-------------------------------------------------------------------------------- FILE ASSIGNMENT -------------------------------------------------------------------------------- Input file : 1L2Y_minim.inp Output file : 1L2Y_minim.out_LJ000 Sidechain potential file : /users/adam/UNRES/PARAM/scinter_LJ.parm SCp potential file : /users/adam/UNRES/PARAM/scp.parm Electrostatic potential file : /users/adam/UNRES/PARAM/electr_631Gdp.parm Cumulant coefficient file : /users/adam/UNRES/PARAM/fourier_opt.parm.1igd_hc_iter3_3 Torsional parameter file : /users/adam/UNRES/PARAM/torsion_631Gdp.parm Double torsional parameter file : /users/adam/UNRES/PARAM/torsion_double_631Gdp.parm SCCOR parameter file : /users/adam/UNRES/PARAM/rotcorr_AM1.parm Bond & inertia constant file : /users/adam/UNRES/PARAM/bond.parm Bending parameter file : /users/adam/UNRES/PARAM/thetaml.5parm Rotamer parameter file : /users/adam/UNRES/PARAM/scgauss.parm Threading database : /users/adam/UNRES/PARAM/patterns.cart -------------------------------------------------------------------------------- ******************************************************************************** United-residue force field calculation - parallel job. ******************************************************************************** ### LAST MODIFIED 03/28/12 23:29 by czarek ++++ Compile info ++++ Version 2.5 build 62 compiled Sun May 13 16:07:22 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: INSTALL_DIR = /users/software/mpich-1.2.7p1_int... FC= ifort OPT = -O3 -ip -w 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 ... LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdr... 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_MP... E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNR... E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort... ++++ End of compile info ++++ Potential is LJ , 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(4)= 0 0 -46 -45086 ran_num 6.422640197456531E-013 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: 0.320158102766798 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 11 TRP 7 7 GLY 11 LEU 8 8 GLY 12 TRP 7 9 GLY 12 LEU 8 10 PRO 13 TRP 7 11 SER 14 GLY 11 12 SER 15 TRP 7 13 SER 15 ASP 10 14 SER 15 GLY 11 15 SER 15 GLY 12 16 ARG 17 TRP 7 17 ARG 17 ASP 10 18 PRO 18 TRP 7 19 PRO 19 TYR 4 20 PRO 19 TRP 7 21 PRO 20 LEU 3 22 PRO 20 TYR 4 23 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 ******************************************************************************** Processor 0: end reading molecular data. ******************************************************************************** Energy evaluation or minimization calculation. Conformations will be energy-minimized. ******************************************************************************** Time for energy evaluation 0.000000000000000E+000 Virtual-chain energies: EVDW= 6.950763E+00 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) EHPB= 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= 1.797273E+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 1189 -4.13326717681629 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 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 PRO 13 SER 15 24 PRO 13 PRO 18 25 SER 14 GLY 16 26 SER 14 ARG 17 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: -34.0939296423320 VDW energy between peptide-group centers: 899.113237730561 Electrostatic contacts before pruning: 1 ASN 2 TYR 4 -10.17518 2 ASN 2 ILE 5 -1.20257 3 LEU 3 ILE 5 -10.90405 4 LEU 3 GLN 6 -1.04733 5 LEU 3 TRP 7 -0.51328 6 TYR 4 GLN 6 -1.11943 7 TYR 4 TRP 7 -0.47363 8 ILE 5 TRP 7 -1.27116 9 GLN 6 LEU 8 -0.57639 10 TRP 7 LYS 9 -1.27183 11 TRP 7 ASP 10 -0.33671 12 LEU 8 ASP 10 -0.74960 13 LEU 8 GLY 11 -0.44794 14 GLY 12 SER 14 -0.51788 Electrostatic contacts after pruning: 1 ASN 2 TYR 4 -10.17518 2 ASN 2 ILE 5 -1.20257 3 LEU 3 ILE 5 -10.90405 4 LEU 3 GLN 6 -1.04733 5 LEU 3 TRP 7 -0.51328 6 TYR 4 GLN 6 -1.11943 7 TYR 4 TRP 7 -0.47363 8 ILE 5 TRP 7 -1.27116 9 GLN 6 LEU 8 -0.57639 10 TRP 7 LYS 9 -1.27183 11 TRP 7 ASP 10 -0.33671 12 LEU 8 ASP 10 -0.74960 13 LEU 8 GLY 11 -0.44794 14 GLY 12 SER 14 -0.51788 Helix 1 1 7 UNRES seq: helix 2 8 Virtual-chain energies: EVDW= 6.783553E+02 WEIGHT= 1.352790D+00 (SC-SC) EVDW2= 2.098526E+04 WEIGHT= 1.593040D+00 (SC-p) EES= -2.316959E+02 WEIGHT= 7.153400D-01 (p-p) EVDWPP= 3.102288E+03 WEIGHT= 1.137100D-01 (p-p VDW) ESTR= 6.779273E-27 WEIGHT= 1.000000D+00 (stretching) EBE= -1.030472E+01 WEIGHT= 1.138730D+00 (bending) ESC= 5.035340E+32 WEIGHT= 1.625800D-01 (SC local) ETORS= 8.256991E+00 WEIGHT= 1.985990D+00 (torsional) ETORSD= 1.541091E+00 WEIGHT= 1.570690D+00 (double torsional) EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.) ECORR4= -1.142431E+02 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= NaN WEIGHT= 1.603600D-01 (electrostatic-local) ETURN3= NaN WEIGHT= 1.687220D+00 (turns, 3rd order) ETURN4= NaN 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= 1.000000E+99 (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 1.684 166.403 -78.295 LEU 3 3.800 118.535 0.000 1.939 98.410 -20.526 TYR 4 3.800 91.262 -84.783 2.484 143.962 -14.485 ILE 5 3.800 0.000 74.731 1.776 126.981 -107.717 GLN 6 3.800 90.125 49.156 2.240 123.165 -131.319 TRP 7 3.800 89.563 53.467 2.605 136.415 -30.509 LEU 8 3.800 89.157 49.735 1.939 155.047 -119.048 LYS 9 3.800 90.266 80.355 2.541 138.316 -137.964 ASP 10 3.800 91.711 42.732 1.709 143.742 -133.222 GLY 11 3.800 91.876 63.556 0.000 180.000 180.000 GLY 12 3.800 115.894 -57.622 0.000 180.000 180.000 PRO 13 3.800 120.076 -75.407 1.345 106.478 -96.392 SER 14 3.800 92.479 -68.391 1.150 133.923 -99.369 SER 15 3.800 94.169 65.963 1.150 114.383 -74.889 GLY 16 3.800 93.692 138.023 0.000 180.000 180.000 ARG 17 3.800 94.409 -73.682 3.020 95.051 -65.680 PRO 18 3.800 130.488 58.633 1.345 120.711 -129.430 PRO 19 3.800 117.860 -103.495 1.345 125.023 -135.544 PRO 20 3.800 116.631 -108.533 1.345 97.647 -118.910 SER 21 3.800 93.213 -137.715 1.150 119.341 -84.219 D 22 3.800 120.091 73.011 0.000 180.000 180.000 RMS deviation from the reference structure: 2.378 % of native contacts: 60.870 % of nonnative contacts: 39.130 contact order: 0.300 SUMSL return code: 4 # of energy evaluations: 431 # of energy evaluations/sec: 3335.758 CG processor 0 is finishing work. Total wall clock time 0.195312500000000 sec