of bounds (-1)
	Warning: Frame 7244 Coordinates out of bounds (-1)
	Warning: Frame 7579 Coordinates out of bounds (-1)
	Warning: Frame 7691 Coordinates out of bounds (-1)
	Warning: Frame 7717 Coordinates out of bounds (-1)
	Warning: Frame 7964 Coordinates out of bounds (-1)
	Warning: Frame 7992 Coordinates out of bounds (-1)
	Warning: Frame 8041 Coordinates out of bounds (-1)
	Warning: Frame 8042 Coordinates out of bounds (-1)
	Warning: Frame 8205 Coordinates out of bounds (-1)
	Warning: Frame 8207 Coordinates out of bounds (-1)
	Warning: Frame 8211 Coordinates out of bounds (-1)
	Warning: Frame 8362 Coordinates out of bounds (-1)
	Warning: Frame 8363 Coordinates out of bounds (-1)
	Warning: Frame 8638 Coordinates out of bounds (-1)
	Warning: Frame 8793 Coordinates out of bounds (-1)
	Warning: Frame 9007 Coordinates out of bounds (-1)
	Warning: Frame 9045 Coordinates out of bounds (-1)
	Warning: Frame 9286 Coordinates out of bounds (-1)
	Warning: Frame 9387 Coordinates out of bounds (-1)
	Warning: Frame 9409 Coordinates out of bounds (-1)
	Warning: Frame 9647 Coordinates out of bounds (-1)
	Warning: Frame 9735 Coordinates out of bounds (-1)
	Warning: Frame 9738 Coordinates out of bounds (-1)
	Warning: Frame 9754 Coordinates out of bounds (-1)
	Warning: Frame 9795 Coordinates out of bounds (-1)
	Warning: Frame 9944 Coordinates out of bounds (-1)
	Warning: Frame 10011 Coordinates out of bounds (-1)
	Warning: Frame 10080 Coordinates out of bounds (-1)
	Warning: Frame 10234 Coordinates out of bounds (-1)
	Warning: Frame 10236 Coordinates out of bounds (-1)
	Warning: Frame 10342 Coordinates out of bounds (-1)
	Warning: Frame 10346 Coordinates out of bounds (-1)
	Warning: Frame 10396 Coordinates out of bounds (-1)
	Warning: Frame 10398 Coordinates out of bounds (-1)
	Warning: Frame 10804 Coordinates out of bounds (-1)
	Warning: Frame 10990 Coordinates out of bounds (-1)
	Warning: Frame 11158 Coordinates out of bounds (-1)
	Warning: Frame 11487 Coordinates out of bounds (-1)
	Warning: Frame 11636 Coordinates out of bounds (-1)
	Warning: Frame 12014 Coordinates out of bounds (-1)
	Warning: Frame 12491 Coordinates out of bounds (-1)
	Warning: Frame 12521 Coordinates out of bounds (-1)
	Warning: Frame 12573 Coordinates out of bounds (-1)
	Warning: Frame 12691 Coordinates out of bounds (-1)
	Warning: Frame 12940 Coordinates out of bounds (-1)
	Warning: Frame 12959 Coordinates out of bounds (-1)
	Warning: Frame 12972 Coordinates out of bounds (-1)
	Warning: Frame 13038 Coordinates out of bounds (-1)
	Warning: Frame 13138 Coordinates out of bounds (-1)
	Warning: Frame 13369 Coordinates out of bounds (-1)
	Warning: Frame 13370 Coordinates out of bounds (-1)
	Warning: Frame 13476 Coordinates out of bounds (-1)
	Warning: Frame 13485 Coordinates out of bounds (-1)
	Warning: Frame 13488 Coordinates out of bounds (-1)
	Warning: Frame 13761 Coordinates out of bounds (-1)
	Warning: Frame 13873 Coordinates out of bounds (-1)
	Warning: Frame 14038 Coordinates out of bounds (-1)
	Warning: Frame 14039 Coordinates out of bounds (-1)
	Warning: Frame 14147 Coordinates out of bounds (-1)
	Warning: Frame 14148 Coordinates out of bounds (-1)
	Warning: Frame 14302 Coordinates out of bounds (-1)
	Warning: Frame 14371 Coordinates out of bounds (-1)
	Warning: Frame 14423 Coordinates out of bounds (-1)
	Warning: Frame 14454 Coordinates out of bounds (-1)
	Warning: Frame 14577 Coordinates out of bounds (-1)
	Warning: Frame 14607 Coordinates out of bounds (-1)
	Warning: Frame 14608 Coordinates out of bounds (-1)
	Warning: Frame 14636 Coordinates out of bounds (-1)
	Warning: Frame 14775 Coordinates out of bounds (-1)
	Warning: Frame 14776 Coordinates out of bounds (-1)
	Warning: Frame 14826 Coordinates out of bounds (-1)
	Warning: Frame 14827 Coordinates out of bounds (-1)
	Warning: Frame 15118 Coordinates out of bounds (-1)
	Warning: Frame 15297 Coordinates out of bounds (-1)
	Warning: Frame 15348 Coordinates out of bounds (-1)
	Warning: Frame 15349 Coordinates out of bounds (-1)
	Warning: Frame 15517 Coordinates out of bounds (-1)
	Warning: Frame 15649 Coordinates out of bounds (-1)
	Warning: Frame 15650 Coordinates out of bounds (-1)
	Warning: Frame 15706 Coordinates out of bounds (-1)
	Warning: Frame 15708 Coordinates out of bounds (-1)
	Warning: Frame 15975 Coordinates out of bounds (-1)
	Warning: Frame 16089 Coordinates out of bounds (-1)
	Warning: Frame 16256 Coordinates out of bounds (-1)
	Warning: Frame 16275 Coordinates out of bounds (-1)
	Warning: Frame 16276 Coordinates out of bounds (-1)
	Warning: Frame 16290 Coordinates out of bounds (-1)
	Warning: Frame 16340 Coordinates out of bounds (-1)
	Warning: Frame 16348 Coordinates out of bounds (-1)
	Warning: Frame 16413 Coordinates out of bounds (-1)
	Warning: Frame 16445 Coordinates out of bounds (-1)
	Warning: Frame 16604 Coordinates out of bounds (-1)
	Warning: Frame 16605 Coordinates out of bounds (-1)
	Warning: Frame 16606 Coordinates out of bounds (-1)
	Warning: Frame 16776 Coordinates out of bounds (-1)
	Warning: Frame 17407 Coordinates out of bounds (-1)
	Warning: Frame 17458 Coordinates out of bounds (-1)
	Warning: Frame 17498 Coordinates out of bounds (-1)
	Warning: Frame 17619 Coordinates out of bounds (-1)
	Warning: Frame 17620 Coordinates out of bounds (-1)
	Warning: Frame 17854 Coordinates out of bounds (-1)
	Warning: Frame 17855 Coordinates out of bounds (-1)
	Warning: Frame 18019 Coordinates out of bounds (-1)
	Warning: Frame 18164 Coordinates out of bounds (-1)
	Warning: Frame 18171 Coordinates out of bounds (-1)
	Warning: Frame 18177 Coordinates out of bounds (-1)
	Warning: Frame 18299 Coordinates out of bounds (-1)
	Warning: Frame 18362 Coordinates out of bounds (-1)
	Warning: Frame 18417 Coordinates out of bounds (-1)
	Warning: Frame 18452 Coordinates out of bounds (-1)
	Warning: Frame 18461 Coordinates out of bounds (-1)
	Warning: Frame 18591 Coordinates out of bounds (-1)
	Warning: Frame 18621 Coordinates out of bounds (-1)
	Warning: Frame 18623 Coordinates out of bounds (-1)
	Warning: Frame 18732 Coordinates out of bounds (-1)
	Warning: Frame 18734 Coordinates out of bounds (-1)
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 18586
  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: 18792 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 18792
  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: 18792 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 18792
  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: 18792 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 18792
  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: 18792 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 18792
  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: 18792 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 18792
  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: 18792 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 18792
  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: 18792 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 18792
  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: 18792 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 18792
  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: 18792 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 18792
  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: 18792 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 18792
  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: 18792 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 18792
  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: 18792 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 18792
  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: 18792 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 18792

TIME: Analyses took 0.0065 seconds.

DATASETS (36 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 18792
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 18792
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 18792
	COM "COM" (double, distance), size is 18792
	g1 "g1" (double, torsion(gamma)), size is 18792
	d1 "d1" (double, torsion(delta)), size is 18792
	e1 "e1" (double, torsion(epsilon)), size is 18792
	z1 "z1" (double, torsion(zeta)), size is 18792
	c1 "c1" (double, torsion(chin)), size is 18792
	a2 "a2" (double, torsion(alpha)), size is 18792
	b2 "b2" (double, torsion(beta)), size is 18792
	g2 "g2" (double, torsion(gamma)), size is 18792
	d2 "d2" (double, torsion(delta)), size is 18792
	c2 "c2" (double, torsion(chin)), size is 18792
	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               : 0.0000 s (  0.03%)
TIME:		Trajectory Process : 0.0762 s ( 55.01%)
TIME:		Action Post        : 0.0000 s (  0.00%)
TIME:		Analysis           : 0.0065 s (  4.69%)
TIME:		Data File Write    : 0.0557 s ( 40.25%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.1385 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 0.6922 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.