1 --------------------------------------------------------------------------------
3 --------------------------------------------------------------------------------
4 Input file : 1L2Y_minim.inp
5 Output file : 1L2Y_minim.out_GB000
7 Sidechain potential file :
8 /users/adam/UNRES/PARAM/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k
9 SCp potential file : /users/adam/UNRES/PARAM/scp.parm
10 Electrostatic potential file : /users/adam/UNRES/PARAM/electr_631Gdp.parm
11 Cumulant coefficient file :
12 /users/adam/UNRES/PARAM/fourier_opt.parm.1igd_hc_iter3_3
13 Torsional parameter file : /users/adam/UNRES/PARAM/torsion_631Gdp.parm
14 Double torsional parameter file :
15 /users/adam/UNRES/PARAM/torsion_double_631Gdp.parm
16 SCCOR parameter file : /users/adam/UNRES/PARAM/rotcorr_AM1.parm
17 Bond & inertia constant file : /users/adam/UNRES/PARAM/bond.parm
18 Bending parameter file : /users/adam/UNRES/PARAM/thetaml.5parm
19 Rotamer parameter file : /users/adam/UNRES/PARAM/scgauss.parm
20 Threading database : /users/adam/UNRES/PARAM/patterns.cart
21 --------------------------------------------------------------------------------
22 ********************************************************************************
23 United-residue force field calculation - parallel job.
24 ********************************************************************************
25 ### LAST MODIFIED 03/28/12 23:29 by czarek
26 ++++ Compile info ++++
28 compiled Sun May 13 16:07:22 2012
29 compiled by adam@matrix.chem.cornell.edu
31 OS release: 2.6.34.9-69.fc13.x86_64
32 OS version: #1 SMP Tue May 3 09:23:03 UTC 2011
34 INSTALL_DIR = /users/software/mpich-1.2.7p1_int...
37 FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include
38 FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)...
39 FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include
40 FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report ...
41 LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdr...
44 object = unres.o arcos.o cartprint.o chainbuild...
45 GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES ...
46 GAB: BIN = ../../../bin/unres/MD/unres_ifort_MP...
47 E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNR...
48 E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort...
49 ++++ End of compile info ++++
51 Potential is GB , exponents are 6 12
53 Disulfide bridge parameters:
54 S-S bridge energy: -5.50
55 d0cm: 3.78 akcm: 15.10
56 akth: 11.00 akct: 12.00
57 v1ss: -1.08 v2ss: 7.61 v3ss: 13.70
58 MPI: node= 0 iseed(4)= 0 0 -46
60 ran_num 6.422640197456531E-013
66 Time limit (min): 960.0
68 Library routine used to diagonalize matrices.
70 ********************************************************************************
71 Options in energy minimization:
72 ********************************************************************************
73 MaxMin: 2000 MaxFun: 5000MinMin: 2000 MinFun: 2000 TolF: 1.00000E-02 RTolF: 1.00000E-04
75 Energy-term weights (unscaled):
77 WSCC= 1.352790 (SC-SC)
79 WELEC= 0.715340 (p-p electr)
80 WVDWPP= 0.113710 (p-p VDW)
81 WBOND= 1.000000 (stretching)
82 WANG= 1.138730 (bending)
83 WSCLOC= 0.162580 (SC local)
84 WTOR= 1.985990 (torsional)
85 WTORD= 1.570690 (double torsional)
86 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
87 WEL_LOC= 0.160360 (multi-body 3-rd order)
88 WCORR4= 0.428870 (multi-body 4th order)
89 WCORR5= 0.000000 (multi-body 5th order)
90 WCORR6= 0.000000 (multi-body 6th order)
91 WSCCOR= 0.000000 (back-scloc correlation)
92 WTURN3= 1.687220 (turns, 3rd order)
93 WTURN4= 0.662300 (turns, 4th order)
94 WTURN6= 0.000000 (turns, 6th order)
96 Hydrogen-bonding correlation between contact pairs of peptide groups
98 Scaling factor of 1,4 SC-p interactions: 0.400
99 General scaling factor of SC-p interactions: 1.000
101 Energy-term weights (scaled):
103 WSCC= 1.352790 (SC-SC)
104 WSCP= 1.593040 (SC-p)
105 WELEC= 0.715340 (p-p electr)
106 WVDWPP= 0.113710 (p-p VDW)
107 WBOND= 1.000000 (stretching)
108 WANG= 1.138730 (bending)
109 WSCLOC= 0.162580 (SC local)
110 WTOR= 1.985990 (torsional)
111 WTORD= 1.570690 (double torsional)
112 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
113 WEL_LOC= 0.160360 (multi-body 3-rd order)
114 WCORR4= 0.428870 (multi-body 4th order)
115 WCORR5= 0.000000 (multi-body 5th order)
116 WCORR6= 0.000000 (multi-body 6th order)
117 WSCCOR= 0.000000 (back-scloc correlatkion)
118 WTURN3= 1.687220 (turns, 3rd order)
119 WTURN4= 0.662300 (turns, 4th order)
120 WTURN6= 0.000000 (turns, 6th order)
121 Reference temperature for weights calculation: 300.000000000000
122 Parameters of the SS-bond potential:
123 D0CM 3.78000000000000 AKCM 15.1000000000000 AKTH
124 11.0000000000000 AKCT 12.0000000000000
125 V1SS -1.08000000000000 V2SS 7.61000000000000 V3SS
127 EBR -5.50000000000000
128 PDB data will be read from file 1L2Y.pdb
130 Backbone and SC coordinates as read from the PDB
131 1 21 D -9.841 4.399 -5.051 -9.841 4.399 -5.051
132 2 14 ASN -8.608 3.135 -1.618 -10.407 3.153 -2.437
133 3 5 LEU -4.923 4.002 -2.452 -4.618 6.091 -1.850
134 4 8 TYR -3.690 2.738 0.981 -1.959 3.143 3.797
135 5 4 ILE -5.857 -0.449 0.613 -7.484 -0.369 1.074
136 6 13 GLN -4.122 -1.167 -2.743 -5.089 -1.450 -4.853
137 7 7 TRP -0.716 -0.631 -0.993 1.727 0.440 1.450
138 8 5 LEU -1.641 -2.932 1.963 -2.244 -2.097 3.799
139 9 19 LYS -3.024 -5.791 -0.269 -3.820 -5.527 -3.146
140 10 16 ASP 0.466 -6.016 -1.905 0.653 -5.125 -3.676
141 11 10 GLY 2.060 -6.618 1.593 2.060 -6.618 1.593
142 12 10 GLY 2.626 -2.967 2.723 2.626 -2.967 2.723
143 13 20 PRO 6.333 -2.533 3.806 5.724 -2.372 5.058
144 14 12 SER 7.049 -6.179 2.704 6.757 -6.938 3.675
145 15 12 SER 6.389 -5.315 -1.015 5.245 -5.350 -1.546
146 16 10 GLY 9.451 -3.116 -1.870 9.451 -3.116 -1.870
147 17 18 ARG 7.289 0.084 -2.054 5.225 -1.826 -3.986
148 18 20 PRO 6.782 3.088 0.345 7.458 3.741 -0.688
149 19 20 PRO 3.287 4.031 1.686 4.025 4.206 2.856
150 20 20 PRO 1.185 6.543 -0.353 0.358 5.421 -0.430
151 21 12 SER 0.852 10.027 1.285 1.151 10.636 1.488
152 22 21 D -1.250 12.539 -0.754 -1.250 12.539 -0.754
153 nsup= 20 nstart_sup= 2
177 Boundaries in phi angle sampling:
201 nsup= 20 nstart_sup= 2 nstart_seq= 2
202 NZ_START= 2 NZ_END= 21
204 Contact order: 0.308441558441558
205 Shifting contacts: 2 2
220 Initial geometry will be read in.
222 Geometry of the virtual chain.
223 Res d Theta Gamma Dsc Alpha Beta
224 D 1 0.000 0.000 0.000 0.000 0.000 0.000
225 ASN 2 3.800 0.000 0.000 1.684 102.356 -82.317
226 LEU 3 3.800 104.929 0.000 1.939 120.092 -56.685
227 TYR 4 3.800 87.695 -100.430 2.484 152.364 85.090
228 ILE 5 3.800 81.904 72.426 1.776 134.976 -88.666
229 GLN 6 3.800 82.466 66.026 2.240 122.343 -140.945
230 TRP 7 3.800 84.466 51.434 2.605 152.178 38.024
231 LEU 8 3.800 83.945 53.508 1.939 159.052 179.471
232 LYS 9 3.800 85.396 60.569 2.541 100.558 -73.090
233 ASP 10 3.800 91.449 44.177 1.709 139.961 -144.797
234 GLY 11 3.800 94.602 67.604 0.000 0.000 0.000
235 GLY 12 3.800 101.862 -72.814 0.000 0.000 0.000
236 PRO 13 3.800 119.363 -61.916 1.345 117.453 -133.163
237 SER 14 3.800 94.363 -75.894 1.150 137.025 -106.659
238 SER 15 3.800 96.264 67.358 1.150 146.290 -130.305
239 GLY 16 3.800 138.119 129.701 0.000 0.000 0.000
240 ARG 17 3.800 96.299 -95.571 3.020 93.901 -102.747
241 PRO 18 3.800 129.702 63.972 1.345 101.025 -111.641
242 PRO 19 3.800 109.445 -74.504 1.345 113.043 -122.044
243 PRO 20 3.800 106.349 -122.306 1.345 93.778 -102.374
244 SER 21 3.800 106.042 -134.605 1.150 153.835 -143.303
245 D 22 3.800 108.718 92.113 0.000 0.000 0.000
248 ********************************************************************************
249 Processor 0: end reading molecular data.
250 ********************************************************************************
253 Energy evaluation or minimization calculation.
255 Conformations will be energy-minimized.
256 ********************************************************************************
258 Time for energy evaluation 0.000000000000000E+000
260 Virtual-chain energies:
262 EVDW= -4.954316E+01 WEIGHT= 1.352790D+00 (SC-SC)
263 EVDW2= 5.228224E+01 WEIGHT= 1.593040D+00 (SC-p)
264 EES= -1.132072E+02 WEIGHT= 7.153400D-01 (p-p)
265 EVDWPP= 2.375178E+01 WEIGHT= 1.137100D-01 (p-p VDW)
266 ESTR= 6.779273E-27 WEIGHT= 1.000000D+00 (stretching)
267 EBE= -1.651995E+01 WEIGHT= 1.138730D+00 (bending)
268 ESC= 7.185904E+01 WEIGHT= 1.625800D-01 (SC local)
269 ETORS= 8.243370E+00 WEIGHT= 1.985990D+00 (torsional)
270 ETORSD= 2.390466E+00 WEIGHT= 1.570690D+00 (double torsional)
271 EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
272 ECORR4= -8.338619E+01 WEIGHT= 4.288700D-01 (multi-body)
273 ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
274 ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
275 EELLO= -5.753258E+00 WEIGHT= 1.603600D-01 (electrostatic-local)
276 ETURN3= 1.901845E+01 WEIGHT= 1.687220D+00 (turns, 3rd order)
277 ETURN4= -7.304754E+00 WEIGHT= 6.623000D-01 (turns, 4th order)
278 ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order)
279 ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr)
280 EDIHC= 0.000000E+00 (dihedral angle constraints)
281 ESS= 0.000000E+00 (disulfide-bridge intrinsic energy)
282 UCONST= 0.000000E+00 (Constraint energy)
283 ETOT= -5.845169E+01 (total)
313 Constants of electrostatic interaction energy expression.
314 1 1 0.7659E+08 -0.1823E+05 -0.1306E+04 0.3727E+01
315 1 2 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00
316 2 1 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00
317 2 2 0.6367E+08 -0.1565E+05 -0.3348E+03 0.5127E+01
318 Total average electrostatic energy: -17.0351458449875
319 VDW energy between peptide-group centers: -10.2064531653452
321 Electrostatic contacts before pruning:
322 1 ASN 2 TYR 4 -1.06027
323 2 LEU 3 ILE 5 -1.59865
324 3 LEU 3 GLN 6 -0.54360
325 4 TYR 4 GLN 6 -2.10033
326 5 TYR 4 TRP 7 -0.84900
327 6 ILE 5 TRP 7 -1.85979
328 7 ILE 5 LEU 8 -0.53540
329 8 GLN 6 LEU 8 -1.48363
330 9 GLN 6 LYS 9 -0.61868
331 10 TRP 7 LYS 9 -1.55464
332 11 TRP 7 GLY 12 -0.37651
333 12 LEU 8 ASP 10 -0.61626
334 13 LEU 8 GLY 11 -0.40662
336 Electrostatic contacts after pruning:
337 1 ASN 2 TYR 4 -1.06027
338 2 LEU 3 ILE 5 -1.59865
339 3 LEU 3 GLN 6 -0.54360
340 4 TYR 4 GLN 6 -2.10033
341 5 TYR 4 TRP 7 -0.84900
342 6 ILE 5 TRP 7 -1.85979
343 7 ILE 5 LEU 8 -0.53540
344 8 GLN 6 LEU 8 -1.48363
345 9 GLN 6 LYS 9 -0.61868
346 10 TRP 7 LYS 9 -1.55464
347 11 TRP 7 GLY 12 -0.37651
348 12 LEU 8 ASP 10 -0.61626
349 13 LEU 8 GLY 11 -0.40662
353 SC_move 1190 -36.8538206659302
388 Constants of electrostatic interaction energy expression.
389 1 1 0.7659E+08 -0.1823E+05 -0.1306E+04 0.3727E+01
390 1 2 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00
391 2 1 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00
392 2 2 0.6367E+08 -0.1565E+05 -0.3348E+03 0.5127E+01
393 Total average electrostatic energy: -37.0692889481661
394 VDW energy between peptide-group centers: 851.859545972044
396 Electrostatic contacts before pruning:
397 1 ASN 2 TYR 4 -9.86113
398 2 ASN 2 ILE 5 -1.53124
399 3 LEU 3 ILE 5 -10.58267
400 4 LEU 3 GLN 6 -1.25110
401 5 LEU 3 TRP 7 -0.80052
402 6 TYR 4 GLN 6 -1.33813
403 7 TYR 4 TRP 7 -0.75936
404 8 ILE 5 TRP 7 -1.25974
405 9 ILE 5 LEU 8 -0.55583
406 10 GLN 6 LEU 8 -1.12670
407 11 GLN 6 LYS 9 -0.55504
408 12 TRP 7 LYS 9 -1.20931
409 13 TRP 7 GLY 12 -0.39500
410 14 LEU 8 ASP 10 -0.66375
411 15 LEU 8 GLY 11 -0.49451
412 16 ASP 10 SER 14 -0.49993
413 17 GLY 11 PRO 13 -0.96815
415 Electrostatic contacts after pruning:
416 1 ASN 2 TYR 4 -9.86113
417 2 ASN 2 ILE 5 -1.53124
418 3 LEU 3 ILE 5 -10.58267
419 4 LEU 3 GLN 6 -1.25110
420 5 LEU 3 TRP 7 -0.80052
421 6 TYR 4 GLN 6 -1.33813
422 7 TYR 4 TRP 7 -0.75936
423 8 ILE 5 TRP 7 -1.25974
424 9 ILE 5 LEU 8 -0.55583
425 10 GLN 6 LEU 8 -1.12670
426 11 GLN 6 LYS 9 -0.55504
427 12 TRP 7 LYS 9 -1.20931
428 13 TRP 7 GLY 12 -0.39500
429 14 LEU 8 ASP 10 -0.66375
430 15 LEU 8 GLY 11 -0.49451
431 16 ASP 10 SER 14 -0.49993
432 17 GLY 11 PRO 13 -0.96815
437 Virtual-chain energies:
439 EVDW= 1.906975E+22 WEIGHT= 1.352790D+00 (SC-SC)
440 EVDW2= 2.099470E+04 WEIGHT= 1.593040D+00 (SC-p)
441 EES= -2.515997E+02 WEIGHT= 7.153400D-01 (p-p)
442 EVDWPP= 2.987216E+03 WEIGHT= 1.137100D-01 (p-p VDW)
443 ESTR= 6.779273E-27 WEIGHT= 1.000000D+00 (stretching)
444 EBE= -9.194128E+00 WEIGHT= 1.138730D+00 (bending)
445 ESC= 5.035340E+32 WEIGHT= 1.625800D-01 (SC local)
446 ETORS= 8.926809E+00 WEIGHT= 1.985990D+00 (torsional)
447 ETORSD= -4.669374E-01 WEIGHT= 1.570690D+00 (double torsional)
448 EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
449 ECORR4= -1.345056E+02 WEIGHT= 4.288700D-01 (multi-body)
450 ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
451 ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
452 EELLO= NaN WEIGHT= 1.603600D-01 (electrostatic-local)
453 ETURN3= NaN WEIGHT= 1.687220D+00 (turns, 3rd order)
454 ETURN4= NaN WEIGHT= 6.623000D-01 (turns, 4th order)
455 ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order)
456 ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr)
457 EDIHC= 0.000000E+00 (dihedral angle constraints)
458 ESS= 0.000000E+00 (disulfide-bridge intrinsic energy)
459 UCONST= 0.000000E+00 (Constraint energy)
460 ETOT= 1.000000E+99 (total)
462 Geometry of the virtual chain.
463 Res d Theta Gamma Dsc Alpha Beta
464 D 1 0.000 0.000 0.000 0.000 0.000 0.000
465 ASN 2 3.800 0.000 0.000 1.684 66.094 -81.746
466 LEU 3 3.800 118.689 0.000 1.939 138.109 -26.893
467 TYR 4 3.800 91.783 -149.590 2.484 123.984 108.154
468 ILE 5 3.800 0.000 84.251 1.776 149.498 -90.988
469 GLN 6 3.800 90.614 45.428 2.240 118.674 -118.972
470 TRP 7 3.800 90.358 42.479 2.605 163.095 48.723
471 LEU 8 3.800 90.561 45.576 1.939 145.280 -129.675
472 LYS 9 3.800 90.389 50.728 2.541 133.176 -134.505
473 ASP 10 3.800 91.852 44.664 1.709 133.932 -129.183
474 GLY 11 3.800 90.570 70.394 0.000 180.000 180.000
475 GLY 12 3.800 105.668 -67.487 0.000 180.000 180.000
476 PRO 13 3.800 99.159 -65.573 1.345 115.572 -113.582
477 SER 14 3.800 92.474 -33.144 1.150 113.504 -79.318
478 SER 15 3.800 94.029 101.491 1.150 124.420 -158.647
479 GLY 16 3.800 115.039 122.531 0.000 180.000 180.000
480 ARG 17 3.800 94.980 -88.208 3.020 101.436 -102.179
481 PRO 18 3.800 125.046 63.779 1.345 121.700 -130.547
482 PRO 19 3.800 117.245 -83.662 1.345 110.939 -109.306
483 PRO 20 3.800 121.153 -109.808 1.345 105.368 -111.814
484 SER 21 3.800 92.281 -149.201 1.150 124.532 -120.711
485 D 22 3.800 116.744 105.020 0.000 180.000 180.000
486 RMS deviation from the reference structure: 2.344
487 % of native contacts: 64.286
488 % of nonnative contacts: 57.143
491 # of energy evaluations: 553
492 # of energy evaluations/sec: 3072.000
493 CG processor 0 is finishing work.
494 Total wall clock time 0.242187500000000 sec