-------------------------------------------------------------------------------- FILE ASSIGNMENT -------------------------------------------------------------------------------- Input file : 1L2Y_minim.inp Output file : 1L2Y_minim.out_GB000 Sidechain potential file : /users/adam/UNRES/PARAM/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k 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 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(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: 0.308441558441558 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 ******************************************************************************** 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= -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) 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= -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 -36.8538206659302 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 LEU 3 LEU 8 7 TYR 4 GLN 6 8 TYR 4 TRP 7 9 TYR 4 LEU 8 10 ILE 5 TRP 7 11 ILE 5 LEU 8 12 ILE 5 LYS 9 13 GLN 6 LEU 8 14 GLN 6 LYS 9 15 TRP 7 LYS 9 16 TRP 7 ASP 10 17 TRP 7 GLY 11 18 TRP 7 GLY 12 19 LEU 8 ASP 10 20 LEU 8 GLY 11 21 LEU 8 GLY 12 22 LYS 9 GLY 11 23 ASP 10 GLY 12 24 ASP 10 PRO 13 25 ASP 10 SER 14 26 GLY 11 PRO 13 27 GLY 11 SER 14 28 GLY 12 SER 14 29 PRO 13 SER 15 30 SER 14 GLY 16 31 SER 15 ARG 17 32 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: -37.0692889481661 VDW energy between peptide-group centers: 851.859545972044 Electrostatic contacts before pruning: 1 ASN 2 TYR 4 -9.86113 2 ASN 2 ILE 5 -1.53124 3 LEU 3 ILE 5 -10.58267 4 LEU 3 GLN 6 -1.25110 5 LEU 3 TRP 7 -0.80052 6 TYR 4 GLN 6 -1.33813 7 TYR 4 TRP 7 -0.75936 8 ILE 5 TRP 7 -1.25974 9 ILE 5 LEU 8 -0.55583 10 GLN 6 LEU 8 -1.12670 11 GLN 6 LYS 9 -0.55504 12 TRP 7 LYS 9 -1.20931 13 TRP 7 GLY 12 -0.39500 14 LEU 8 ASP 10 -0.66375 15 LEU 8 GLY 11 -0.49451 16 ASP 10 SER 14 -0.49993 17 GLY 11 PRO 13 -0.96815 Electrostatic contacts after pruning: 1 ASN 2 TYR 4 -9.86113 2 ASN 2 ILE 5 -1.53124 3 LEU 3 ILE 5 -10.58267 4 LEU 3 GLN 6 -1.25110 5 LEU 3 TRP 7 -0.80052 6 TYR 4 GLN 6 -1.33813 7 TYR 4 TRP 7 -0.75936 8 ILE 5 TRP 7 -1.25974 9 ILE 5 LEU 8 -0.55583 10 GLN 6 LEU 8 -1.12670 11 GLN 6 LYS 9 -0.55504 12 TRP 7 LYS 9 -1.20931 13 TRP 7 GLY 12 -0.39500 14 LEU 8 ASP 10 -0.66375 15 LEU 8 GLY 11 -0.49451 16 ASP 10 SER 14 -0.49993 17 GLY 11 PRO 13 -0.96815 Helix 1 3 10 UNRES seq: helix 4 11 Virtual-chain energies: EVDW= 1.906975E+22 WEIGHT= 1.352790D+00 (SC-SC) EVDW2= 2.099470E+04 WEIGHT= 1.593040D+00 (SC-p) EES= -2.515997E+02 WEIGHT= 7.153400D-01 (p-p) EVDWPP= 2.987216E+03 WEIGHT= 1.137100D-01 (p-p VDW) ESTR= 6.779273E-27 WEIGHT= 1.000000D+00 (stretching) EBE= -9.194128E+00 WEIGHT= 1.138730D+00 (bending) ESC= 5.035340E+32 WEIGHT= 1.625800D-01 (SC local) ETORS= 8.926809E+00 WEIGHT= 1.985990D+00 (torsional) ETORSD= -4.669374E-01 WEIGHT= 1.570690D+00 (double torsional) EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.) ECORR4= -1.345056E+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 66.094 -81.746 LEU 3 3.800 118.689 0.000 1.939 138.109 -26.893 TYR 4 3.800 91.783 -149.590 2.484 123.984 108.154 ILE 5 3.800 0.000 84.251 1.776 149.498 -90.988 GLN 6 3.800 90.614 45.428 2.240 118.674 -118.972 TRP 7 3.800 90.358 42.479 2.605 163.095 48.723 LEU 8 3.800 90.561 45.576 1.939 145.280 -129.675 LYS 9 3.800 90.389 50.728 2.541 133.176 -134.505 ASP 10 3.800 91.852 44.664 1.709 133.932 -129.183 GLY 11 3.800 90.570 70.394 0.000 180.000 180.000 GLY 12 3.800 105.668 -67.487 0.000 180.000 180.000 PRO 13 3.800 99.159 -65.573 1.345 115.572 -113.582 SER 14 3.800 92.474 -33.144 1.150 113.504 -79.318 SER 15 3.800 94.029 101.491 1.150 124.420 -158.647 GLY 16 3.800 115.039 122.531 0.000 180.000 180.000 ARG 17 3.800 94.980 -88.208 3.020 101.436 -102.179 PRO 18 3.800 125.046 63.779 1.345 121.700 -130.547 PRO 19 3.800 117.245 -83.662 1.345 110.939 -109.306 PRO 20 3.800 121.153 -109.808 1.345 105.368 -111.814 SER 21 3.800 92.281 -149.201 1.150 124.532 -120.711 D 22 3.800 116.744 105.020 0.000 180.000 180.000 RMS deviation from the reference structure: 2.344 % of native contacts: 64.286 % of nonnative contacts: 57.143 contact order: 0.253 SUMSL return code: 4 # of energy evaluations: 553 # of energy evaluations/sec: 3072.000 CG processor 0 is finishing work. Total wall clock time 0.242187500000000 sec