-------------------------------------------------------------------------------- FILE ASSIGNMENT -------------------------------------------------------------------------------- Input file : 1L2Y_minim.inp Output file : 1L2Y_minim.out_GB Sidechain potential file : ../../../../PARAM/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k SCp potential file : ../../../../PARAM/scp.parm Electrostatic potential file : ../../../../PARAM/electr_631Gdp.parm Cumulant coefficient file : ../../../../PARAM/fourier_opt.parm.1igd_hc_iter3_3 Torsional parameter file : ../../../../PARAM/torsion_631Gdp.parm Double torsional parameter file : ../../../../PARAM/torsion_double_631Gdp.parm SCCOR parameter file : ../../../../PARAM/rotcorr_AM1.parm Bond & inertia constant file : ../../../../PARAM/bond.parm Bending parameter file : ../../../../PARAM/thetaml.5parm Rotamer parameter file : ../../../../PARAM/scgauss.parm Threading database : ../../../../PARAM/patterns.cart -------------------------------------------------------------------------------- ### LAST MODIFIED 03/28/12 23:29 by czarek ++++ Compile info ++++ Version 2.5 build 34 compiled Mon Apr 2 08:16:44 2012 compiled by adam@matrix.chem.cornell.edu OS name: Linux OS release: 2.6.34.9-69.fc13.x86_64 OS version: #1 SMP Tue May 3 09:23:03 UTC 2011 flags: FC = ifort FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)... FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report ... CC = cc CFLAGS = -DLINUX -DPGI -c OPT = -O3 -ip -w LIBS = -Lxdrf -lxdrf ARCH = LINUX PP = /lib/cpp -P object = unres.o arcos.o cartprint.o chainbuild... GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES ... GAB: BIN = ../../../bin/unres/MD/unres_ifort_si... E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNR... E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort... ++++ End of compile info ++++ 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 ran_num 0.930227314089531 RMSDBC = 3.0 RMSDBC1 = 0.5 RMSDBC1MAX = 1.5 DRMS = 0.1 RMSDBCM = 3.0 Time limit (min): 960.0 RESCALE_MODE 1 Library routine used to diagonalize matrices. ******************************************************************************** Options in energy minimization: ******************************************************************************** MaxMin: 2000 MaxFun: 5000MinMin: 2000 MinFun: 2000 TolF: 1.00000E-02 RTolF: 1.00000E-04 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) 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) 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 -10.407 3.153 -2.437 3 5 LEU -4.923 4.002 -2.452 -4.618 6.091 -1.850 4 8 TYR -3.690 2.738 0.981 -1.959 3.143 3.797 5 4 ILE -5.857 -0.449 0.613 -7.484 -0.369 1.074 6 13 GLN -4.122 -1.167 -2.743 -5.089 -1.450 -4.853 7 7 TRP -0.716 -0.631 -0.993 1.727 0.440 1.450 8 5 LEU -1.641 -2.932 1.963 -2.244 -2.097 3.799 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 nsup= 20 nsup= 20 nstart_sup= 2 nstart_seq= 2 NZ_START= 2 NZ_END= 21 IZ_SC= 0 Contact order: 0.308441558441558 Shifting contacts: 2 2 1 ILE 5 ASN 2 2 TRP 7 TYR 4 3 LEU 8 TYR 4 4 LEU 8 ILE 5 5 LYS 9 GLN 6 6 GLY 12 TRP 7 7 GLY 12 LEU 8 8 SER 14 GLY 11 9 SER 15 ASP 10 10 SER 15 GLY 11 11 PRO 19 TRP 7 12 PRO 20 LEU 3 13 PRO 20 TYR 4 14 PRO 20 TRP 7 Initial geometry will be read in. 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 3.800 0.000 0.000 1.684 102.356 -82.317 LEU 3 3.800 104.929 0.000 1.939 120.092 -56.685 TYR 4 3.800 87.695 -100.430 2.484 152.364 85.090 ILE 5 3.800 81.904 72.426 1.776 134.976 -88.666 GLN 6 3.800 82.466 66.026 2.240 122.343 -140.945 TRP 7 3.800 84.466 51.434 2.605 152.178 38.024 LEU 8 3.800 83.945 53.508 1.939 159.052 179.471 LYS 9 3.800 85.396 60.569 2.541 100.558 -73.090 ASP 10 3.800 91.449 44.177 1.709 139.961 -144.797 GLY 11 3.800 94.602 67.604 0.000 0.000 0.000 GLY 12 3.800 101.862 -72.814 0.000 0.000 0.000 PRO 13 3.800 119.363 -61.916 1.345 117.453 -133.163 SER 14 3.800 94.363 -75.894 1.150 137.025 -106.659 SER 15 3.800 96.264 67.358 1.150 146.290 -130.305 GLY 16 3.800 138.119 129.701 0.000 0.000 0.000 ARG 17 3.800 96.299 -95.571 3.020 93.901 -102.747 PRO 18 3.800 129.702 63.972 1.345 101.025 -111.641 PRO 19 3.800 109.445 -74.504 1.345 113.043 -122.044 PRO 20 3.800 106.349 -122.306 1.345 93.778 -102.374 SER 21 3.800 106.042 -134.605 1.150 153.835 -143.303 D 22 3.800 108.718 92.113 0.000 0.000 0.000 Energy evaluation or minimization calculation. Conformations will be energy-minimized. ******************************************************************************** Time for energy evaluation 0.000000000000000E+000 Virtual-chain energies: EVDW= -4.954316E+01 WEIGHT= 1.352790D+00 (SC-SC) EVDW2= 5.228224E+01 WEIGHT= 1.593040D+00 (SC-p) EES= -1.132072E+02 WEIGHT= 7.153400D-01 (p-p) EVDWPP= 2.375178E+01 WEIGHT= 1.137100D-01 (p-p VDW) ESTR= 6.779273E-27 WEIGHT= 1.000000D+00 (stretching) EBE= -1.651995E+01 WEIGHT= 1.138730D+00 (bending) ESC= 7.185904E+01 WEIGHT= 1.625800D-01 (SC local) ETORS= 8.243370E+00 WEIGHT= 1.985990D+00 (torsional) ETORSD= 2.390466E+00 WEIGHT= 1.570690D+00 (double torsional) EHBP= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.) ECORR4= -8.338619E+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= -5.753258E+00 WEIGHT= 1.603600D-01 (electrostatic-local) ETURN3= 1.901845E+01 WEIGHT= 1.687220D+00 (turns, 3rd order) ETURN4= -7.304754E+00 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) ETOT= -5.845169E+01 (total) PP contact map: 1 ASN 2 TYR 4 2 ASN 2 ILE 5 3 LEU 3 ILE 5 4 LEU 3 GLN 6 5 TYR 4 GLN 6 6 TYR 4 TRP 7 7 TYR 4 LEU 8 8 ILE 5 TRP 7 9 ILE 5 LEU 8 10 GLN 6 LEU 8 11 GLN 6 LYS 9 12 TRP 7 LYS 9 13 TRP 7 ASP 10 14 TRP 7 GLY 11 15 TRP 7 GLY 12 16 LEU 8 ASP 10 17 LEU 8 GLY 11 18 LYS 9 GLY 11 19 ASP 10 GLY 12 20 GLY 11 PRO 13 21 GLY 11 SER 14 22 GLY 12 SER 14 23 SER 14 GLY 16 24 SER 15 ARG 17 25 GLY 16 PRO 18 26 ARG 17 PRO 19 27 PRO 18 PRO 20 Hairpins: Constants of electrostatic interaction energy expression. 1 1 0.7659E+08 -0.1823E+05 -0.1306E+04 0.3727E+01 1 2 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00 2 1 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00 2 2 0.6367E+08 -0.1565E+05 -0.3348E+03 0.5127E+01 Total average electrostatic energy: -17.0351458449875 VDW energy between peptide-group centers: -10.2064531653452 Electrostatic contacts before pruning: 1 ASN 2 TYR 4 -1.06027 2 LEU 3 ILE 5 -1.59865 3 LEU 3 GLN 6 -0.54360 4 TYR 4 GLN 6 -2.10033 5 TYR 4 TRP 7 -0.84900 6 ILE 5 TRP 7 -1.85979 7 ILE 5 LEU 8 -0.53540 8 GLN 6 LEU 8 -1.48363 9 GLN 6 LYS 9 -0.61868 10 TRP 7 LYS 9 -1.55464 11 TRP 7 GLY 12 -0.37651 12 LEU 8 ASP 10 -0.61626 13 LEU 8 GLY 11 -0.40662 Electrostatic contacts after pruning: 1 ASN 2 TYR 4 -1.06027 2 LEU 3 ILE 5 -1.59865 3 LEU 3 GLN 6 -0.54360 4 TYR 4 GLN 6 -2.10033 5 TYR 4 TRP 7 -0.84900 6 ILE 5 TRP 7 -1.85979 7 ILE 5 LEU 8 -0.53540 8 GLN 6 LEU 8 -1.48363 9 GLN 6 LYS 9 -0.61868 10 TRP 7 LYS 9 -1.55464 11 TRP 7 GLY 12 -0.37651 12 LEU 8 ASP 10 -0.61626 13 LEU 8 GLY 11 -0.40662 Helix 1 2 10 UNRES seq: helix 3 11 SC_move 1190 -14.2312827671102 PP contact map: 1 ASN 2 TYR 4 2 ASN 2 ILE 5 3 LEU 3 ILE 5 4 LEU 3 GLN 6 5 LEU 3 TRP 7 6 TYR 4 GLN 6 7 TYR 4 TRP 7 8 TYR 4 LEU 8 9 ILE 5 TRP 7 10 ILE 5 LEU 8 11 ILE 5 LYS 9 12 GLN 6 LEU 8 13 GLN 6 LYS 9 14 TRP 7 LYS 9 15 TRP 7 ASP 10 16 TRP 7 GLY 11 17 TRP 7 GLY 12 18 LEU 8 ASP 10 19 LEU 8 GLY 11 20 LYS 9 GLY 11 21 ASP 10 GLY 12 22 GLY 11 PRO 13 23 GLY 11 SER 14 24 GLY 12 SER 14 25 PRO 13 SER 15 26 SER 14 GLY 16 27 SER 15 ARG 17 28 PRO 18 PRO 20 Hairpins: Constants of electrostatic interaction energy expression. 1 1 0.7659E+08 -0.1823E+05 -0.1306E+04 0.3727E+01 1 2 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00 2 1 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00 2 2 0.6367E+08 -0.1565E+05 -0.3348E+03 0.5127E+01 Total average electrostatic energy: -14.3281191505659 VDW energy between peptide-group centers: -22.1278543766753 Electrostatic contacts before pruning: 1 ASN 2 TYR 4 -0.80580 2 LEU 3 ILE 5 -1.08899 3 LEU 3 GLN 6 -0.51166 4 TYR 4 GLN 6 -1.35288 5 TYR 4 TRP 7 -0.71638 6 ILE 5 TRP 7 -1.25245 7 ILE 5 LEU 8 -0.56094 8 GLN 6 LEU 8 -1.12103 9 GLN 6 LYS 9 -0.52058 10 TRP 7 LYS 9 -1.15119 11 LEU 8 ASP 10 -0.71444 12 LEU 8 GLY 11 -0.38113 13 GLY 12 SER 14 -0.61187 Electrostatic contacts after pruning: 1 ASN 2 TYR 4 -0.80580 2 LEU 3 ILE 5 -1.08899 3 LEU 3 GLN 6 -0.51166 4 TYR 4 GLN 6 -1.35288 5 TYR 4 TRP 7 -0.71638 6 ILE 5 TRP 7 -1.25245 7 ILE 5 LEU 8 -0.56094 8 GLN 6 LEU 8 -1.12103 9 GLN 6 LYS 9 -0.52058 10 TRP 7 LYS 9 -1.15119 11 LEU 8 ASP 10 -0.71444 12 LEU 8 GLY 11 -0.38113 13 GLY 12 SER 14 -0.61187 Helix 1 2 10 UNRES seq: helix 3 11 Virtual-chain energies: EVDW= -5.340090E+01 WEIGHT= 1.352790D+00 (SC-SC) EVDW2= 4.677947E+01 WEIGHT= 1.593040D+00 (SC-p) EES= -9.503008E+01 WEIGHT= 7.153400D-01 (p-p) EVDWPP= -2.608496E+01 WEIGHT= 1.137100D-01 (p-p VDW) ESTR= 6.779273E-27 WEIGHT= 1.000000D+00 (stretching) EBE= -3.660091E+01 WEIGHT= 1.138730D+00 (bending) ESC= 8.674390E+01 WEIGHT= 1.625800D-01 (SC local) ETORS= 9.615105E+00 WEIGHT= 1.985990D+00 (torsional) ETORSD= 4.819701E-01 WEIGHT= 1.570690D+00 (double torsional) EHBP= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.) ECORR4= -7.040856E+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= -7.334513E+00 WEIGHT= 1.603600D-01 (electrostatic-local) ETURN3= 1.856553E+01 WEIGHT= 1.687220D+00 (turns, 3rd order) ETURN4= -3.312436E+00 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) ETOT= -7.862875E+01 (total) 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 3.800 0.000 0.000 1.684 110.702 -85.685 LEU 3 3.800 118.494 0.000 1.939 141.228 -49.540 TYR 4 3.800 91.717 -100.428 2.484 118.549 113.868 ILE 5 3.800 90.036 63.646 1.776 146.652 -96.973 GLN 6 3.800 89.040 55.793 2.240 104.893 -50.566 TRP 7 3.800 90.433 45.276 2.605 138.711 59.219 LEU 8 3.800 90.769 45.241 1.939 136.395 -145.480 LYS 9 3.800 90.500 50.320 2.541 134.179 -136.318 ASP 10 3.800 92.103 46.289 1.709 143.475 -124.446 GLY 11 3.800 91.360 65.751 0.000 180.000 180.000 GLY 12 3.800 111.681 -71.670 0.000 180.000 180.000 PRO 13 3.800 113.684 -58.655 1.345 129.775 -154.011 SER 14 3.800 93.263 -78.152 1.150 115.010 -77.057 SER 15 3.800 93.932 57.849 1.150 124.898 -144.294 GLY 16 3.800 115.865 137.415 0.000 180.000 180.000 ARG 17 3.800 94.303 -84.359 3.020 90.176 -107.687 PRO 18 3.800 121.756 61.635 1.345 116.339 -177.378 PRO 19 3.800 117.856 -81.085 1.345 141.987 -158.715 PRO 20 3.800 115.623 -108.327 1.345 97.877 -97.653 SER 21 3.800 93.855 -137.450 1.150 144.130 -129.546 D 22 3.800 117.793 46.049 0.000 180.000 180.000 RMS deviation from the reference structure: 2.067 % of native contacts: 78.571 % of nonnative contacts: 54.167 contact order: 0.348 SUMSL return code: 4 # of energy evaluations: 348 # of energy evaluations/sec: 3154.545 ***** Computation time: 0 hours 0 minutes 0 seconds *****