------------------------------------------------------- Amber 16 SANDER 2016 ------------------------------------------------------- | Run on 07/26/2016 at 11:00:15 | Executable path: ../../bin/sander | Working directory: /shared/home/wesley/amber16_mpi/test/rdc | Hostname: headnode [-O]verwriting output File Assignments: | MDIN: mdin | MDOUT: gcg.dip.o |INPCRD: gcg.old.x | PARM: prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDFRC: mdfrc | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: inptraj | REMLOG: rem.log | REMTYPE: rem.type | REMSTRIP: | SAVEENE: saveene |CLUSTERINF: cluster.info | RESERVOIR: reserv/frame | REMDDIM: Here is the input file: test of distance, angle, rdc and chemical shifts restraints for a DNA duplex &cntrl pencut=0.05, nmropt=2, imin=1, maxcyc=10, igb=1, rgbmax=15., ntpr=1, ipnlty=1, cut=12.0, ntb=0, iscale=5, scalm=300., ntc=1, ntb=0, / &wt type='SHIFTS', value1=2.0, / &wt type='REST', istep1=0, istep2=15000, value1=0.0, value2=0.0, / &wt type='END' / LISTOUT=POUT DISANG=RST.allang DIPOLE=RST.dip SHIFTS=gcg10.shf END -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: MPI | New format PARM file being parsed. | Version = 1.000 Date = 06/02/03 Time = 15:18:49 NATOM = 632 NTYPES = 15 NBONH = 228 MBONA = 452 NTHETH = 536 MTHETA = 694 NPHIH = 946 MPHIA = 1142 NHPARM = 0 NPARM = 0 NNB = 3508 NRES = 20 NBONA = 452 NTHETA = 694 NPHIA = 1142 NUMBND = 37 NUMANG = 76 NPTRA = 34 NATYP = 25 NPHB = 0 IFBOX = 0 NMXRS = 33 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 203249 | Hollerith 1918 | Integer 180058 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 2298 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 1, nmropt = 2 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 2, ntpr = 1, ntrx = 1, ntwr = 1 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 1, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 12.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500 rdt = 0.00000, rgbmax = 15.00000 extdiel = 78.50000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 10, ncyc = 10, ntmin = 1 dx0 = 0.01000, drms = 0.00010 NMR refinement options: iscale = 5, noeskp = 1, ipnlty = 1, mxsub = 1 scalm = 300.00000, pencut = 0.05000, tausw = 0.10000 | MPI Timing options: | profile_mpi = 0 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Begin reading energy term weight changes/NMR restraints WEIGHT CHANGES: SHIFTS 0 0 2.000000 0.000000 0 0 REST 0 15000 0.000000 0.000000 0 0 RESTRAINTS: Requested file redirections: LISTOUT = POUT DISANG = RST.allang DIPOLE = RST.dip SHIFTS = gcg10.shf Restraints will be read from file: RST.allang Here are comments from the DISANG input file: # # 1 GUA H1' 1 GUA H3' 4.6 Number of restraints read = 793 Done reading weight changes/NMR restraints Alignment info will be read from file: RST.dip Here are comments from the alignment input file: Number of triangulated 3-point waters found: 0 | Atom division among processors: | 0 61 94 126 158 222 252 285 | 316 377 410 442 474 538 568 601 | 632 | Running AMBER/MPI version on 16 nodes -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- Chemical shifts will be read from file: gcg10.shf NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.1090E+03 5.2176E+00 2.6863E+01 C6 140 BOND = 15.2816 ANGLE = 88.9731 DIHED = 368.4253 VDWAALS = -324.4472 EEL = 202.5241 EGB = -2428.8371 1-4 VDW = 173.0467 1-4 EEL = -2389.4169 RESTRAINT = 185.4482 EAMBER = -4294.4503 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 : Noesy= 0.000 Shift = 155.846 Pcshift = 0.000 Energy (this step): Align= 29.602 CSA= 0.000 Alignment tensor: -14.357 1.286 -29.811 1.286 -18.844 -44.361 -29.811 -44.361 33.201 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 2 -4.1114E+03 4.7445E+00 2.3827E+01 C6 140 BOND = 15.5261 ANGLE = 88.5298 DIHED = 368.3326 VDWAALS = -324.4720 EEL = 222.1654 EGB = -2448.8796 1-4 VDW = 172.6280 1-4 EEL = -2389.8546 RESTRAINT = 184.6742 EAMBER = -4296.0244 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 : Noesy= 0.000 Shift = 155.847 Pcshift = 0.000 Energy (this step): Align= 28.827 CSA= 0.000 Alignment tensor: -14.357 1.286 -29.811 1.286 -18.844 -44.361 -29.811 -44.361 33.201 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 3 -4.1142E+03 4.2232E+00 2.0411E+01 C6 140 BOND = 16.0100 ANGLE = 88.0572 DIHED = 368.2185 VDWAALS = -324.5015 EEL = 222.3259 EGB = -2449.7920 1-4 VDW = 172.1277 1-4 EEL = -2390.4085 RESTRAINT = 183.8099 EAMBER = -4297.9628 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 : Noesy= 0.000 Shift = 155.848 Pcshift = 0.000 Energy (this step): Align= 27.962 CSA= 0.000 Alignment tensor: -14.357 1.286 -29.811 1.286 -18.844 -44.361 -29.811 -44.361 33.201 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 4 -4.1170E+03 3.6716E+00 1.7087E+01 H1' 518 BOND = 16.8130 ANGLE = 87.5739 DIHED = 368.0786 VDWAALS = -324.5391 EEL = 231.7369 EGB = -2459.9326 1-4 VDW = 171.5323 1-4 EEL = -2391.1164 RESTRAINT = 182.8604 EAMBER = -4299.8534 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 : Noesy= 0.000 Shift = 155.849 Pcshift = 0.000 Energy (this step): Align= 27.012 CSA= 0.000 Alignment tensor: -14.357 1.286 -29.811 1.286 -18.844 -44.361 -29.811 -44.361 33.201 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 5 -4.1200E+03 3.1255E+00 1.6361E+01 H3 466 BOND = 17.9881 ANGLE = 87.1104 DIHED = 367.9091 VDWAALS = -324.5865 EEL = 234.6520 EGB = -2463.7217 1-4 VDW = 170.8303 1-4 EEL = -2392.0276 RESTRAINT = 181.8384 EAMBER = -4301.8458 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 : Noesy= 0.000 Shift = 155.850 Pcshift = 0.000 Energy (this step): Align= 25.989 CSA= 0.000 Alignment tensor: -14.357 1.286 -29.811 1.286 -18.844 -44.361 -29.811 -44.361 33.201 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 6 -4.1230E+03 2.6361E+00 1.5579E+01 H3 466 BOND = 19.4893 ANGLE = 86.7119 DIHED = 367.7115 VDWAALS = -324.6501 EEL = 246.5435 EGB = -2476.3442 1-4 VDW = 170.0176 1-4 EEL = -2393.1996 RESTRAINT = 180.7691 EAMBER = -4303.7202 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 : Noesy= 0.000 Shift = 155.850 Pcshift = 0.000 Energy (this step): Align= 24.919 CSA= 0.000 Alignment tensor: -14.357 1.285 -29.811 1.285 -18.844 -44.361 -29.811 -44.361 33.201 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 7 -4.1261E+03 2.2446E+00 1.4441E+01 H3 466 BOND = 21.0779 ANGLE = 86.4326 DIHED = 367.4996 VDWAALS = -324.7432 EEL = 249.1895 EGB = -2479.6388 1-4 VDW = 169.1062 1-4 EEL = -2394.6781 RESTRAINT = 179.6920 EAMBER = -4305.7542 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 : Noesy= 0.000 Shift = 155.849 Pcshift = 0.000 Energy (this step): Align= 23.843 CSA= 0.000 Alignment tensor: -14.357 1.285 -29.811 1.285 -18.844 -44.361 -29.811 -44.361 33.201 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 8 -4.1293E+03 1.9400E+00 1.2959E+01 H3 466 BOND = 22.3793 ANGLE = 86.3175 DIHED = 367.3074 VDWAALS = -324.8895 EEL = 251.8008 EGB = -2482.4849 1-4 VDW = 168.1206 1-4 EEL = -2396.4657 RESTRAINT = 178.6416 EAMBER = -4307.9146 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 : Noesy= 0.000 Shift = 155.847 Pcshift = 0.000 Energy (this step): Align= 22.794 CSA= 0.000 Alignment tensor: -14.357 1.285 -29.812 1.285 -18.844 -44.361 -29.812 -44.361 33.201 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 9 -4.1324E+03 1.6761E+00 1.1263E+01 H3 466 BOND = 23.2396 ANGLE = 86.3853 DIHED = 367.1773 VDWAALS = -325.1267 EEL = 267.5009 EGB = -2497.7503 1-4 VDW = 167.0676 1-4 EEL = -2398.5394 RESTRAINT = 177.5985 EAMBER = -4310.0457 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 : Noesy= 0.000 Shift = 155.842 Pcshift = 0.000 Energy (this step): Align= 21.757 CSA= 0.000 Alignment tensor: -14.357 1.285 -29.812 1.285 -18.843 -44.361 -29.812 -44.361 33.200 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 10 -4.1355E+03 1.4325E+00 9.4257E+00 H3 466 BOND = 23.8784 ANGLE = 86.6483 DIHED = 367.1374 VDWAALS = -325.5089 EEL = 298.0289 EGB = -2527.2500 1-4 VDW = 165.9372 1-4 EEL = -2400.9245 RESTRAINT = 176.5076 EAMBER = -4312.0532 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 : Noesy= 0.000 Shift = 155.830 Pcshift = 0.000 Energy (this step): Align= 20.678 CSA= 0.000 Alignment tensor: -14.357 1.284 -29.812 1.284 -18.843 -44.362 -29.812 -44.362 33.200 =============================================================================== Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 10 -4.1355E+03 1.4325E+00 9.4257E+00 H3 466 BOND = 23.8784 ANGLE = 86.6483 DIHED = 367.1374 VDWAALS = -325.5089 EEL = 298.0289 EGB = -2527.2500 1-4 VDW = 165.9372 1-4 EEL = -2400.9245 RESTRAINT = 176.5076 EAMBER = -4312.0532 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 : Noesy= 0.000 Shift = 155.830 Pcshift = 0.000 Energy (this step): Align= 20.678 CSA= 0.000 Alignment tensor: -14.357 1.284 -29.812 1.284 -18.843 -44.362 -29.812 -44.362 33.200 =============================================================================== ------------------------------------------------------------------------------ Final Restraint Analysis for coords: restrt Restraints, deviations, and energy contributions: pencut = 0.05 ------------------------------------------------------------------------------ First atom Last atom curr. value target deviation penalty ------------------------------------------------------------------------------ Total distance penalty: 0.000 Total angle penalty: 0.000 Total torsion penalty: 0.000 ------------------------------------------------------------------------------ Chemical shifts analysis: Proton Calc. Observed Penalty --------------------------------------------- 170 H1' DA 6 -0.62 0.65 2.54 186 H3' DA 6 0.01 0.68 1.35 167 H4' DA 6 -0.02 0.41 0.86 202 H1' DA 7 -0.22 0.82 2.09 218 H3' DA 7 0.00 0.64 1.27 199 H4' DA 7 0.04 0.44 0.79 43 H1' DC 2 -0.26 0.53 1.59 57 H3' DC 2 -0.01 0.53 1.07 234 H1' DC 8 -0.51 0.32 1.66 248 H3' DC 8 -0.05 0.40 0.89 182 H2 DA 6 -2.70 -1.76 1.86 214 H2 DA 7 -0.77 -1.09 0.63 10 H1' DG5 1 -0.24 0.76 2.00 27 H3' DG5 1 -0.05 0.49 1.10 7 H4' DG5 1 -0.11 0.26 0.74 73 H1' DG 3 -0.13 0.82 1.90 90 H3' DG 3 -0.03 0.64 1.35 70 H4' DG 3 -0.01 0.42 0.86 264 H1' DG 9 -0.45 0.70 2.30 281 H3' DG 9 -0.14 0.59 1.47 261 H4' DG 9 -0.15 0.34 0.97 486 H1' DA 16 -0.35 0.65 2.00 502 H3' DA 16 -0.02 0.68 1.41 483 H4' DA 16 -0.04 0.41 0.89 518 H1' DA 17 -0.20 0.82 2.04 534 H3' DA 17 -0.01 0.64 1.31 515 H4' DA 17 0.08 0.44 0.71 297 H1' DC3 10 -0.17 0.95 2.24 311 H3' DC3 10 -0.18 0.13 0.62 359 H1' DC 12 -0.14 0.53 1.34 373 H3' DC 12 0.03 0.53 1.00 550 H1' DC 18 -0.35 0.32 1.35 564 H3' DC 18 -0.02 0.40 0.83 613 H1' DC3 20 -0.16 0.95 2.22 498 H2 DA 16 -2.14 -1.76 0.74 326 H1' DG5 11 -0.39 0.76 2.30 343 H3' DG5 11 -0.09 0.49 1.17 323 H4' DG5 11 -0.12 0.26 0.76 389 H1' DG 13 -0.12 0.82 1.87 406 H3' DG 13 -0.02 0.64 1.32 386 H4' DG 13 0.00 0.42 0.83 580 H1' DG 19 -0.32 0.70 2.04 597 H3' DG 19 -0.10 0.59 1.38 577 H4' DG 19 -0.09 0.34 0.86 13 H8 DG5 1 -0.14 0.26 0.81 76 H8 DG 3 -0.34 0.24 1.17 267 H8 DG 9 -0.62 0.15 1.53 188 H2'1 DA 6 -0.07 0.50 1.14 164 H5'1 DA 6 0.05 0.54 0.99 220 H2'1 DA 7 -0.07 0.33 0.81 196 H5'1 DA 7 0.14 0.63 0.96 189 H2'2 DA 6 0.02 0.71 1.39 165 H5'2 DA 6 0.02 0.37 0.71 221 H2'2 DA 7 -0.01 0.62 1.25 197 H5'2 DA 7 0.06 0.51 0.89 37 H5'1 DC 2 0.03 0.54 1.01 228 H5'1 DC 8 0.16 0.63 0.93 106 H1' DT 4 -0.22 0.77 1.97 122 H3' DT 4 -0.05 0.49 1.07 138 H1' DT 5 -0.15 0.44 1.17 154 H3' DT 5 0.05 0.51 0.93 38 H5'2 DC 2 -0.00 0.42 0.84 251 H2'2 DC 8 -0.25 0.09 0.67 229 H5'2 DC 8 0.05 0.38 0.66 329 H8 DG5 11 -0.15 0.26 0.83 392 H8 DG 13 -0.30 0.24 1.09 583 H8 DG 19 -0.50 0.15 1.29 29 H2'1 DG5 1 -0.05 0.37 0.84 92 H2'1 DG 3 -0.08 0.43 1.02 67 H5'1 DG 3 0.00 0.55 1.10 283 H2'1 DG 9 -0.29 0.34 1.26 258 H5'1 DG 9 -0.09 0.41 1.01 504 H2'1 DA 16 -0.13 0.50 1.26 480 H5'1 DA 16 -0.01 0.54 1.11 536 H2'1 DA 17 -0.13 0.33 0.93 512 H5'1 DA 17 0.13 0.63 0.98 30 H2'2 DG5 1 -0.05 0.63 1.35 93 H2'2 DG 3 -0.01 0.66 1.33 68 H5'2 DG 3 -0.02 0.37 0.78 284 H2'2 DG 9 -0.30 0.54 1.67 259 H5'2 DG 9 -0.08 0.37 0.91 505 H2'2 DA 16 -0.03 0.71 1.48 481 H5'2 DA 16 -0.02 0.37 0.78 537 H2'2 DA 17 -0.09 0.62 1.41 513 H5'2 DA 17 0.05 0.51 0.92 291 H5'1 DC3 10 -0.05 0.44 0.97 353 H5'1 DC 12 0.01 0.54 1.06 566 H2'1 DC 18 -0.10 -0.41 0.61 544 H5'1 DC 18 0.17 0.63 0.91 607 H5'1 DC3 20 -0.01 0.44 0.90 422 H1' DT 14 -0.25 0.77 2.03 438 H3' DT 14 -0.03 0.49 1.03 454 H1' DT 15 -0.27 0.44 1.42 470 H3' DT 15 -0.00 0.51 1.03 292 H5'2 DC3 10 -0.08 0.51 1.17 354 H5'2 DC 12 0.01 0.42 0.81 567 H2'2 DC 18 -0.21 0.09 0.60 545 H5'2 DC 18 0.07 0.38 0.61 608 H5'2 DC3 20 -0.05 0.51 1.12 109 H6 DT 4 -0.55 -0.20 0.69 345 H2'1 DG5 11 -0.11 0.37 0.95 408 H2'1 DG 13 -0.06 0.43 0.99 383 H5'1 DG 13 0.03 0.55 1.05 599 H2'1 DG 19 -0.20 0.34 1.08 574 H5'1 DG 19 -0.03 0.41 0.90 346 H2'2 DG5 11 -0.02 0.63 1.30 409 H2'2 DG 13 -0.00 0.66 1.32 384 H5'2 DG 13 -0.00 0.37 0.75 600 H2'2 DG 19 -0.17 0.54 1.40 575 H5'2 DG 19 -0.04 0.37 0.83 100 H5'1 DT 4 0.07 0.69 1.23 156 H2'1 DT 5 0.10 -0.23 0.65 132 H5'1 DT 5 -0.00 0.53 1.07 125 H2'2 DT 4 -0.05 0.36 0.82 101 H5'2 DT 4 0.01 0.45 0.87 133 H5'2 DT 5 0.01 0.41 0.81 430 H73 DT 14 -0.83 -0.43 0.80 416 H5'1 DT 14 0.11 0.69 1.17 448 H5'1 DT 15 -0.03 0.53 1.13 441 H2'2 DT 14 -0.05 0.36 0.81 417 H5'2 DT 14 0.02 0.45 0.85 449 H5'2 DT 15 -0.02 0.41 0.86 Total shift constraint: 155.83 # Pearson r rms error ----------------------------------- Shift correlation: 174 0.73702 0.52468 ------------------------------------------------------------------------------ Residual dipolar splittings: ------------------------------------------------------------------------------ First atom Last atom curr. value target deviation penalty distance ------------------------------------------------------------------------------ C1' DG5 1 -- H1' DG5 1: 4.498 4.390 0.108 0.001 1.095 C1' DC 2 -- H1' DC 2: 10.032 9.810 0.222 0.005 1.093 C1' DG 3 -- H1' DG 3: 13.495 12.490 1.005 0.101 1.103 C1' DT 4 -- H1' DT 4: 7.951 9.410 -1.459 0.213 1.085 C1' DT 5 -- H1' DT 5: 9.867 8.120 1.747 0.305 1.102 C1' DA 6 -- H1' DA 6: 9.973 9.920 0.053 0.000 1.095 C1' DA 7 -- H1' DA 7: 13.341 12.490 0.851 0.072 1.102 C1' DC 8 -- H1' DC 8: 12.181 12.020 0.161 0.003 1.096 C1' DG 9 -- H1' DG 9: 5.034 4.440 0.594 0.035 1.095 C1' DC3 10 -- H1' DC3 10: 2.105 1.950 0.155 0.002 1.094 C1' DG5 11 -- H1' DG5 11: 5.293 4.390 0.903 0.082 1.097 C1' DC 12 -- H1' DC 12: 9.303 9.810 -0.507 0.026 1.088 C1' DG 13 -- H1' DG 13: 11.679 12.490 -0.811 0.066 1.088 C1' DT 14 -- H1' DT 14: 7.423 9.410 -1.987 0.395 1.083 C1' DT 15 -- H1' DT 15: 7.370 8.120 -0.750 0.056 1.087 C1' DA 16 -- H1' DA 16: 11.163 9.920 1.243 0.154 1.100 C1' DA 17 -- H1' DA 17: 13.993 12.490 1.503 0.226 1.107 C1' DC 18 -- H1' DC 18: 12.715 12.020 0.695 0.048 1.102 C1' DG 19 -- H1' DG 19: 3.862 4.440 -0.578 0.033 1.090 C1' DC3 20 -- H1' DC3 20: 4.228 1.950 2.278 0.519 1.100 C4' DT 5 -- H4' DT 5: -0.666 -1.190 0.524 0.027 1.091 C4' DC 8 -- H4' DC 8: 14.251 14.830 -0.579 0.033 1.086 C4' DC3 10 -- H4' DC3 10: 9.102 8.660 0.442 0.020 1.097 C4' DT 15 -- H4' DT 15: -1.015 -1.190 0.175 0.003 1.090 C4' DC 18 -- H4' DC 18: 13.572 14.830 -1.258 0.158 1.078 C4' DC3 20 -- H4' DC3 20: 8.061 8.660 -0.599 0.036 1.089 C2 DA 6 -- H2 DA 6: 15.893 15.990 -0.097 0.001 1.080 C2 DA 7 -- H2 DA 7: 24.677 25.550 -0.873 0.076 1.065 C2 DA 16 -- H2 DA 16: 16.253 15.990 0.263 0.007 1.086 C2 DA 17 -- H2 DA 17: 24.965 25.550 -0.585 0.034 1.069 C6 DC 2 -- H6 DC 2: 8.570 8.320 0.250 0.006 1.082 C6 DT 4 -- H6 DT 4: 11.491 13.610 -2.119 0.449 1.064 C6 DT 5 -- H6 DT 5: 18.812 19.680 -0.868 0.075 1.070 C6 DC 8 -- H6 DC 8: 5.882 5.150 0.732 0.054 1.082 C6 DC3 10 -- H6 DC3 10: 5.337 6.640 -1.303 0.170 1.074 C6 DC 12 -- H6 DC 12: 9.417 8.320 1.097 0.120 1.090 C6 DT 14 -- H6 DT 14: 11.702 13.610 -1.908 0.364 1.065 C6 DT 15 -- H6 DT 15: 18.979 19.680 -0.701 0.049 1.072 C6 DC 18 -- H6 DC 18: 5.681 5.150 0.531 0.028 1.080 C6 DC3 20 -- H6 DC3 20: 9.343 6.640 2.703 0.730 1.098 C8 DG5 1 -- H8 DG5 1: 21.639 21.950 -0.311 0.010 1.078 C8 DG 3 -- H8 DG 3: 6.433 7.820 -1.387 0.192 1.076 C8 DA 6 -- H8 DA 6: 21.074 21.260 -0.186 0.003 1.078 C8 DA 7 -- H8 DA 7: 17.082 17.610 -0.528 0.028 1.075 C8 DG 9 -- H8 DG 9: 7.495 7.450 0.045 0.000 1.082 C8 DG5 11 -- H8 DG5 11: 21.575 21.950 -0.375 0.014 1.076 C8 DG 13 -- H8 DG 13: 6.951 7.820 -0.869 0.075 1.076 C8 DA 16 -- H8 DA 16: 21.207 21.260 -0.053 0.000 1.081 C8 DA 17 -- H8 DA 17: 18.074 17.610 0.464 0.022 1.088 C8 DG 19 -- H8 DG 19: 5.777 7.450 -1.673 0.280 1.076 N3 DT 4 -- H3 DT 4: 3.176 5.230 -2.054 0.422 1.007 N3 DT 5 -- H3 DT 5: 4.233 8.210 -3.977 1.582 1.003 N3 DT 14 -- H3 DT 14: -0.698 5.230 -5.928 3.514 1.016 N3 DT 15 -- H3 DT 15: 3.231 8.210 -4.979 2.479 1.004 N1 DG 9 -- H1 DG 9: 1.336 3.810 -2.474 0.612 1.007 N1 DG 3 -- H1 DG 3: 2.555 4.020 -1.465 0.214 1.006 N1 DG 19 -- H1 DG 19: -1.262 3.810 -5.072 2.572 1.014 N1 DG 13 -- H1 DG 13: -1.642 4.020 -5.662 3.206 1.015 N7 DG5 1 -- H8 DG5 1: 1.903 1.430 0.473 0.022 2.102 N7 DG 3 -- H8 DG 3: 0.567 1.000 -0.433 0.019 2.093 N7 DG 9 -- H8 DG 9: 1.191 0.040 1.151 0.132 2.098 N7 DG5 11 -- H8 DG5 11: 1.937 1.430 0.507 0.026 2.094 N7 DG 13 -- H8 DG 13: 1.096 1.000 0.096 0.001 2.095 N7 DG 19 -- H8 DG 19: 1.652 0.040 1.612 0.260 2.100 N7 DA 7 -- H8 DA 7: 1.115 2.110 -0.995 0.099 2.090 N7 DA 17 -- H8 DA 17: 1.076 2.110 -1.034 0.107 2.107 Total align constraint: 20.68 Diagonalize the alignment matrix: -50.55971 0.41603 0.73400 0.53682 -16.82559 0.85339 -0.51903 0.04831 67.38531 -0.31408 -0.43802 0.84231 Diagonalize the moment of interia tensor: 280640.06643 -0.11634 -0.50682 0.85416 21.63501 679836.06997 -0.96366 0.26581 0.02646 11.72616 731292.16561 -0.24046 -0.82005 -0.51933 9.74128 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.00 ( 0.99% of Total) | Fast Water setup 0.00 ( 0.01% of Total) | Calc gb radii 0.01 (25.79% of Gen B) | Communicate gb radii 0.00 ( 6.31% of Gen B) | Calc gb diag 0.01 (41.97% of Gen B) | Calc gb off-diag 0.01 (25.87% of Gen B) | Other 0.00 ( 0.06% of Gen B) | Gen Born time 0.03 (100.0% of Nonbo) | Nonbond force 0.03 (21.96% of Force) | Bond/Angle/Dihedral 0.00 ( 0.58% of Force) | FRC Collect time 0.00 ( 1.10% of Force) | shift der time 0.01 ( 7.31% of Noe c) | Ringcurr time 0.07 (91.39% of Noe c) | Electro. noe time 0.00 ( 1.11% of Noe c) | Anisotr. noe time 0.00 ( 0.19% of Noe c) | Noe calc time 0.08 (69.15% of Force) | Other 0.01 ( 7.21% of Force) | Force time 0.12 (100.0% of Runmd) | Runmd Time 0.12 (57.26% of Total) | Other 0.08 (41.74% of Total) | Total time 0.20 (99.62% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 11:00:15.068 on 07/26/2016 | Setup done at 11:00:15.132 on 07/26/2016 | Run done at 11:00:15.270 on 07/26/2016 | wallclock() was called 12286 times