CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 05/26/16 12:24:10
| Available memory: 6.982 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.c6]
	Reading '../ctraj.c6' 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 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6]
    DISTANCE: :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :1@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, 66 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (1 total):
 0: 'ctraj.c6' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 316 of 316)
  Coordinate processing will occur on 316 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*](42)
	Reference mask: [:1,2&!@H*](42)
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 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6]
	:2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :1@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.c6 (1-316, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 316 frames and processed 316 frames.
TIME: Avg. throughput= 72979.2148 frames / second.

ACTION OUTPUT:

DATASETS (14 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 316
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 316
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 316
	COM "COM" (double, distance), size is 316
	g1 "g1" (double, torsion(gamma)), size is 316
	d1 "d1" (double, torsion(delta)), size is 316
	e1 "e1" (double, torsion(epsilon)), size is 316
	z1 "z1" (double, torsion(zeta)), size is 316
	c1 "c1" (double, torsion(chin)), size is 316
	a2 "a2" (double, torsion(alpha)), size is 316
	b2 "b2" (double, torsion(beta)), size is 316
	g2 "g2" (double, torsion(gamma)), size is 316
	d2 "d2" (double, torsion(delta)), size is 316
	c2 "c2" (double, torsion(chin)), size is 316

RUN TIMING:
TIME:		Init               : 0.0000 s (  0.54%)
TIME:		Trajectory Process : 0.0043 s ( 98.10%)
TIME:		Action Post        : 0.0000 s (  0.07%)
TIME:		Analysis           : 0.0000 s (  0.00%)
TIME:		Data File Write    : 0.0000 s (  0.70%)
TIME:		Other              : 0.0000 s (  0.01%)
TIME:	Run Total 0.0044 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, 66 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (1 total):
 0: 'ctraj.c6' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 316 of 316)
  Coordinate processing will occur on 316 frames.

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

BEGIN TRAJECTORY PROCESSING:
----- ctraj.c6 (1-316, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 316 frames and processed 316 frames.
TIME: Avg. throughput= 150763.3588 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: 316 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 316
  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: 316 data points in each dimension.
	Hist: Allocating histogram, total bins = 100
	Warning: Frame 1 Coordinates out of bounds (-1)
	Warning: Frame 2 Coordinates out of bounds (-1)
	Warning: Frame 6 Coordinates out of bounds (-1)
	Warning: Frame 7 Coordinates out of bounds (-1)
	Warning: Frame 8 Coordinates out of bounds (-1)
	Warning: Frame 9 Coordinates out of bounds (-1)
	Warning: Frame 19 Coordinates out of bounds (-1)
	Warning: Frame 20 Coordinates out of bounds (-1)
	Warning: Frame 21 Coordinates out of bounds (-1)
	Warning: Frame 23 Coordinates out of bounds (-1)
	Warning: Frame 26 Coordinates out of bounds (-1)
	Warning: Frame 27 Coordinates out of bounds (-1)
	Warning: Frame 28 Coordinates out of bounds (-1)
	Warning: Frame 29 Coordinates out of bounds (-1)
	Warning: Frame 31 Coordinates out of bounds (-1)
	Warning: Frame 32 Coordinates out of bounds (-1)
	Warning: Frame 34 Coordinates out of bounds (-1)
	Warning: Frame 35 Coordinates out of bounds (-1)
	Warning: Frame 36 Coordinates out of bounds (-1)
	Warning: Frame 37 Coordinates out of bounds (-1)
	Warning: Frame 38 Coordinates out of bounds (-1)
	Warning: Frame 39 Coordinates out of bounds (-1)
	Warning: Frame 40 Coordinates out of bounds (-1)
	Warning: Frame 41 Coordinates out of bounds (-1)
	Warning: Frame 45 Coordinates out of bounds (-1)
	Warning: Frame 46 Coordinates out of bounds (-1)
	Warning: Frame 50 Coordinates out of bounds (-1)
	Warning: Frame 51 Coordinates out of bounds (-1)
	Warning: Frame 52 Coordinates out of bounds (-1)
	Warning: Frame 53 Coordinates out of bounds (-1)
	Warning: Frame 55 Coordinates out of bounds (-1)
	Warning: Frame 56 Coordinates out of bounds (-1)
	Warning: Frame 57 Coordinates out of bounds (-1)
	Warning: Frame 58 Coordinates out of bounds (-1)
	Warning: Frame 66 Coordinates out of bounds (-1)
	Warning: Frame 67 Coordinates out of bounds (-1)
	Warning: Frame 68 Coordinates out of bounds (-1)
	Warning: Frame 70 Coordinates out of bounds (-1)
	Warning: Frame 71 Coordinates out of bounds (-1)
	Warning: Frame 74 Coordinates out of bounds (-1)
	Warning: Frame 75 Coordinates out of bounds (-1)
	Warning: Frame 77 Coordinates out of bounds (-1)
	Warning: Frame 78 Coordinates out of bounds (-1)
	Warning: Frame 79 Coordinates out of bounds (-1)
	Warning: Frame 85 Coordinates out of bounds (-1)
	Warning: Frame 86 Coordinates out of bounds (-1)
	Warning: Frame 87 Coordinates out of bounds (-1)
	Warning: Frame 88 Coordinates out of bounds (-1)
	Warning: Frame 89 Coordinates out of bounds (-1)
	Warning: Frame 90 Coordinates out of bounds (-1)
	Warning: Frame 93 Coordinates out of bounds (-1)
	Warning: Frame 94 Coordinates out of bounds (-1)
	Warning: Frame 95 Coordinates out of bounds (-1)
	Warning: Frame 96 Coordinates out of bounds (-1)
	Warning: Frame 103 Coordinates out of bounds (-1)
	Warning: Frame 104 Coordinates out of bounds (-1)
	Warning: Frame 105 Coordinates out of bounds (-1)
	Warning: Frame 106 Coordinates out of bounds (-1)
	Warning: Frame 110 Coordinates out of bounds (-1)
	Warning: Frame 111 Coordinates out of bounds (-1)
	Warning: Frame 112 Coordinates out of bounds (-1)
	Warning: Frame 113 Coordinates out of bounds (-1)
	Warning: Frame 119 Coordinates out of bounds (-1)
	Warning: Frame 120 Coordinates out of bounds (-1)
	Warning: Frame 121 Coordinates out of bounds (-1)
	Warning: Frame 124 Coordinates out of bounds (-1)
	Warning: Frame 128 Coordinates out of bounds (-1)
	Warning: Frame 131 Coordinates out of bounds (-1)
	Warning: Frame 132 Coordinates out of bounds (-1)
	Warning: Frame 133 Coordinates out of bounds (-1)
	Warning: Frame 134 Coordinates out of bounds (-1)
	Warning: Frame 135 Coordinates out of bounds (-1)
	Warning: Frame 136 Coordinates out of bounds (-1)
	Warning: Frame 137 Coordinates out of bounds (-1)
	Warning: Frame 138 Coordinates out of bounds (-1)
	Warning: Frame 139 Coordinates out of bounds (-1)
	Warning: Frame 140 Coordinates out of bounds (-1)
	Warning: Frame 142 Coordinates out of bounds (-1)
	Warning: Frame 143 Coordinates out of bounds (-1)
	Warning: Frame 144 Coordinates out of bounds (-1)
	Warning: Frame 145 Coordinates out of bounds (-1)
	Warning: Frame 148 Coordinates out of bounds (-1)
	Warning: Frame 149 Coordinates out of bounds (-1)
	Warning: Frame 152 Coordinates out of bounds (-1)
	Warning: Frame 154 Coordinates out of bounds (-1)
	Warning: Frame 155 Coordinates out of bounds (-1)
	Warning: Frame 156 Coordinates out of bounds (-1)
	Warning: Frame 157 Coordinates out of bounds (-1)
	Warning: Frame 160 Coordinates out of bounds (-1)
	Warning: Frame 162 Coordinates out of bounds (-1)
	Warning: Frame 163 Coordinates out of bounds (-1)
	Warning: Frame 164 Coordinates out of bounds (-1)
	Warning: Frame 165 Coordinates out of bounds (-1)
	Warning: Frame 166 Coordinates out of bounds (-1)
	Warning: Frame 167 Coordinates out of bounds (-1)
	Warning: Frame 168 Coordinates out of bounds (-1)
	Warning: Frame 169 Coordinates out of bounds (-1)
	Warning: Frame 170 Coordinates out of bounds (-1)
	Warning: Frame 171 Coordinates out of bounds (-1)
	Warning: Frame 172 Coordinates out of bounds (-1)
	Warning: Frame 174 Coordinates out of bounds (-1)
	Warning: Frame 175 Coordinates out of bounds (-1)
	Warning: Frame 176 Coordinates out of bounds (-1)
	Warning: Frame 179 Coordinates out of bounds (-1)
	Warning: Frame 180 Coordinates out of bounds (-1)
	Warning: Frame 184 Coordinates out of bounds (-1)
	Warning: Frame 186 Coordinates out of bounds (-1)
	Warning: Frame 195 Coordinates out of bounds (-1)
	Warning: Frame 196 Coordinates out of bounds (-1)
	Warning: Frame 197 Coordinates out of bounds (-1)
	Warning: Frame 198 Coordinates out of bounds (-1)
	Warning: Frame 199 Coordinates out of bounds (-1)
	Warning: Frame 200 Coordinates out of bounds (-1)
	Warning: Frame 201 Coordinates out of bounds (-1)
	Warning: Frame 203 Coordinates out of bounds (-1)
	Warning: Frame 204 Coordinates out of bounds (-1)
	Warning: Frame 205 Coordinates out of bounds (-1)
	Warning: Frame 208 Coordinates out of bounds (-1)
	Warning: Frame 209 Coordinates out of bounds (-1)
	Warning: Frame 210 Coordinates out of bounds (-1)
	Warning: Frame 211 Coordinates out of bounds (-1)
	Warning: Frame 216 Coordinates out of bounds (-1)
	Warning: Frame 217 Coordinates out of bounds (-1)
	Warning: Frame 221 Coordinates out of bounds (-1)
	Warning: Frame 228 Coordinates out of bounds (-1)
	Warning: Frame 229 Coordinates out of bounds (-1)
	Warning: Frame 230 Coordinates out of bounds (-1)
	Warning: Frame 231 Coordinates out of bounds (-1)
	Warning: Frame 233 Coordinates out of bounds (-1)
	Warning: Frame 234 Coordinates out of bounds (-1)
	Warning: Frame 235 Coordinates out of bounds (-1)
	Warning: Frame 240 Coordinates out of bounds (-1)
	Warning: Frame 241 Coordinates out of bounds (-1)
	Warning: Frame 242 Coordinates out of bounds (-1)
	Warning: Frame 243 Coordinates out of bounds (-1)
	Warning: Frame 245 Coordinates out of bounds (-1)
	Warning: Frame 253 Coordinates out of bounds (-1)
	Warning: Frame 254 Coordinates out of bounds (-1)
	Warning: Frame 257 Coordinates out of bounds (-1)
	Warning: Frame 259 Coordinates out of bounds (-1)
	Warning: Frame 262 Coordinates out of bounds (-1)
	Warning: Frame 272 Coordinates out of bounds (-1)
	Warning: Frame 273 Coordinates out of bounds (-1)
	Warning: Frame 274 Coordinates out of bounds (-1)
	Warning: Frame 275 Coordinates out of bounds (-1)
	Warning: Frame 278 Coordinates out of bounds (-1)
	Warning: Frame 279 Coordinates out of bounds (-1)
	Warning: Frame 280 Coordinates out of bounds (-1)
	Warning: Frame 281 Coordinates out of bounds (-1)
	Warning: Frame 283 Coordinates out of bounds (-1)
	Warning: Frame 284 Coordinates out of bounds (-1)
	Warning: Frame 290 Coordinates out of bounds (-1)
	Warning: Frame 297 Coordinates out of bounds (-1)
	Warning: Frame 300 Coordinates out of bounds (-1)
	Warning: Frame 305 Coordinates out of bounds (-1)
	Warning: Frame 307 Coordinates out of bounds (-1)
	Warning: Frame 313 Coordinates out of bounds (-1)
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 159
  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: 316 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 316
  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: 316 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 316
  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: 316 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 316
  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: 316 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 316
  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: 316 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 316
  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: 316 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 316
  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: 316 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 316
  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: 316 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 316
  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: 316 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 316
  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: 316 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 316
  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: 316 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 316
  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: 316 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 316
  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: 316 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 316

TIME: Analyses took 0.0005 seconds.

DATASETS (36 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 316
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 316
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 316
	COM "COM" (double, distance), size is 316
	g1 "g1" (double, torsion(gamma)), size is 316
	d1 "d1" (double, torsion(delta)), size is 316
	e1 "e1" (double, torsion(epsilon)), size is 316
	z1 "z1" (double, torsion(zeta)), size is 316
	c1 "c1" (double, torsion(chin)), size is 316
	a2 "a2" (double, torsion(alpha)), size is 316
	b2 "b2" (double, torsion(beta)), size is 316
	g2 "g2" (double, torsion(gamma)), size is 316
	d2 "d2" (double, torsion(delta)), size is 316
	c2 "c2" (double, torsion(chin)), size is 316
	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 (  0.11%)
TIME:		Trajectory Process : 0.0021 s (  7.78%)
TIME:		Action Post        : 0.0000 s (  0.00%)
TIME:		Analysis           : 0.0005 s (  2.02%)
TIME:		Data File Write    : 0.0243 s ( 90.00%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.0270 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 0.0433 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.