--- /dev/null
+--------------------------------------------------------------------------------
+ FILE ASSIGNMENT
+--------------------------------------------------------------------------------
+ Input file : 1l2y_pdb.inp
+ Output file : 1l2y_pdb.out_GB000
+
+ Sidechain potential file :
+ /users/bartek/UNRESPACK/unres/PARAM/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-
+ 10-8k
+ SCp potential file : /users/bartek/UNRESPACK/unres/PARAM/scp.parm
+ Electrostatic potential file :
+ /users/bartek/UNRESPACK/unres/PARAM/electr_631Gdp.parm
+ Cumulant coefficient file :
+ /users/bartek/UNRESPACK/unres/PARAM/fourier_opt.parm.1igd_hc_iter3_3
+ Torsional parameter file :
+ /users/bartek/UNRESPACK/unres/PARAM/torsion_631Gdp.parm
+ Double torsional parameter file :
+ /users/bartek/UNRESPACK/unres/PARAM/torsion_double_631Gdp.parm
+ SCCOR parameter file : /users/bartek/UNRESPACK/unres/PARAM/rotcorr_AM1.parm
+ Bond & inertia constant file : /users/bartek/UNRESPACK/unres/PARAM/bond.parm
+ Bending parameter file :
+ /users/bartek/UNRESPACK/unres/PARAM/thetaml.5parm
+ Rotamer parameter file :
+ /users/bartek/UNRESPACK/unres/PARAM/scgauss.parm
+ Threading database :
+ /users/bartek/UNRESPACK/unres/PARAM/patterns.cart
+--------------------------------------------------------------------------------
+********************************************************************************
+United-residue force field calculation - parallel job.
+********************************************************************************
+ ### LAST MODIFIED 11/03/09 1:19PM by czarek
+ ++++ Compile info ++++
+ Version CSA and DFA only
+
+Potential is GB , exponents are 6 12
+
+Disulfide bridge parameters:
+S-S bridge energy: -5.50
+d0cm: 3.78 akcm: 15.10
+akth: 11.00 akct: 12.00
+v1ss: -1.08 v2ss: 7.61 v3ss: 13.70
+ MPI: node= 0 iseed= -3059742
+ ran_num 0.273754117333397
+RMSDBC = 3.0
+RMSDBC1 = 0.5
+RMSDBC1MAX = 1.5
+DRMS = 0.1
+RMSDBCM = 3.0
+Time limit (min): 960.0
+ RESCALE_MODE 0
+Library routine used to diagonalize matrices.
+
+Energy-term weights (unscaled):
+
+WSCC= 1.352790 (SC-SC)
+WSCP= 1.593040 (SC-p)
+WELEC= 0.715340 (p-p electr)
+WVDWPP= 0.113710 (p-p VDW)
+WBOND= 1.000000 (stretching)
+WANG= 1.138730 (bending)
+WSCLOC= 0.162580 (SC local)
+WTOR= 1.985990 (torsional)
+WTORD= 1.570690 (double torsional)
+WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
+WEL_LOC= 0.160360 (multi-body 3-rd order)
+WCORR4= 0.428870 (multi-body 4th order)
+WCORR5= 0.000000 (multi-body 5th order)
+WCORR6= 0.000000 (multi-body 6th order)
+WSCCOR= 0.000000 (back-scloc correlation)
+WTURN3= 1.687220 (turns, 3rd order)
+WTURN4= 0.662300 (turns, 4th order)
+WTURN6= 0.000000 (turns, 6th order)
+WDFA_D= 0.000000 (DFA, distance)
+WDFA_T= 0.000000 (DFA, torsional)
+WDFA_N= 0.000000 (DFA, number of neighbor)
+WDFA_B= 0.000000 (DFA, beta formation)
+
+Hydrogen-bonding correlation between contact pairs of peptide groups
+
+Scaling factor of 1,4 SC-p interactions: 0.400
+General scaling factor of SC-p interactions: 1.000
+
+Energy-term weights (scaled):
+
+WSCC= 1.352790 (SC-SC)
+WSCP= 1.593040 (SC-p)
+WELEC= 0.715340 (p-p electr)
+WVDWPP= 0.113710 (p-p VDW)
+WBOND= 1.000000 (stretching)
+WANG= 1.138730 (bending)
+WSCLOC= 0.162580 (SC local)
+WTOR= 1.985990 (torsional)
+WTORD= 1.570690 (double torsional)
+WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
+WEL_LOC= 0.160360 (multi-body 3-rd order)
+WCORR4= 0.428870 (multi-body 4th order)
+WCORR5= 0.000000 (multi-body 5th order)
+WCORR6= 0.000000 (multi-body 6th order)
+WSCCOR= 0.000000 (back-scloc correlatkion)
+WTURN3= 1.687220 (turns, 3rd order)
+WTURN4= 0.662300 (turns, 4th order)
+WTURN6= 0.000000 (turns, 6th order)
+WDFA_D= 0.000000 (DFA, distance)
+WDFA_T= 0.000000 (DFA, torsional)
+WDFA_N= 0.000000 (DFA, number of neighbor)
+WDFA_B= 0.000000 (DFA, beta formation)
+ Reference temperature for weights calculation: 300.000000000000
+ Parameters of the SS-bond potential:
+ D0CM 3.78000000000000 AKCM 15.1000000000000 AKTH
+ 11.0000000000000 AKCT 12.0000000000000
+ V1SS -1.08000000000000 V2SS 7.61000000000000 V3SS
+ 13.7000000000000
+ EBR -5.50000000000000
+PDB data will be read from file 1l2y.pdb
+ Nres: 21
+Backbone and SC coordinates as read from the PDB
+ 1 21 D -9.841 4.399 -5.051 -9.841 4.399 -5.051
+ 2 14 ASN -8.608 3.135 -1.618 -10.909 3.249 -2.846
+ 3 5 LEU -4.923 4.002 -2.452 -4.502 6.849 -1.550
+ 4 8 TYR -3.690 2.738 0.981 -1.959 3.143 3.797
+ 5 4 ILE -5.857 -0.449 0.613 -7.910 -0.417 1.393
+ 6 13 GLN -4.122 -1.167 -2.743 -5.540 -1.315 -5.233
+ 7 7 TRP -0.716 -0.631 -0.993 1.727 0.440 1.450
+ 8 5 LEU -1.641 -2.932 1.963 -2.262 -1.871 4.556
+ 9 19 LYS -3.024 -5.791 -0.269 -3.820 -5.527 -3.146
+ 10 16 ASP 0.466 -6.016 -1.905 0.653 -5.125 -3.676
+ 11 10 GLY 2.060 -6.618 1.593 2.060 -6.618 1.593
+ 12 10 GLY 2.626 -2.967 2.723 2.626 -2.967 2.723
+ 13 20 PRO 6.333 -2.533 3.806 5.724 -2.372 5.058
+ 14 12 SER 7.049 -6.179 2.704 6.757 -6.938 3.675
+ 15 12 SER 6.389 -5.315 -1.015 5.245 -5.350 -1.546
+ 16 10 GLY 9.451 -3.116 -1.870 9.451 -3.116 -1.870
+ 17 18 ARG 7.289 0.084 -2.054 5.225 -1.826 -3.986
+ 18 20 PRO 6.782 3.088 0.345 7.458 3.741 -0.688
+ 19 20 PRO 3.287 4.031 1.686 4.025 4.206 2.856
+ 20 20 PRO 1.185 6.543 -0.353 0.358 5.421 -0.430
+ 21 12 SER 0.852 10.027 1.285 1.151 10.636 1.488
+ 22 21 D -1.250 12.539 -0.754 -1.250 12.539 -0.754
+nsup= 20 nstart_sup= 2
+ ITEL
+ 1 21 0
+ 2 14 1
+ 3 5 1
+ 4 8 1
+ 5 4 1
+ 6 13 1
+ 7 7 1
+ 8 5 1
+ 9 19 1
+ 10 16 1
+ 11 10 1
+ 12 10 2
+ 13 20 1
+ 14 12 1
+ 15 12 1
+ 16 10 1
+ 17 18 2
+ 18 20 2
+ 19 20 2
+ 20 20 1
+ 21 12 0
+ ns= 0 iss:
+Boundaries in phi angle sampling:
+D 1 -180.0 180.0
+ASN 2 -180.0 180.0
+LEU 3 -180.0 180.0
+TYR 4 -180.0 180.0
+ILE 5 -180.0 180.0
+GLN 6 -180.0 180.0
+TRP 7 -180.0 180.0
+LEU 8 -180.0 180.0
+LYS 9 -180.0 180.0
+ASP 10 -180.0 180.0
+GLY 11 -180.0 180.0
+GLY 12 -180.0 180.0
+PRO 13 -180.0 180.0
+SER 14 -180.0 180.0
+SER 15 -180.0 180.0
+GLY 16 -180.0 180.0
+ARG 17 -180.0 180.0
+PRO 18 -180.0 180.0
+PRO 19 -180.0 180.0
+PRO 20 -180.0 180.0
+SER 21 -180.0 180.0
+D 22 -180.0 180.0
+dist_dfa.dat is opened!
+phi_dfa.dat is opened!
+theta_dfa.dat is opened!
+nei_dfa.dat is opened!
+beta_dfa.dat is opened!
+nsup= 20
+ nsup= 20 nstart_sup= 2 nstart_seq= 2
+ NZ_START= 2 NZ_END= 21
+ IZ_SC= 0
+ Processor 0 CG group 0 absolute rank 0 nhpb
+ 0 link_start= 1 link_end 0
+ Contact order: 0.337121212121212
+ Shifting contacts: 2 2
+ 1 TRP 7 TYR 4
+ 2 LEU 8 TYR 4
+ 3 LYS 9 GLN 6
+ 4 GLY 12 TRP 7
+ 5 GLY 12 LEU 8
+ 6 SER 14 GLY 11
+ 7 SER 15 ASP 10
+ 8 SER 15 GLY 11
+ 9 PRO 19 TRP 7
+ 10 PRO 20 LEU 3
+ 11 PRO 20 TYR 4
+ 12 PRO 20 TRP 7
+
+Geometry of the virtual chain.
+ Res d Theta Gamma Dsc Alpha Beta
+D 1 0.000 0.000 0.000 0.000 0.000 0.000
+ASN 2 3.861 0.000 0.000 2.611 90.531 -178.452
+LEU 3 3.876 92.239 0.000 3.016 101.575 -78.530
+TYR 4 3.861 92.239 -180.000 3.330 163.195 -7.440
+ILE 5 3.871 90.357 45.849 2.196 148.228 -110.333
+GLN 6 3.846 89.090 55.194 2.869 164.593 -141.638
+TRP 7 3.867 88.657 49.396 3.617 123.650 -21.913
+LEU 8 3.859 93.032 48.298 2.869 156.202 -108.750
+LYS 9 3.882 94.826 46.843 2.997 106.974 -55.960
+ASP 10 3.861 87.966 59.623 1.991 153.447 -128.646
+GLY 11 3.891 89.908 56.679 0.000 0.000 0.000
+GLY 12 3.864 100.181 -87.304 0.000 0.000 0.000
+PRO 13 3.886 109.073 -127.499 1.402 101.771 -115.580
+SER 14 3.876 89.537 4.261 1.267 144.515 -129.218
+SER 15 3.875 91.815 66.108 1.262 161.047 -100.177
+GLY 16 3.866 101.784 70.140 0.000 0.000 0.000
+ARG 17 3.866 92.201 -108.949 3.411 139.846 -132.716
+PRO 18 3.878 133.225 103.824 1.397 115.610 -118.024
+PRO 19 3.860 121.502 -122.527 1.395 118.575 -122.417
+PRO 20 3.858 117.950 -90.285 1.396 118.959 -126.207
+SER 21 3.864 114.201 -108.328 0.708 128.925 -37.341
+D 22 3.858 114.201 180.000 0.000 0.000 0.000
+
+
+********************************************************************************
+ Processor 0: end reading molecular data.
+********************************************************************************
+
+
+Energy evaluation or minimization calculation.
+
+********************************************************************************
+
+ Time for energy evaluation 0.000000000000000E+000
+
+Virtual-chain energies:
+
+EVDW= -1.313715E+01 WEIGHT= 1.352790D+00 (SC-SC)
+EVDW2= 4.471415E+01 WEIGHT= 1.593040D+00 (SC-p)
+EES= -9.165378E+01 WEIGHT= 7.153400D-01 (p-p)
+EVDWPP= -3.362882E+01 WEIGHT= 1.137100D-01 (p-p VDW)
+ESTR= 1.489925E+03 WEIGHT= 1.000000D+00 (stretching)
+EBE= -3.261471E+01 WEIGHT= 1.138730D+00 (bending)
+ESC= 6.169976E+01 WEIGHT= 1.625800D-01 (SC local)
+ETORS= 1.479510E+01 WEIGHT= 1.985990D+00 (torsional)
+ETORSD= 1.006444E+00 WEIGHT= 1.570690D+00 (double torsional)
+EHBP= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
+ECORR4= -6.528803E+01 WEIGHT= 4.288700D-01 (multi-body)
+ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
+ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
+EELLO= -4.012900E+00 WEIGHT= 1.603600D-01 (electrostatic-local)
+ETURN3= 1.829789E+01 WEIGHT= 1.687220D+00 (turns, 3rd order)
+ETURN4= 6.580750E-01 WEIGHT= 6.623000D-01 (turns, 4th order)
+ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order)
+ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr)
+EDIHC= 0.000000E+00 (dihedral angle constraints)
+ESS= 0.000000E+00 (disulfide-bridge intrinsic energy)
+UCONST= 0.000000E+00 (Constraint energy)
+EDFAD= 0.000000E+00 (DFA distance energy)
+EDFAT= 0.000000E+00 (DFA torsion energy)
+EDFAN= 0.000000E+00 (DFA NCa energy)
+EDFAB= 0.000000E+00 (DFA Beta energy)
+ETOT= 1.480518E+03 (total)
+RMS deviation from the reference structure: 0.000
+ % of native contacts: 100.000
+ % of nonnative contacts: 0.000
+ contact order: 0.337
+CG processor 0 is finishing work.
+ Total wall clock time 1.12500000000000 sec
projects / unres.git / blobdiff