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, BO, 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): 2000/01/25 01:03:23.422 fndatmi_285W> Only 464 residues out of 463 contain atoms of type CA check_ali___> Checking pairwise structural superpositions. Equivalent CA pairs with distance difference larger than 6.0 angstroms: ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------------- 258 1 2 275 226 K S 7.644 259 1 2 276 227 D D 9.903 260 1 2 277 228 N N 8.826 261 1 2 278 229 Q G 6.201 262 1 2 279 230 K N 6.251 263 1 2 280 231 S A 6.277 264 1 2 281 232 E G 6.305 408 1 2 417 373 G P 10.476 409 1 2 418 374 N A 9.318 461 1 2 466 426 N L 6.905 END OF TABLE check_ali___> Checking the sequence-structure alignment. Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- END OF TABLE read_to_681_> topology.submodel read from topology file: 3 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 4 454 atom names : C +N atom indices : 3618 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 4 454 atom names : C CA +N O atom indices : 3618 3612 0 3619 fndatmi_285W> Only 464 residues out of 463 contain atoms of type CA delete__442E> One or more atoms absent from MODEL: O: 454: C: 454: N: 455: CA: 455: omgdel__425W> Unselected all O C +N +CA dihedrals: 474 mdtrsr__446W> A potential that relies on one protein is used, yet you have at least one known structure available. MDT, not library, potential is used. iup2crm_280W> No topology library in memory or assigning a BLK residue. Default CHARMM atom type assigned: FE --> C This message is written only for the first such atom. add_res_442E> One or more atoms absent from MODEL: NH1:124 O1D:491