MODELLER 6a, Dec 13, 2000 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2000 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M. A. Marti-Renom, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant 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, IRIX64 viol 6.5 IP28 Date and time of compilation : 2000/04/29 20:19:04 Job starting time (YY/MM/DD HH:MM:SS): 2001/08/01 13:56:55.660 TOP_________> 115 828 READ_MODEL FILE = '4mdhA' openf5__224_> Open 11 OLD SEQUENTIAL ./4mdhA.pdb Dynamically allocated memory at amaxbnd [B,kB,MB]: 4863479 4749.491 4.638 openf5__224_> Open 11 OLD SEQUENTIAL ./4mdhA.pdb rdatm___297_> Segments, residues, atoms: 1 334 2553 rdatm___298_> Segment: 1 0 A 0 A 2553 iatmcls_286W> MODEL atom not classified: ALA:OT1 ALA iatmcls_286W> MODEL atom not classified: ALA:OT2 ALA TOP_________> 116 829 SEQUENCE_TO_ALI ALIGN_CODES = '4mdhA' TOP_________> 117 830 READ_ALIGNMENT FILE = 'TvLDH.ali' , ALIGN_CODES = ALIGN_; CODES 'TvLDH' , ADD_SEQUENCE = ON Dynamically allocated memory at amaxseq [B,kB,MB]: 5145223 5024.632 4.907 openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.ali Dynamically allocated memory at amaxbnd [B,kB,MB]: 5174679 5053.397 4.935 openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.ali read_al_374_> Non-standard residue type,position,sequence: e 1 1 read_al_374_> Non-standard residue type,position,sequence: / 335 1 Read the alignment from file : TvLDH.ali Total number of alignment positions: 336 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 4mdhA 334 2 4mdhA undefined 2 TvLDH 335 1 TvLDH TOP_________> 118 831 WRITE_ALIGNMENT FILE ='test' openf5__224_> Open 14 UNKNOWN SEQUENTIAL test TOP_________> 119 832 ALIGN2D Dynamically allocated memory at amaxbnd [B,kB,MB]: 10577559 10329.647 10.088 openf5__224_> Open 11 OLD SEQUENTIAL ./4mdhA.pdb mkapsa__293W> No TOPOLOGY_LIB is in memory. Use READ_TOPOLOGY to read one. iup2crm_280W> No TOPOLOGY_LIB in memory or assigning a BLK residue. Default CHARMM atom type assigned: C --> CT2 This message is written only for the first such atom. fndatmi_285W> Number of residues <> number of atoms; atom code: 334 333 CA openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib//as1.sim.mat rdrrwgh_268_> Number of residue types: 20 Pairwise dynamic programming alignment (ALIGN2D): Residue-residue metric : ${MODINSTALL6a}/modlib//as1.sim.mat Diagonal : 100 Overhang : 0 Maximal gap length : 999999 Local alignment : F MATRIX_OFFSET (local aln): 0.0000 FIX_OFFSETS : 0.0 1000.0 2000.0 3000.0 4000.0 Alignment block : 1 Gap introduction penalty : -900.0000 Gap extension penalty : -50.0000 Gap diagonal penalty : 0.0000 Structure gap penalties : 0.350 1.200 0.900 1.200 0.600 8.600 1.200 Length of alignment : 336 Score : 199173.8281 TOP_________> 120 833 WRITE_ALIGNMENT FILE ='TvLDH-4mdhA.ali', ALIGNMENT_FORMAT; = 'PIR' openf5__224_> Open 14 UNKNOWN SEQUENTIAL TvLDH-4mdhA.ali TOP_________> 121 834 WRITE_ALIGNMENT FILE ='TvLDH-4mdhA.pap', ALIGNMENT_FORMAT; = 'PAP' openf5__224_> Open 14 UNKNOWN SEQUENTIAL TvLDH-4mdhA.pap Dynamically allocated memory at finish [B,kB,MB]: 10577559 10329.647 10.088 Starting time : 2001/08/01 13:56:55.660 Closing time : 2001/08/01 14:09:02.922 Total CPU time [seconds] : 0.00