1 --------------------------------------------------------------------------------
3 --------------------------------------------------------------------------------
4 Input file : 1L2Y_minim.inp
5 Output file : 1L2Y_minim.out_GB
7 Sidechain potential file :
8 ../../../../PARAM/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k
9 SCp potential file : ../../../../PARAM/scp.parm
10 Electrostatic potential file : ../../../../PARAM/electr_631Gdp.parm
11 Cumulant coefficient file :
12 ../../../../PARAM/fourier_opt.parm.1igd_hc_iter3_3
13 Torsional parameter file : ../../../../PARAM/torsion_631Gdp.parm
14 Double torsional parameter file : ../../../../PARAM/torsion_double_631Gdp.parm
15 SCCOR parameter file : ../../../../PARAM/rotcorr_AM1.parm
16 Bond & inertia constant file : ../../../../PARAM/bond.parm
17 Bending parameter file : ../../../../PARAM/thetaml.5parm
18 Rotamer parameter file : ../../../../PARAM/scgauss.parm
19 Threading database : ../../../../PARAM/patterns.cart
20 --------------------------------------------------------------------------------
21 ### LAST MODIFIED 03/28/12 23:29 by czarek
22 ++++ Compile info ++++
24 compiled Mon Apr 2 08:16:44 2012
25 compiled by adam@matrix.chem.cornell.edu
27 OS release: 2.6.34.9-69.fc13.x86_64
28 OS version: #1 SMP Tue May 3 09:23:03 UTC 2011
31 FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include
32 FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)...
33 FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include
34 FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report ...
36 CFLAGS = -DLINUX -DPGI -c
41 object = unres.o arcos.o cartprint.o chainbuild...
42 GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES ...
43 GAB: BIN = ../../../bin/unres/MD/unres_ifort_si...
44 E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNR...
45 E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort...
46 ++++ End of compile info ++++
48 Potential is GB , exponents are 6 12
50 Disulfide bridge parameters:
51 S-S bridge energy: -5.50
52 d0cm: 3.78 akcm: 15.10
53 akth: 11.00 akct: 12.00
54 v1ss: -1.08 v2ss: 7.61 v3ss: 13.70
55 ran_num 0.930227314089531
61 Time limit (min): 960.0
63 Library routine used to diagonalize matrices.
65 ********************************************************************************
66 Options in energy minimization:
67 ********************************************************************************
68 MaxMin: 2000 MaxFun: 5000MinMin: 2000 MinFun: 2000 TolF: 1.00000E-02 RTolF: 1.00000E-04
70 Energy-term weights (unscaled):
72 WSCC= 1.352790 (SC-SC)
74 WELEC= 0.715340 (p-p electr)
75 WVDWPP= 0.113710 (p-p VDW)
76 WBOND= 1.000000 (stretching)
77 WANG= 1.138730 (bending)
78 WSCLOC= 0.162580 (SC local)
79 WTOR= 1.985990 (torsional)
80 WTORD= 1.570690 (double torsional)
81 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
82 WEL_LOC= 0.160360 (multi-body 3-rd order)
83 WCORR4= 0.428870 (multi-body 4th order)
84 WCORR5= 0.000000 (multi-body 5th order)
85 WCORR6= 0.000000 (multi-body 6th order)
86 WSCCOR= 0.000000 (back-scloc correlation)
87 WTURN3= 1.687220 (turns, 3rd order)
88 WTURN4= 0.662300 (turns, 4th order)
89 WTURN6= 0.000000 (turns, 6th order)
91 Hydrogen-bonding correlation between contact pairs of peptide groups
93 Scaling factor of 1,4 SC-p interactions: 0.400
94 General scaling factor of SC-p interactions: 1.000
96 Energy-term weights (scaled):
98 WSCC= 1.352790 (SC-SC)
100 WELEC= 0.715340 (p-p electr)
101 WVDWPP= 0.113710 (p-p VDW)
102 WBOND= 1.000000 (stretching)
103 WANG= 1.138730 (bending)
104 WSCLOC= 0.162580 (SC local)
105 WTOR= 1.985990 (torsional)
106 WTORD= 1.570690 (double torsional)
107 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
108 WEL_LOC= 0.160360 (multi-body 3-rd order)
109 WCORR4= 0.428870 (multi-body 4th order)
110 WCORR5= 0.000000 (multi-body 5th order)
111 WCORR6= 0.000000 (multi-body 6th order)
112 WSCCOR= 0.000000 (back-scloc correlatkion)
113 WTURN3= 1.687220 (turns, 3rd order)
114 WTURN4= 0.662300 (turns, 4th order)
115 WTURN6= 0.000000 (turns, 6th order)
116 Reference temperature for weights calculation: 300.000000000000
117 Parameters of the SS-bond potential:
118 D0CM 3.78000000000000 AKCM 15.1000000000000 AKTH
119 11.0000000000000 AKCT 12.0000000000000
120 V1SS -1.08000000000000 V2SS 7.61000000000000 V3SS
122 EBR -5.50000000000000
123 PDB data will be read from file 1L2Y.pdb
125 Backbone and SC coordinates as read from the PDB
126 1 21 D -9.841 4.399 -5.051 -9.841 4.399 -5.051
127 2 14 ASN -8.608 3.135 -1.618 -10.407 3.153 -2.437
128 3 5 LEU -4.923 4.002 -2.452 -4.618 6.091 -1.850
129 4 8 TYR -3.690 2.738 0.981 -1.959 3.143 3.797
130 5 4 ILE -5.857 -0.449 0.613 -7.484 -0.369 1.074
131 6 13 GLN -4.122 -1.167 -2.743 -5.089 -1.450 -4.853
132 7 7 TRP -0.716 -0.631 -0.993 1.727 0.440 1.450
133 8 5 LEU -1.641 -2.932 1.963 -2.244 -2.097 3.799
134 9 19 LYS -3.024 -5.791 -0.269 -3.820 -5.527 -3.146
135 10 16 ASP 0.466 -6.016 -1.905 0.653 -5.125 -3.676
136 11 10 GLY 2.060 -6.618 1.593 2.060 -6.618 1.593
137 12 10 GLY 2.626 -2.967 2.723 2.626 -2.967 2.723
138 13 20 PRO 6.333 -2.533 3.806 5.724 -2.372 5.058
139 14 12 SER 7.049 -6.179 2.704 6.757 -6.938 3.675
140 15 12 SER 6.389 -5.315 -1.015 5.245 -5.350 -1.546
141 16 10 GLY 9.451 -3.116 -1.870 9.451 -3.116 -1.870
142 17 18 ARG 7.289 0.084 -2.054 5.225 -1.826 -3.986
143 18 20 PRO 6.782 3.088 0.345 7.458 3.741 -0.688
144 19 20 PRO 3.287 4.031 1.686 4.025 4.206 2.856
145 20 20 PRO 1.185 6.543 -0.353 0.358 5.421 -0.430
146 21 12 SER 0.852 10.027 1.285 1.151 10.636 1.488
147 22 21 D -1.250 12.539 -0.754 -1.250 12.539 -0.754
148 nsup= 20 nstart_sup= 2
172 Boundaries in phi angle sampling:
196 nsup= 20 nstart_sup= 2 nstart_seq= 2
197 NZ_START= 2 NZ_END= 21
199 Contact order: 0.308441558441558
200 Shifting contacts: 2 2
215 Initial geometry will be read in.
217 Geometry of the virtual chain.
218 Res d Theta Gamma Dsc Alpha Beta
219 D 1 0.000 0.000 0.000 0.000 0.000 0.000
220 ASN 2 3.800 0.000 0.000 1.684 102.356 -82.317
221 LEU 3 3.800 104.929 0.000 1.939 120.092 -56.685
222 TYR 4 3.800 87.695 -100.430 2.484 152.364 85.090
223 ILE 5 3.800 81.904 72.426 1.776 134.976 -88.666
224 GLN 6 3.800 82.466 66.026 2.240 122.343 -140.945
225 TRP 7 3.800 84.466 51.434 2.605 152.178 38.024
226 LEU 8 3.800 83.945 53.508 1.939 159.052 179.471
227 LYS 9 3.800 85.396 60.569 2.541 100.558 -73.090
228 ASP 10 3.800 91.449 44.177 1.709 139.961 -144.797
229 GLY 11 3.800 94.602 67.604 0.000 0.000 0.000
230 GLY 12 3.800 101.862 -72.814 0.000 0.000 0.000
231 PRO 13 3.800 119.363 -61.916 1.345 117.453 -133.163
232 SER 14 3.800 94.363 -75.894 1.150 137.025 -106.659
233 SER 15 3.800 96.264 67.358 1.150 146.290 -130.305
234 GLY 16 3.800 138.119 129.701 0.000 0.000 0.000
235 ARG 17 3.800 96.299 -95.571 3.020 93.901 -102.747
236 PRO 18 3.800 129.702 63.972 1.345 101.025 -111.641
237 PRO 19 3.800 109.445 -74.504 1.345 113.043 -122.044
238 PRO 20 3.800 106.349 -122.306 1.345 93.778 -102.374
239 SER 21 3.800 106.042 -134.605 1.150 153.835 -143.303
240 D 22 3.800 108.718 92.113 0.000 0.000 0.000
241 Energy evaluation or minimization calculation.
243 Conformations will be energy-minimized.
244 ********************************************************************************
246 Time for energy evaluation 0.000000000000000E+000
248 Virtual-chain energies:
250 EVDW= -4.954316E+01 WEIGHT= 1.352790D+00 (SC-SC)
251 EVDW2= 5.228224E+01 WEIGHT= 1.593040D+00 (SC-p)
252 EES= -1.132072E+02 WEIGHT= 7.153400D-01 (p-p)
253 EVDWPP= 2.375178E+01 WEIGHT= 1.137100D-01 (p-p VDW)
254 ESTR= 6.779273E-27 WEIGHT= 1.000000D+00 (stretching)
255 EBE= -1.651995E+01 WEIGHT= 1.138730D+00 (bending)
256 ESC= 7.185904E+01 WEIGHT= 1.625800D-01 (SC local)
257 ETORS= 8.243370E+00 WEIGHT= 1.985990D+00 (torsional)
258 ETORSD= 2.390466E+00 WEIGHT= 1.570690D+00 (double torsional)
259 EHBP= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
260 ECORR4= -8.338619E+01 WEIGHT= 4.288700D-01 (multi-body)
261 ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
262 ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
263 EELLO= -5.753258E+00 WEIGHT= 1.603600D-01 (electrostatic-local)
264 ETURN3= 1.901845E+01 WEIGHT= 1.687220D+00 (turns, 3rd order)
265 ETURN4= -7.304754E+00 WEIGHT= 6.623000D-01 (turns, 4th order)
266 ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order)
267 ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr)
268 EDIHC= 0.000000E+00 (dihedral angle constraints)
269 ESS= 0.000000E+00 (disulfide-bridge intrinsic energy)
270 UCONST= 0.000000E+00 (Constraint energy)
271 ETOT= -5.845169E+01 (total)
301 Constants of electrostatic interaction energy expression.
302 1 1 0.7659E+08 -0.1823E+05 -0.1306E+04 0.3727E+01
303 1 2 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00
304 2 1 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00
305 2 2 0.6367E+08 -0.1565E+05 -0.3348E+03 0.5127E+01
306 Total average electrostatic energy: -17.0351458449875
307 VDW energy between peptide-group centers: -10.2064531653452
309 Electrostatic contacts before pruning:
310 1 ASN 2 TYR 4 -1.06027
311 2 LEU 3 ILE 5 -1.59865
312 3 LEU 3 GLN 6 -0.54360
313 4 TYR 4 GLN 6 -2.10033
314 5 TYR 4 TRP 7 -0.84900
315 6 ILE 5 TRP 7 -1.85979
316 7 ILE 5 LEU 8 -0.53540
317 8 GLN 6 LEU 8 -1.48363
318 9 GLN 6 LYS 9 -0.61868
319 10 TRP 7 LYS 9 -1.55464
320 11 TRP 7 GLY 12 -0.37651
321 12 LEU 8 ASP 10 -0.61626
322 13 LEU 8 GLY 11 -0.40662
324 Electrostatic contacts after pruning:
325 1 ASN 2 TYR 4 -1.06027
326 2 LEU 3 ILE 5 -1.59865
327 3 LEU 3 GLN 6 -0.54360
328 4 TYR 4 GLN 6 -2.10033
329 5 TYR 4 TRP 7 -0.84900
330 6 ILE 5 TRP 7 -1.85979
331 7 ILE 5 LEU 8 -0.53540
332 8 GLN 6 LEU 8 -1.48363
333 9 GLN 6 LYS 9 -0.61868
334 10 TRP 7 LYS 9 -1.55464
335 11 TRP 7 GLY 12 -0.37651
336 12 LEU 8 ASP 10 -0.61626
337 13 LEU 8 GLY 11 -0.40662
341 SC_move 1190 -14.2312827671102
372 Constants of electrostatic interaction energy expression.
373 1 1 0.7659E+08 -0.1823E+05 -0.1306E+04 0.3727E+01
374 1 2 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00
375 2 1 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00
376 2 2 0.6367E+08 -0.1565E+05 -0.3348E+03 0.5127E+01
377 Total average electrostatic energy: -14.3281191505659
378 VDW energy between peptide-group centers: -22.1278543766753
380 Electrostatic contacts before pruning:
381 1 ASN 2 TYR 4 -0.80580
382 2 LEU 3 ILE 5 -1.08899
383 3 LEU 3 GLN 6 -0.51166
384 4 TYR 4 GLN 6 -1.35288
385 5 TYR 4 TRP 7 -0.71638
386 6 ILE 5 TRP 7 -1.25245
387 7 ILE 5 LEU 8 -0.56094
388 8 GLN 6 LEU 8 -1.12103
389 9 GLN 6 LYS 9 -0.52058
390 10 TRP 7 LYS 9 -1.15119
391 11 LEU 8 ASP 10 -0.71444
392 12 LEU 8 GLY 11 -0.38113
393 13 GLY 12 SER 14 -0.61187
395 Electrostatic contacts after pruning:
396 1 ASN 2 TYR 4 -0.80580
397 2 LEU 3 ILE 5 -1.08899
398 3 LEU 3 GLN 6 -0.51166
399 4 TYR 4 GLN 6 -1.35288
400 5 TYR 4 TRP 7 -0.71638
401 6 ILE 5 TRP 7 -1.25245
402 7 ILE 5 LEU 8 -0.56094
403 8 GLN 6 LEU 8 -1.12103
404 9 GLN 6 LYS 9 -0.52058
405 10 TRP 7 LYS 9 -1.15119
406 11 LEU 8 ASP 10 -0.71444
407 12 LEU 8 GLY 11 -0.38113
408 13 GLY 12 SER 14 -0.61187
413 Virtual-chain energies:
415 EVDW= -5.340090E+01 WEIGHT= 1.352790D+00 (SC-SC)
416 EVDW2= 4.677947E+01 WEIGHT= 1.593040D+00 (SC-p)
417 EES= -9.503008E+01 WEIGHT= 7.153400D-01 (p-p)
418 EVDWPP= -2.608496E+01 WEIGHT= 1.137100D-01 (p-p VDW)
419 ESTR= 6.779273E-27 WEIGHT= 1.000000D+00 (stretching)
420 EBE= -3.660091E+01 WEIGHT= 1.138730D+00 (bending)
421 ESC= 8.674390E+01 WEIGHT= 1.625800D-01 (SC local)
422 ETORS= 9.615105E+00 WEIGHT= 1.985990D+00 (torsional)
423 ETORSD= 4.819701E-01 WEIGHT= 1.570690D+00 (double torsional)
424 EHBP= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
425 ECORR4= -7.040856E+01 WEIGHT= 4.288700D-01 (multi-body)
426 ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
427 ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
428 EELLO= -7.334513E+00 WEIGHT= 1.603600D-01 (electrostatic-local)
429 ETURN3= 1.856553E+01 WEIGHT= 1.687220D+00 (turns, 3rd order)
430 ETURN4= -3.312436E+00 WEIGHT= 6.623000D-01 (turns, 4th order)
431 ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order)
432 ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr)
433 EDIHC= 0.000000E+00 (dihedral angle constraints)
434 ESS= 0.000000E+00 (disulfide-bridge intrinsic energy)
435 UCONST= 0.000000E+00 (Constraint energy)
436 ETOT= -7.862875E+01 (total)
438 Geometry of the virtual chain.
439 Res d Theta Gamma Dsc Alpha Beta
440 D 1 0.000 0.000 0.000 0.000 0.000 0.000
441 ASN 2 3.800 0.000 0.000 1.684 110.702 -85.685
442 LEU 3 3.800 118.494 0.000 1.939 141.228 -49.540
443 TYR 4 3.800 91.717 -100.428 2.484 118.549 113.868
444 ILE 5 3.800 90.036 63.646 1.776 146.652 -96.973
445 GLN 6 3.800 89.040 55.793 2.240 104.893 -50.566
446 TRP 7 3.800 90.433 45.276 2.605 138.711 59.219
447 LEU 8 3.800 90.769 45.241 1.939 136.395 -145.480
448 LYS 9 3.800 90.500 50.320 2.541 134.179 -136.318
449 ASP 10 3.800 92.103 46.289 1.709 143.475 -124.446
450 GLY 11 3.800 91.360 65.751 0.000 180.000 180.000
451 GLY 12 3.800 111.681 -71.670 0.000 180.000 180.000
452 PRO 13 3.800 113.684 -58.655 1.345 129.775 -154.011
453 SER 14 3.800 93.263 -78.152 1.150 115.010 -77.057
454 SER 15 3.800 93.932 57.849 1.150 124.898 -144.294
455 GLY 16 3.800 115.865 137.415 0.000 180.000 180.000
456 ARG 17 3.800 94.303 -84.359 3.020 90.176 -107.687
457 PRO 18 3.800 121.756 61.635 1.345 116.339 -177.378
458 PRO 19 3.800 117.856 -81.085 1.345 141.987 -158.715
459 PRO 20 3.800 115.623 -108.327 1.345 97.877 -97.653
460 SER 21 3.800 93.855 -137.450 1.150 144.130 -129.546
461 D 22 3.800 117.793 46.049 0.000 180.000 180.000
462 RMS deviation from the reference structure: 2.067
463 % of native contacts: 78.571
464 % of nonnative contacts: 54.167
467 # of energy evaluations: 348
468 # of energy evaluations/sec: 3154.545
471 ***** Computation time: 0 hours 0 minutes 0 seconds *****