1 --------------------------------------------------------------------------------
3 --------------------------------------------------------------------------------
4 Input file : 1L2Y_minim.inp
5 Output file : 1L2Y_minim.out_LJ000
7 Sidechain potential file : /users/adam/UNRES/PARAM/scinter_LJ.parm
8 SCp potential file : /users/adam/UNRES/PARAM/scp.parm
9 Electrostatic potential file : /users/adam/UNRES/PARAM/electr_631Gdp.parm
10 Cumulant coefficient file :
11 /users/adam/UNRES/PARAM/fourier_opt.parm.1igd_hc_iter3_3
12 Torsional parameter file : /users/adam/UNRES/PARAM/torsion_631Gdp.parm
13 Double torsional parameter file :
14 /users/adam/UNRES/PARAM/torsion_double_631Gdp.parm
15 SCCOR parameter file : /users/adam/UNRES/PARAM/rotcorr_AM1.parm
16 Bond & inertia constant file : /users/adam/UNRES/PARAM/bond.parm
17 Bending parameter file : /users/adam/UNRES/PARAM/thetaml.5parm
18 Rotamer parameter file : /users/adam/UNRES/PARAM/scgauss.parm
19 Threading database : /users/adam/UNRES/PARAM/patterns.cart
20 --------------------------------------------------------------------------------
21 ********************************************************************************
22 United-residue force field calculation - parallel job.
23 ********************************************************************************
24 ### LAST MODIFIED 03/28/12 23:29 by czarek
25 ++++ Compile info ++++
27 compiled Sun May 13 16:07:22 2012
28 compiled by adam@matrix.chem.cornell.edu
30 OS release: 2.6.34.9-69.fc13.x86_64
31 OS version: #1 SMP Tue May 3 09:23:03 UTC 2011
33 INSTALL_DIR = /users/software/mpich-1.2.7p1_int...
36 FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include
37 FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)...
38 FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include
39 FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report ...
40 LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdr...
43 object = unres.o arcos.o cartprint.o chainbuild...
44 GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES ...
45 GAB: BIN = ../../../bin/unres/MD/unres_ifort_MP...
46 E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNR...
47 E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort...
48 ++++ End of compile info ++++
50 Potential is LJ , exponents are 6 12
52 Disulfide bridge parameters:
53 S-S bridge energy: -5.50
54 d0cm: 3.78 akcm: 15.10
55 akth: 11.00 akct: 12.00
56 v1ss: -1.08 v2ss: 7.61 v3ss: 13.70
57 MPI: node= 0 iseed(4)= 0 0 -46
59 ran_num 6.422640197456531E-013
65 Time limit (min): 960.0
67 Library routine used to diagonalize matrices.
69 ********************************************************************************
70 Options in energy minimization:
71 ********************************************************************************
72 MaxMin: 2000 MaxFun: 5000MinMin: 2000 MinFun: 2000 TolF: 1.00000E-02 RTolF: 1.00000E-04
74 Energy-term weights (unscaled):
76 WSCC= 1.352790 (SC-SC)
78 WELEC= 0.715340 (p-p electr)
79 WVDWPP= 0.113710 (p-p VDW)
80 WBOND= 1.000000 (stretching)
81 WANG= 1.138730 (bending)
82 WSCLOC= 0.162580 (SC local)
83 WTOR= 1.985990 (torsional)
84 WTORD= 1.570690 (double torsional)
85 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
86 WEL_LOC= 0.160360 (multi-body 3-rd order)
87 WCORR4= 0.428870 (multi-body 4th order)
88 WCORR5= 0.000000 (multi-body 5th order)
89 WCORR6= 0.000000 (multi-body 6th order)
90 WSCCOR= 0.000000 (back-scloc correlation)
91 WTURN3= 1.687220 (turns, 3rd order)
92 WTURN4= 0.662300 (turns, 4th order)
93 WTURN6= 0.000000 (turns, 6th order)
95 Hydrogen-bonding correlation between contact pairs of peptide groups
97 Scaling factor of 1,4 SC-p interactions: 0.400
98 General scaling factor of SC-p interactions: 1.000
100 Energy-term weights (scaled):
102 WSCC= 1.352790 (SC-SC)
103 WSCP= 1.593040 (SC-p)
104 WELEC= 0.715340 (p-p electr)
105 WVDWPP= 0.113710 (p-p VDW)
106 WBOND= 1.000000 (stretching)
107 WANG= 1.138730 (bending)
108 WSCLOC= 0.162580 (SC local)
109 WTOR= 1.985990 (torsional)
110 WTORD= 1.570690 (double torsional)
111 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
112 WEL_LOC= 0.160360 (multi-body 3-rd order)
113 WCORR4= 0.428870 (multi-body 4th order)
114 WCORR5= 0.000000 (multi-body 5th order)
115 WCORR6= 0.000000 (multi-body 6th order)
116 WSCCOR= 0.000000 (back-scloc correlatkion)
117 WTURN3= 1.687220 (turns, 3rd order)
118 WTURN4= 0.662300 (turns, 4th order)
119 WTURN6= 0.000000 (turns, 6th order)
120 Reference temperature for weights calculation: 300.000000000000
121 Parameters of the SS-bond potential:
122 D0CM 3.78000000000000 AKCM 15.1000000000000 AKTH
123 11.0000000000000 AKCT 12.0000000000000
124 V1SS -1.08000000000000 V2SS 7.61000000000000 V3SS
126 EBR -5.50000000000000
127 PDB data will be read from file 1L2Y.pdb
129 Backbone and SC coordinates as read from the PDB
130 1 21 D -9.841 4.399 -5.051 -9.841 4.399 -5.051
131 2 14 ASN -8.608 3.135 -1.618 -10.407 3.153 -2.437
132 3 5 LEU -4.923 4.002 -2.452 -4.618 6.091 -1.850
133 4 8 TYR -3.690 2.738 0.981 -1.959 3.143 3.797
134 5 4 ILE -5.857 -0.449 0.613 -7.484 -0.369 1.074
135 6 13 GLN -4.122 -1.167 -2.743 -5.089 -1.450 -4.853
136 7 7 TRP -0.716 -0.631 -0.993 1.727 0.440 1.450
137 8 5 LEU -1.641 -2.932 1.963 -2.244 -2.097 3.799
138 9 19 LYS -3.024 -5.791 -0.269 -3.820 -5.527 -3.146
139 10 16 ASP 0.466 -6.016 -1.905 0.653 -5.125 -3.676
140 11 10 GLY 2.060 -6.618 1.593 2.060 -6.618 1.593
141 12 10 GLY 2.626 -2.967 2.723 2.626 -2.967 2.723
142 13 20 PRO 6.333 -2.533 3.806 5.724 -2.372 5.058
143 14 12 SER 7.049 -6.179 2.704 6.757 -6.938 3.675
144 15 12 SER 6.389 -5.315 -1.015 5.245 -5.350 -1.546
145 16 10 GLY 9.451 -3.116 -1.870 9.451 -3.116 -1.870
146 17 18 ARG 7.289 0.084 -2.054 5.225 -1.826 -3.986
147 18 20 PRO 6.782 3.088 0.345 7.458 3.741 -0.688
148 19 20 PRO 3.287 4.031 1.686 4.025 4.206 2.856
149 20 20 PRO 1.185 6.543 -0.353 0.358 5.421 -0.430
150 21 12 SER 0.852 10.027 1.285 1.151 10.636 1.488
151 22 21 D -1.250 12.539 -0.754 -1.250 12.539 -0.754
152 nsup= 20 nstart_sup= 2
176 Boundaries in phi angle sampling:
200 nsup= 20 nstart_sup= 2 nstart_seq= 2
201 NZ_START= 2 NZ_END= 21
203 Contact order: 0.320158102766798
204 Shifting contacts: 2 2
228 Initial geometry will be read in.
230 Geometry of the virtual chain.
231 Res d Theta Gamma Dsc Alpha Beta
232 D 1 0.000 0.000 0.000 0.000 0.000 0.000
233 ASN 2 3.800 0.000 0.000 1.684 102.356 -82.317
234 LEU 3 3.800 104.929 0.000 1.939 120.092 -56.685
235 TYR 4 3.800 87.695 -100.430 2.484 152.364 85.090
236 ILE 5 3.800 81.904 72.426 1.776 134.976 -88.666
237 GLN 6 3.800 82.466 66.026 2.240 122.343 -140.945
238 TRP 7 3.800 84.466 51.434 2.605 152.178 38.024
239 LEU 8 3.800 83.945 53.508 1.939 159.052 179.471
240 LYS 9 3.800 85.396 60.569 2.541 100.558 -73.090
241 ASP 10 3.800 91.449 44.177 1.709 139.961 -144.797
242 GLY 11 3.800 94.602 67.604 0.000 0.000 0.000
243 GLY 12 3.800 101.862 -72.814 0.000 0.000 0.000
244 PRO 13 3.800 119.363 -61.916 1.345 117.453 -133.163
245 SER 14 3.800 94.363 -75.894 1.150 137.025 -106.659
246 SER 15 3.800 96.264 67.358 1.150 146.290 -130.305
247 GLY 16 3.800 138.119 129.701 0.000 0.000 0.000
248 ARG 17 3.800 96.299 -95.571 3.020 93.901 -102.747
249 PRO 18 3.800 129.702 63.972 1.345 101.025 -111.641
250 PRO 19 3.800 109.445 -74.504 1.345 113.043 -122.044
251 PRO 20 3.800 106.349 -122.306 1.345 93.778 -102.374
252 SER 21 3.800 106.042 -134.605 1.150 153.835 -143.303
253 D 22 3.800 108.718 92.113 0.000 0.000 0.000
256 ********************************************************************************
257 Processor 0: end reading molecular data.
258 ********************************************************************************
261 Energy evaluation or minimization calculation.
263 Conformations will be energy-minimized.
264 ********************************************************************************
266 Time for energy evaluation 0.000000000000000E+000
268 Virtual-chain energies:
270 EVDW= 6.950763E+00 WEIGHT= 1.352790D+00 (SC-SC)
271 EVDW2= 5.228224E+01 WEIGHT= 1.593040D+00 (SC-p)
272 EES= -1.132072E+02 WEIGHT= 7.153400D-01 (p-p)
273 EVDWPP= 2.375178E+01 WEIGHT= 1.137100D-01 (p-p VDW)
274 ESTR= 6.779273E-27 WEIGHT= 1.000000D+00 (stretching)
275 EBE= -1.651995E+01 WEIGHT= 1.138730D+00 (bending)
276 ESC= 7.185904E+01 WEIGHT= 1.625800D-01 (SC local)
277 ETORS= 8.243370E+00 WEIGHT= 1.985990D+00 (torsional)
278 ETORSD= 2.390466E+00 WEIGHT= 1.570690D+00 (double torsional)
279 EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
280 ECORR4= -8.338619E+01 WEIGHT= 4.288700D-01 (multi-body)
281 ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
282 ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
283 EELLO= -5.753258E+00 WEIGHT= 1.603600D-01 (electrostatic-local)
284 ETURN3= 1.901845E+01 WEIGHT= 1.687220D+00 (turns, 3rd order)
285 ETURN4= -7.304754E+00 WEIGHT= 6.623000D-01 (turns, 4th order)
286 ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order)
287 ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr)
288 EDIHC= 0.000000E+00 (dihedral angle constraints)
289 ESS= 0.000000E+00 (disulfide-bridge intrinsic energy)
290 UCONST= 0.000000E+00 (Constraint energy)
291 ETOT= 1.797273E+01 (total)
321 Constants of electrostatic interaction energy expression.
322 1 1 0.7659E+08 -0.1823E+05 -0.1306E+04 0.3727E+01
323 1 2 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00
324 2 1 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00
325 2 2 0.6367E+08 -0.1565E+05 -0.3348E+03 0.5127E+01
326 Total average electrostatic energy: -17.0351458449875
327 VDW energy between peptide-group centers: -10.2064531653452
329 Electrostatic contacts before pruning:
330 1 ASN 2 TYR 4 -1.06027
331 2 LEU 3 ILE 5 -1.59865
332 3 LEU 3 GLN 6 -0.54360
333 4 TYR 4 GLN 6 -2.10033
334 5 TYR 4 TRP 7 -0.84900
335 6 ILE 5 TRP 7 -1.85979
336 7 ILE 5 LEU 8 -0.53540
337 8 GLN 6 LEU 8 -1.48363
338 9 GLN 6 LYS 9 -0.61868
339 10 TRP 7 LYS 9 -1.55464
340 11 TRP 7 GLY 12 -0.37651
341 12 LEU 8 ASP 10 -0.61626
342 13 LEU 8 GLY 11 -0.40662
344 Electrostatic contacts after pruning:
345 1 ASN 2 TYR 4 -1.06027
346 2 LEU 3 ILE 5 -1.59865
347 3 LEU 3 GLN 6 -0.54360
348 4 TYR 4 GLN 6 -2.10033
349 5 TYR 4 TRP 7 -0.84900
350 6 ILE 5 TRP 7 -1.85979
351 7 ILE 5 LEU 8 -0.53540
352 8 GLN 6 LEU 8 -1.48363
353 9 GLN 6 LYS 9 -0.61868
354 10 TRP 7 LYS 9 -1.55464
355 11 TRP 7 GLY 12 -0.37651
356 12 LEU 8 ASP 10 -0.61626
357 13 LEU 8 GLY 11 -0.40662
361 SC_move 1189 -4.13326717681629
392 Constants of electrostatic interaction energy expression.
393 1 1 0.7659E+08 -0.1823E+05 -0.1306E+04 0.3727E+01
394 1 2 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00
395 2 1 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00
396 2 2 0.6367E+08 -0.1565E+05 -0.3348E+03 0.5127E+01
397 Total average electrostatic energy: -34.0939296423320
398 VDW energy between peptide-group centers: 899.113237730561
400 Electrostatic contacts before pruning:
401 1 ASN 2 TYR 4 -10.17518
402 2 ASN 2 ILE 5 -1.20257
403 3 LEU 3 ILE 5 -10.90405
404 4 LEU 3 GLN 6 -1.04733
405 5 LEU 3 TRP 7 -0.51328
406 6 TYR 4 GLN 6 -1.11943
407 7 TYR 4 TRP 7 -0.47363
408 8 ILE 5 TRP 7 -1.27116
409 9 GLN 6 LEU 8 -0.57639
410 10 TRP 7 LYS 9 -1.27183
411 11 TRP 7 ASP 10 -0.33671
412 12 LEU 8 ASP 10 -0.74960
413 13 LEU 8 GLY 11 -0.44794
414 14 GLY 12 SER 14 -0.51788
416 Electrostatic contacts after pruning:
417 1 ASN 2 TYR 4 -10.17518
418 2 ASN 2 ILE 5 -1.20257
419 3 LEU 3 ILE 5 -10.90405
420 4 LEU 3 GLN 6 -1.04733
421 5 LEU 3 TRP 7 -0.51328
422 6 TYR 4 GLN 6 -1.11943
423 7 TYR 4 TRP 7 -0.47363
424 8 ILE 5 TRP 7 -1.27116
425 9 GLN 6 LEU 8 -0.57639
426 10 TRP 7 LYS 9 -1.27183
427 11 TRP 7 ASP 10 -0.33671
428 12 LEU 8 ASP 10 -0.74960
429 13 LEU 8 GLY 11 -0.44794
430 14 GLY 12 SER 14 -0.51788
435 Virtual-chain energies:
437 EVDW= 6.783553E+02 WEIGHT= 1.352790D+00 (SC-SC)
438 EVDW2= 2.098526E+04 WEIGHT= 1.593040D+00 (SC-p)
439 EES= -2.316959E+02 WEIGHT= 7.153400D-01 (p-p)
440 EVDWPP= 3.102288E+03 WEIGHT= 1.137100D-01 (p-p VDW)
441 ESTR= 6.779273E-27 WEIGHT= 1.000000D+00 (stretching)
442 EBE= -1.030472E+01 WEIGHT= 1.138730D+00 (bending)
443 ESC= 5.035340E+32 WEIGHT= 1.625800D-01 (SC local)
444 ETORS= 8.256991E+00 WEIGHT= 1.985990D+00 (torsional)
445 ETORSD= 1.541091E+00 WEIGHT= 1.570690D+00 (double torsional)
446 EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
447 ECORR4= -1.142431E+02 WEIGHT= 4.288700D-01 (multi-body)
448 ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
449 ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
450 EELLO= NaN WEIGHT= 1.603600D-01 (electrostatic-local)
451 ETURN3= NaN WEIGHT= 1.687220D+00 (turns, 3rd order)
452 ETURN4= NaN WEIGHT= 6.623000D-01 (turns, 4th order)
453 ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order)
454 ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr)
455 EDIHC= 0.000000E+00 (dihedral angle constraints)
456 ESS= 0.000000E+00 (disulfide-bridge intrinsic energy)
457 UCONST= 0.000000E+00 (Constraint energy)
458 ETOT= 1.000000E+99 (total)
460 Geometry of the virtual chain.
461 Res d Theta Gamma Dsc Alpha Beta
462 D 1 0.000 0.000 0.000 0.000 0.000 0.000
463 ASN 2 3.800 0.000 0.000 1.684 166.403 -78.295
464 LEU 3 3.800 118.535 0.000 1.939 98.410 -20.526
465 TYR 4 3.800 91.262 -84.783 2.484 143.962 -14.485
466 ILE 5 3.800 0.000 74.731 1.776 126.981 -107.717
467 GLN 6 3.800 90.125 49.156 2.240 123.165 -131.319
468 TRP 7 3.800 89.563 53.467 2.605 136.415 -30.509
469 LEU 8 3.800 89.157 49.735 1.939 155.047 -119.048
470 LYS 9 3.800 90.266 80.355 2.541 138.316 -137.964
471 ASP 10 3.800 91.711 42.732 1.709 143.742 -133.222
472 GLY 11 3.800 91.876 63.556 0.000 180.000 180.000
473 GLY 12 3.800 115.894 -57.622 0.000 180.000 180.000
474 PRO 13 3.800 120.076 -75.407 1.345 106.478 -96.392
475 SER 14 3.800 92.479 -68.391 1.150 133.923 -99.369
476 SER 15 3.800 94.169 65.963 1.150 114.383 -74.889
477 GLY 16 3.800 93.692 138.023 0.000 180.000 180.000
478 ARG 17 3.800 94.409 -73.682 3.020 95.051 -65.680
479 PRO 18 3.800 130.488 58.633 1.345 120.711 -129.430
480 PRO 19 3.800 117.860 -103.495 1.345 125.023 -135.544
481 PRO 20 3.800 116.631 -108.533 1.345 97.647 -118.910
482 SER 21 3.800 93.213 -137.715 1.150 119.341 -84.219
483 D 22 3.800 120.091 73.011 0.000 180.000 180.000
484 RMS deviation from the reference structure: 2.378
485 % of native contacts: 60.870
486 % of nonnative contacts: 39.130
489 # of energy evaluations: 431
490 # of energy evaluations/sec: 3335.758
491 CG processor 0 is finishing work.
492 Total wall clock time 0.195312500000000 sec