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

| Date/time: 06/02/16 18:13:29
| Available memory: 3.783 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,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.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 24389 of 24389)
  Coordinate processing will occur on 24389 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.c1 (1-24389, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 24389 frames and processed 24389 frames.
TIME: Avg. throughput= 109486.5280 frames / second.

ACTION OUTPUT:

DATASETS (14 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 24389
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 24389
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 24389
	COM "COM" (double, distance), size is 24389
	g1 "g1" (double, torsion(gamma)), size is 24389
	d1 "d1" (double, torsion(delta)), size is 24389
	e1 "e1" (double, torsion(epsilon)), size is 24389
	z1 "z1" (double, torsion(zeta)), size is 24389
	c1 "c1" (double, torsion(chin)), size is 24389
	a2 "a2" (double, torsion(alpha)), size is 24389
	b2 "b2" (double, torsion(beta)), size is 24389
	g2 "g2" (double, torsion(gamma)), size is 24389
	d2 "d2" (double, torsion(delta)), size is 24389
	c2 "c2" (double, torsion(chin)), size is 24389

RUN TIMING:
TIME:		Init               : 0.0000 s (  0.02%)
TIME:		Trajectory Process : 0.2228 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 0.2229 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.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 24389 of 24389)
  Coordinate processing will occur on 24389 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 (1-24389, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 24389 frames and processed 24389 frames.
TIME: Avg. throughput= 254952.3839 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: 24389 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 24389
  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: 24389 data points in each dimension.
	Hist: Allocating histogram, total bins = 100
	Warning: Frame 33 Coordinates out of bounds (-1)
	Warning: Frame 69 Coordinates out of bounds (-1)
	Warning: Frame 592 Coordinates out of bounds (-1)
	Warning: Frame 600 Coordinates out of bounds (-1)
	Warning: Frame 601 Coordinates out of bounds (-1)
	Warning: Frame 723 Coordinates out of bounds (-1)
	Warning: Frame 750 Coordinates out of bounds (-1)
	Warning: Frame 777 Coordinates out of bounds (-1)
	Warning: Frame 829 Coordinates out of bounds (-1)
	Warning: Frame 1149 Coordinates out of bounds (-1)
	Warning: Frame 1150 Coordinates out of bounds (-1)
	Warning: Frame 1187 Coordinates out of bounds (-1)
	Warning: Frame 1193 Coordinates out of bounds (-1)
	Warning: Frame 1701 Coordinates out of bounds (-1)
	Warning: Frame 1801 Coordinates out of bounds (-1)
	Warning: Frame 1817 Coordinates out of bounds (-1)
	Warning: Frame 1825 Coordinates out of bounds (-1)
	Warning: Frame 2371 Coordinates out of bounds (-1)
	Warning: Frame 2648 Coordinates out of bounds (-1)
	Warning: Frame 2807 Coordinates out of bounds (-1)
	Warning: Frame 3156 Coordinates out of bounds (-1)
	Warning: Frame 3223 Coordinates out of bounds (-1)
	Warning: Frame 3402 Coordinates out of bounds (-1)
	Warning: Frame 3714 Coordinates out of bounds (-1)
	Warning: Frame 3722 Coordinates out of bounds (-1)
	Warning: Frame 3723 Coordinates out of bounds (-1)
	Warning: Frame 3787 Coordinates out of bounds (-1)
	Warning: Frame 3788 Coordinates out of bounds (-1)
	Warning: Frame 4163 Coordinates out of bounds (-1)
	Warning: Frame 4302 Coordinates out of bounds (-1)
	Warning: Frame 4683 Coordinates out of bounds (-1)
	Warning: Frame 4996 Coordinates out of bounds (-1)
	Warning: Frame 5012 Coordinates out of bounds (-1)
	Warning: Frame 5018 Coordinates out of bounds (-1)
	Warning: Frame 5023 Coordinates out of bounds (-1)
	Warning: Frame 5239 Coordinates out of bounds (-1)
	Warning: Frame 5504 Coordinates out of bounds (-1)
	Warning: Frame 6248 Coordinates out of bounds (-1)
	Warning: Frame 6626 Coordinates out of bounds (-1)
	Warning: Frame 8010 Coordinates out of bounds (-1)
	Warning: Frame 8358 Coordinates out of bounds (-1)
	Warning: Frame 8366 Coordinates out of bounds (-1)
	Warning: Frame 8377 Coordinates out of bounds (-1)
	Warning: Frame 8633 Coordinates out of bounds (-1)
	Warning: Frame 8790 Coordinates out of bounds (-1)
	Warning: Frame 9296 Coordinates out of bounds (-1)
	Warning: Frame 9298 Coordinates out of bounds (-1)
	Warning: Frame 9463 Coordinates out of bounds (-1)
	Warning: Frame 9468 Coordinates out of bounds (-1)
	Warning: Frame 9548 Coordinates out of bounds (-1)
	Warning: Frame 9549 Coordinates out of bounds (-1)
	Warning: Frame 9704 Coordinates out of bounds (-1)
	Warning: Frame 9721 Coordinates out of bounds (-1)
	Warning: Frame 9870 Coordinates out of bounds (-1)
	Warning: Frame 9941 Coordinates out of bounds (-1)
	Warning: Frame 10153 Coordinates out of bounds (-1)
	Warning: Frame 10195 Coordinates out of bounds (-1)
	Warning: Frame 10248 Coordinates out of bounds (-1)
	Warning: Frame 11172 Coordinates out of bounds (-1)
	Warning: Frame 11311 Coordinates out of bounds (-1)
	Warning: Frame 11349 Coordinates out of bounds (-1)
	Warning: Frame 11565 Coordinates out of bounds (-1)
	Warning: Frame 11566 Coordinates out of bounds (-1)
	Warning: Frame 11651 Coordinates out of bounds (-1)
	Warning: Frame 11759 Coordinates out of bounds (-1)
	Warning: Frame 12038 Coordinates out of bounds (-1)
	Warning: Frame 12693 Coordinates out of bounds (-1)
	Warning: Frame 12820 Coordinates out of bounds (-1)
	Warning: Frame 13282 Coordinates out of bounds (-1)
	Warning: Frame 13504 Coordinates out of bounds (-1)
	Warning: Frame 13779 Coordinates out of bounds (-1)
	Warning: Frame 14168 Coordinates out of bounds (-1)
	Warning: Frame 14169 Coordinates out of bounds (-1)
	Warning: Frame 14325 Coordinates out of bounds (-1)
	Warning: Frame 14326 Coordinates out of bounds (-1)
	Warning: Frame 14526 Coordinates out of bounds (-1)
	Warning: Frame 14794 Coordinates out of bounds (-1)
	Warning: Frame 15061 Coordinates out of bounds (-1)
	Warning: Frame 15880 Coordinates out of bounds (-1)
	Warning: Frame 16105 Coordinates out of bounds (-1)
	Warning: Frame 16152 Coordinates out of bounds (-1)
	Warning: Frame 16395 Coordinates out of bounds (-1)
	Warning: Frame 16480 Coordinates out of bounds (-1)
	Warning: Frame 16513 Coordinates out of bounds (-1)
	Warning: Frame 16601 Coordinates out of bounds (-1)
	Warning: Frame 16602 Coordinates out of bounds (-1)
	Warning: Frame 16603 Coordinates out of bounds (-1)
	Warning: Frame 16671 Coordinates out of bounds (-1)
	Warning: Frame 16780 Coordinates out of bounds (-1)
	Warning: Frame 16967 Coordinates out of bounds (-1)
	Warning: Frame 17406 Coordinates out of bounds (-1)
	Warning: Frame 17752 Coordinates out of bounds (-1)
	Warning: Frame 17871 Coordinates out of bounds (-1)
	Warning: Frame 17982 Coordinates out of bounds (-1)
	Warning: Frame 18118 Coordinates out of bounds (-1)
	Warning: Frame 18510 Coordinates out of bounds (-1)
	Warning: Frame 19210 Coordinates out of bounds (-1)
	Warning: Frame 19213 Coordinates out of bounds (-1)
	Warning: Frame 19216 Coordinates out of bounds (-1)
	Warning: Frame 19218 Coordinates out of bounds (-1)
	Warning: Frame 19616 Coordinates out of bounds (-1)
	Warning: Frame 19884 Coordinates out of bounds (-1)
	Warning: Frame 19905 Coordinates out of bounds (-1)
	Warning: Frame 20031 Coordinates out of bounds (-1)
	Warning: Frame 20113 Coordinates out of bounds (-1)
	Warning: Frame 20300 Coordinates out of bounds (-1)
	Warning: Frame 20301 Coordinates out of bounds (-1)
	Warning: Frame 20413 Coordinates out of bounds (-1)
	Warning: Frame 20761 Coordinates out of bounds (-1)
	Warning: Frame 20887 Coordinates out of bounds (-1)
	Warning: Frame 21010 Coordinates out of bounds (-1)
	Warning: Frame 21011 Coordinates out of bounds (-1)
	Warning: Frame 21155 Coordinates out of bounds (-1)
	Warning: Frame 21157 Coordinates out of bounds (-1)
	Warning: Frame 21158 Coordinates out of bounds (-1)
	Warning: Frame 21253 Coordinates out of bounds (-1)
	Warning: Frame 21346 Coordinates out of bounds (-1)
	Warning: Frame 21361 Coordinates out of bounds (-1)
	Warning: Frame 21372 Coordinates out of bounds (-1)
	Warning: Frame 22373 Coordinates out of bounds (-1)
	Warning: Frame 22467 Coordinates out of bounds (-1)
	Warning: Frame 22657 Coordinates out of bounds (-1)
	Warning: Frame 22765 Coordinates out of bounds (-1)
	Warning: Frame 22796 Coordinates out of bounds (-1)
	Warning: Frame 22850 Coordinates out of bounds (-1)
	Warning: Frame 22914 Coordinates out of bounds (-1)
	Warning: Frame 22915 Coordinates out of bounds (-1)
	Warning: Frame 23390 Coordinates out of bounds (-1)
	Warning: Frame 24035 Coordinates out of bounds (-1)
	Warning: Frame 24036 Coordinates out of bounds (-1)
	Warning: Frame 24291 Coordinates out of bounds (-1)
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 24258
  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: 24389 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 24389
  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: 24389 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 24389
  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: 24389 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 24389
  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: 24389 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 24389
  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: 24389 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 24389
  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: 24389 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 24389
  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: 24389 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 24389
  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: 24389 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 24389
  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: 24389 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 24389
  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: 24389 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 24389
  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: 24389 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 24389
  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: 24389 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 24389
  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: 24389 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 24389

TIME: Analyses took 0.0084 seconds.

DATASETS (36 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 24389
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 24389
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 24389
	COM "COM" (double, distance), size is 24389
	g1 "g1" (double, torsion(gamma)), size is 24389
	d1 "d1" (double, torsion(delta)), size is 24389
	e1 "e1" (double, torsion(epsilon)), size is 24389
	z1 "z1" (double, torsion(zeta)), size is 24389
	c1 "c1" (double, torsion(chin)), size is 24389
	a2 "a2" (double, torsion(alpha)), size is 24389
	b2 "b2" (double, torsion(beta)), size is 24389
	g2 "g2" (double, torsion(gamma)), size is 24389
	d2 "d2" (double, torsion(delta)), size is 24389
	c2 "c2" (double, torsion(chin)), size is 24389
	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 : 0.0957 s ( 47.70%)
TIME:		Action Post        : 0.0000 s (  0.00%)
TIME:		Analysis           : 0.0084 s (  4.17%)
TIME:		Data File Write    : 0.0964 s ( 48.08%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.2006 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 0.4501 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.