+++ /dev/null
---------------------------------------------------------------------------------
- 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 *****
projects / unres.git / blobdiff