MODELLER 9.16, 2016/01/07, r10745 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2016 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux sunflower.rnet.missouri.edu 2.6.32-431.23.3.el6.x86_64 x86_64 Date and time of compilation : 2016/01/07 10:19:44 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2016/04/05 22:42:10 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v16}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v16}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191562 187.072 0.183 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192090 187.588 0.183 openf___224_> Open ${MODINSTALL9v16}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240690 235.049 0.230 rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf___224_> Open ${MODINSTALL9v16}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253990 248.037 0.242 openf___224_> Open ${MODINSTALL9v16}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v16}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v16}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v16}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v16}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v16}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 openf___224_> Open 1cuk-a2.mrc MRC file 1cuk-a2.mrc read in 32-bit mode: grid 40x40x40 MAP > Writing EM density map. MAP > ============================================== openf___224_> Open EM_map.MRC MRC file EM_map.MRC written: grid 40x40x40 CCF > grid_sqr_sum= 569.89 openf___224_> Open test-cr.log openf___224_> Open 1cuk-a2.pdb openf___224_> Open 1cuk-a2.pdb dock > Docking protein no. 1: 1cuk-a2.pdb dock > ===================================================================== openf___224_> Open bestCC_1cuk openf___224_> Open 1cuk_init_1.pdb C2MAP > probe_grid_sqr_sum= 4086559.9841 MAP > Writing density map. 1: 1cuk-a2.pdb MAP > ==================================================================== openf___224_> Open 1cuk_init.MRC MRC file 1cuk_init.MRC written: grid 40x40x40 CCF > improved score= 40370.0614 dock > The first center of mass of the protein on the grid (x, y, z): 20.5 20.5 20.5 dock > The first global score is: 0.8365 dock > Starting translation/rotation search dock > =============================================================== rotate > Summary of search round 1 - increase in the score rotate > Orientation range: rotate > phi= 0.0->360.0 theta= 0.0->180.0 psi= 0.0->360.0 rotate > Step size: 30.00 rotate > The rotation angles (phi, teta, psi) for the best fit are: rotate > 0.0 0.0 0.0 rotate > The translation vector (x, y, z) for the best fit is: rotate > 0.0 0.0 0.0 rotate > The simple score is: 1464.61 rotate > -------------------------------------------------------------- rotate > Summary of search round 2 - increase in the score rotate > Orientation range: rotate > phi=-20.0-> 20.0 theta=-20.0-> 20.0 psi=-20.0-> 20.0 rotate > Step size: 6.00 rotate > The rotation angles (phi, teta, psi) for the best fit are: rotate > -2.0 -2.0 4.0 rotate > The translation vector (x, y, z) for the best fit is: rotate > 0.7 -1.5 0.7 rotate > The simple score is: 1479.25 rotate > -------------------------------------------------------------- rotate > Search round 3 - no increase in the score rotate > -------------------------------------------------------------- rotate > Search round 4 - no increase in the score rotate > -------------------------------------------------------------- CCF > improved score= 40371.4684 openf___224_> Open 1cuk_1_1.pdb Grid unit 1 The best score(s): center of mass of the best position X=20.5 Y=20.5 Z=20.5 Solution 1 0.8366 C2MAP > probe_grid_sqr_sum= 4119208.6907 MAP > Writing density map. 1: 1cuk-a2.pdb MAP > ==================================================================== openf___224_> Open 1cuk_best.MRC MRC file 1cuk_best.MRC written: grid 40x40x40 Dynamically allocated memory at finish [B,KiB,MiB]: 510402 498.439 0.487 Starting time : 2016/04/05 22:42:10 Closing time : 2016/04/05 22:42:10 Total CPU time [seconds] : 0.19