1 --------------------------------------------------------------------------------
3 --------------------------------------------------------------------------------
4 Input file : 1l2y_pdb.inp
5 Output file : 1l2y_pdb.out_GB000
7 Sidechain potential file :
8 /users/bartek/UNRESPACK/unres/PARAM/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-
10 SCp potential file : /users/bartek/UNRESPACK/unres/PARAM/scp.parm
11 Electrostatic potential file :
12 /users/bartek/UNRESPACK/unres/PARAM/electr_631Gdp.parm
13 Cumulant coefficient file :
14 /users/bartek/UNRESPACK/unres/PARAM/fourier_opt.parm.1igd_hc_iter3_3
15 Torsional parameter file :
16 /users/bartek/UNRESPACK/unres/PARAM/torsion_631Gdp.parm
17 Double torsional parameter file :
18 /users/bartek/UNRESPACK/unres/PARAM/torsion_double_631Gdp.parm
19 SCCOR parameter file : /users/bartek/UNRESPACK/unres/PARAM/rotcorr_AM1.parm
20 Bond & inertia constant file : /users/bartek/UNRESPACK/unres/PARAM/bond.parm
21 Bending parameter file :
22 /users/bartek/UNRESPACK/unres/PARAM/thetaml.5parm
23 Rotamer parameter file :
24 /users/bartek/UNRESPACK/unres/PARAM/scgauss.parm
26 /users/bartek/UNRESPACK/unres/PARAM/patterns.cart
27 --------------------------------------------------------------------------------
28 ********************************************************************************
29 United-residue force field calculation - parallel job.
30 ********************************************************************************
31 ### LAST MODIFIED 11/03/09 1:19PM by czarek
32 ++++ Compile info ++++
33 Version CSA and DFA only
35 Potential is GB , exponents are 6 12
37 Disulfide bridge parameters:
38 S-S bridge energy: -5.50
39 d0cm: 3.78 akcm: 15.10
40 akth: 11.00 akct: 12.00
41 v1ss: -1.08 v2ss: 7.61 v3ss: 13.70
42 MPI: node= 0 iseed= -3059742
43 ran_num 0.273754117333397
49 Time limit (min): 960.0
51 Library routine used to diagonalize matrices.
53 Energy-term weights (unscaled):
55 WSCC= 1.352790 (SC-SC)
57 WELEC= 0.715340 (p-p electr)
58 WVDWPP= 0.113710 (p-p VDW)
59 WBOND= 1.000000 (stretching)
60 WANG= 1.138730 (bending)
61 WSCLOC= 0.162580 (SC local)
62 WTOR= 1.985990 (torsional)
63 WTORD= 1.570690 (double torsional)
64 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
65 WEL_LOC= 0.160360 (multi-body 3-rd order)
66 WCORR4= 0.428870 (multi-body 4th order)
67 WCORR5= 0.000000 (multi-body 5th order)
68 WCORR6= 0.000000 (multi-body 6th order)
69 WSCCOR= 0.000000 (back-scloc correlation)
70 WTURN3= 1.687220 (turns, 3rd order)
71 WTURN4= 0.662300 (turns, 4th order)
72 WTURN6= 0.000000 (turns, 6th order)
73 WDFA_D= 0.000000 (DFA, distance)
74 WDFA_T= 0.000000 (DFA, torsional)
75 WDFA_N= 0.000000 (DFA, number of neighbor)
76 WDFA_B= 0.000000 (DFA, beta formation)
78 Hydrogen-bonding correlation between contact pairs of peptide groups
80 Scaling factor of 1,4 SC-p interactions: 0.400
81 General scaling factor of SC-p interactions: 1.000
83 Energy-term weights (scaled):
85 WSCC= 1.352790 (SC-SC)
87 WELEC= 0.715340 (p-p electr)
88 WVDWPP= 0.113710 (p-p VDW)
89 WBOND= 1.000000 (stretching)
90 WANG= 1.138730 (bending)
91 WSCLOC= 0.162580 (SC local)
92 WTOR= 1.985990 (torsional)
93 WTORD= 1.570690 (double torsional)
94 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
95 WEL_LOC= 0.160360 (multi-body 3-rd order)
96 WCORR4= 0.428870 (multi-body 4th order)
97 WCORR5= 0.000000 (multi-body 5th order)
98 WCORR6= 0.000000 (multi-body 6th order)
99 WSCCOR= 0.000000 (back-scloc correlatkion)
100 WTURN3= 1.687220 (turns, 3rd order)
101 WTURN4= 0.662300 (turns, 4th order)
102 WTURN6= 0.000000 (turns, 6th order)
103 WDFA_D= 0.000000 (DFA, distance)
104 WDFA_T= 0.000000 (DFA, torsional)
105 WDFA_N= 0.000000 (DFA, number of neighbor)
106 WDFA_B= 0.000000 (DFA, beta formation)
107 Reference temperature for weights calculation: 300.000000000000
108 Parameters of the SS-bond potential:
109 D0CM 3.78000000000000 AKCM 15.1000000000000 AKTH
110 11.0000000000000 AKCT 12.0000000000000
111 V1SS -1.08000000000000 V2SS 7.61000000000000 V3SS
113 EBR -5.50000000000000
114 PDB data will be read from file 1l2y.pdb
116 Backbone and SC coordinates as read from the PDB
117 1 21 D -9.841 4.399 -5.051 -9.841 4.399 -5.051
118 2 14 ASN -8.608 3.135 -1.618 -10.909 3.249 -2.846
119 3 5 LEU -4.923 4.002 -2.452 -4.502 6.849 -1.550
120 4 8 TYR -3.690 2.738 0.981 -1.959 3.143 3.797
121 5 4 ILE -5.857 -0.449 0.613 -7.910 -0.417 1.393
122 6 13 GLN -4.122 -1.167 -2.743 -5.540 -1.315 -5.233
123 7 7 TRP -0.716 -0.631 -0.993 1.727 0.440 1.450
124 8 5 LEU -1.641 -2.932 1.963 -2.262 -1.871 4.556
125 9 19 LYS -3.024 -5.791 -0.269 -3.820 -5.527 -3.146
126 10 16 ASP 0.466 -6.016 -1.905 0.653 -5.125 -3.676
127 11 10 GLY 2.060 -6.618 1.593 2.060 -6.618 1.593
128 12 10 GLY 2.626 -2.967 2.723 2.626 -2.967 2.723
129 13 20 PRO 6.333 -2.533 3.806 5.724 -2.372 5.058
130 14 12 SER 7.049 -6.179 2.704 6.757 -6.938 3.675
131 15 12 SER 6.389 -5.315 -1.015 5.245 -5.350 -1.546
132 16 10 GLY 9.451 -3.116 -1.870 9.451 -3.116 -1.870
133 17 18 ARG 7.289 0.084 -2.054 5.225 -1.826 -3.986
134 18 20 PRO 6.782 3.088 0.345 7.458 3.741 -0.688
135 19 20 PRO 3.287 4.031 1.686 4.025 4.206 2.856
136 20 20 PRO 1.185 6.543 -0.353 0.358 5.421 -0.430
137 21 12 SER 0.852 10.027 1.285 1.151 10.636 1.488
138 22 21 D -1.250 12.539 -0.754 -1.250 12.539 -0.754
139 nsup= 20 nstart_sup= 2
163 Boundaries in phi angle sampling:
186 dist_dfa.dat is opened!
187 phi_dfa.dat is opened!
188 theta_dfa.dat is opened!
189 nei_dfa.dat is opened!
190 beta_dfa.dat is opened!
192 nsup= 20 nstart_sup= 2 nstart_seq= 2
193 NZ_START= 2 NZ_END= 21
195 Processor 0 CG group 0 absolute rank 0 nhpb
196 0 link_start= 1 link_end 0
197 Contact order: 0.337121212121212
198 Shifting contacts: 2 2
212 Geometry of the virtual chain.
213 Res d Theta Gamma Dsc Alpha Beta
214 D 1 0.000 0.000 0.000 0.000 0.000 0.000
215 ASN 2 3.861 0.000 0.000 2.611 90.531 -178.452
216 LEU 3 3.876 92.239 0.000 3.016 101.575 -78.530
217 TYR 4 3.861 92.239 -180.000 3.330 163.195 -7.440
218 ILE 5 3.871 90.357 45.849 2.196 148.228 -110.333
219 GLN 6 3.846 89.090 55.194 2.869 164.593 -141.638
220 TRP 7 3.867 88.657 49.396 3.617 123.650 -21.913
221 LEU 8 3.859 93.032 48.298 2.869 156.202 -108.750
222 LYS 9 3.882 94.826 46.843 2.997 106.974 -55.960
223 ASP 10 3.861 87.966 59.623 1.991 153.447 -128.646
224 GLY 11 3.891 89.908 56.679 0.000 0.000 0.000
225 GLY 12 3.864 100.181 -87.304 0.000 0.000 0.000
226 PRO 13 3.886 109.073 -127.499 1.402 101.771 -115.580
227 SER 14 3.876 89.537 4.261 1.267 144.515 -129.218
228 SER 15 3.875 91.815 66.108 1.262 161.047 -100.177
229 GLY 16 3.866 101.784 70.140 0.000 0.000 0.000
230 ARG 17 3.866 92.201 -108.949 3.411 139.846 -132.716
231 PRO 18 3.878 133.225 103.824 1.397 115.610 -118.024
232 PRO 19 3.860 121.502 -122.527 1.395 118.575 -122.417
233 PRO 20 3.858 117.950 -90.285 1.396 118.959 -126.207
234 SER 21 3.864 114.201 -108.328 0.708 128.925 -37.341
235 D 22 3.858 114.201 180.000 0.000 0.000 0.000
238 ********************************************************************************
239 Processor 0: end reading molecular data.
240 ********************************************************************************
243 Energy evaluation or minimization calculation.
245 ********************************************************************************
247 Time for energy evaluation 0.000000000000000E+000
249 Virtual-chain energies:
251 EVDW= -1.313715E+01 WEIGHT= 1.352790D+00 (SC-SC)
252 EVDW2= 4.471415E+01 WEIGHT= 1.593040D+00 (SC-p)
253 EES= -9.165378E+01 WEIGHT= 7.153400D-01 (p-p)
254 EVDWPP= -3.362882E+01 WEIGHT= 1.137100D-01 (p-p VDW)
255 ESTR= 1.489925E+03 WEIGHT= 1.000000D+00 (stretching)
256 EBE= -3.261471E+01 WEIGHT= 1.138730D+00 (bending)
257 ESC= 6.169976E+01 WEIGHT= 1.625800D-01 (SC local)
258 ETORS= 1.479510E+01 WEIGHT= 1.985990D+00 (torsional)
259 ETORSD= 1.006444E+00 WEIGHT= 1.570690D+00 (double torsional)
260 EHBP= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
261 ECORR4= -6.528803E+01 WEIGHT= 4.288700D-01 (multi-body)
262 ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
263 ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
264 EELLO= -4.012900E+00 WEIGHT= 1.603600D-01 (electrostatic-local)
265 ETURN3= 1.829789E+01 WEIGHT= 1.687220D+00 (turns, 3rd order)
266 ETURN4= 6.580750E-01 WEIGHT= 6.623000D-01 (turns, 4th order)
267 ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order)
268 ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr)
269 EDIHC= 0.000000E+00 (dihedral angle constraints)
270 ESS= 0.000000E+00 (disulfide-bridge intrinsic energy)
271 UCONST= 0.000000E+00 (Constraint energy)
272 EDFAD= 0.000000E+00 (DFA distance energy)
273 EDFAT= 0.000000E+00 (DFA torsion energy)
274 EDFAN= 0.000000E+00 (DFA NCa energy)
275 EDFAB= 0.000000E+00 (DFA Beta energy)
276 ETOT= 1.480518E+03 (total)
277 RMS deviation from the reference structure: 0.000
278 % of native contacts: 100.000
279 % of nonnative contacts: 0.000
281 CG processor 0 is finishing work.
282 Total wall clock time 1.12500000000000 sec