MODELLER 8v1, Jun 20, 2005 11:37am PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2005 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, 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, WinXP build 2600 Service Pack 2, SPACERSKY, uni, x86 Family 15 Model 2 Stepping 7 Date and time of compilation : 06/21/2005 10:55:30 MODELLER executable type : i386-w32 Job starting time (YY/MM/DD HH:MM:SS): 2005/09/12 16:08:02.234 openf5__224_> Open 11 OLD SEQUENTIAL $(LIB)/restyp.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/resdih.lib 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 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/radii.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/radii14.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch1.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch2.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch3.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 runcmd______> alignment.append(align_codes=['1u13', '1ptg'], atom_files=[], file='Apnew.ali', (def)remove_gaps=True, (def)alignment_format='PIR', add_sequence=True, (def)rewind_file=False, (def)close_file=True) openf___224_> Open Apnew.ali rdpir___376W> Not enough fields in the second line of the sequence entry: 1u13 474 aa Actual fields, should be: 1 10 (Fields are separated by a colon, :) Dynamically allocated memory at amaxalignment [B,kB,MB]: 2124923 2075.120 2.026 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2126623 2076.780 2.028 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2130023 2080.101 2.031 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2136823 2086.741 2.038 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2150423 2100.022 2.051 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2644501 2582.521 2.522 rdpir___376W> Not enough fields in the second line of the sequence entry: 1ptg 474 aa Actual fields, should be: 1 10 (Fields are separated by a colon, :) Read the alignment from file : Apnew.ali Total number of alignment positions: 474 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1u13 480 1 2 1ptg 507 1 runcmd______> alignment.check() check_a_343_> >> BEGINNING OF COMMAND check_a_337E> Structure not read in: 1