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 22:42:04 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 openf___224_> Open ${MODINSTALL9v16}/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 openf___224_> Open ${MODINSTALL9v16}/modlib/radii.lib 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 toxin.ali Read the alignment from file : toxin.ali Total number of alignment positions: 77 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 2ctx 71 1 2ctx alpha-cobratoxin 2 2abx 74 1 2abx alpha-bungarotoxin 3 2nbt 66 1 2nbt neuronal bungarotoxin 4 1fas 61 1 1fas fasciculin 1 openf___224_> Open toxin.pap openf___224_> Open toxin.fasta check_a_343_> >> BEGINNING OF COMMAND openf___224_> Open ../atom_files/pdb2ctx.ent openf___224_> Open ../atom_files/pdb2abx.ent openf___224_> Open ../atom_files/2nbt.pdb 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 ---------------------------------------------------- 5 1 2 5 5 I T 6.260 7 1 2 7 7 P A 6.689 10 1 2 10 10 T P 6.001 74 1 2 68 71 R R 6.778 75 1 2 69 72 K Q 12.104 76 1 2 70 73 R P 16.762 77 1 2 71 74 P G 15.091 1 1 3 1 1 I R 7.634 5 1 3 5 5 I I 11.003 6 1 3 6 6 T S 17.482 7 1 3 7 7 P P 18.661 8 1 3 8 8 D S 13.040 9 1 3 9 9 I S 7.857 16 1 3 13 13 D T 7.571 18 1 3 15 15 P P 7.291 32 1 3 28 29 A K 6.940 33 1 3 29 30 F F 8.486 34 1 3 30 31 C C 6.838 35 1 3 31 32 S S 8.770 36 1 3 32 33 I I 9.240 37 1 3 33 34 R R 6.950 38 1 3 34 35 G G 6.063 51 1 3 47 48 T Q 6.149 52 1 3 48 49 V F 6.114 53 1 3 49 50 K R 8.298 55 1 3 50 52 T N 6.399 57 1 3 52 54 V R 7.067 70 1 3 64 66 P H 7.495 1 2 3 1 1 I R 8.250 2 2 3 2 2 V T 6.359 5 2 3 5 5 T I 9.186 6 2 3 6 6 T S 14.715 7 2 3 7 7 A P 16.420 8 2 3 8 8 T S 17.281 9 2 3 9 9 I S 13.920 32 2 3 31 29 A K 6.407 33 2 3 32 30 F F 6.600 34 2 3 33 31 C C 7.053 35 2 3 34 32 S S 6.786 36 2 3 35 33 S I 9.399 37 2 3 36 34 R R 8.033 38 2 3 37 35 G G 6.216 39 2 3 38 36 K P 6.934 52 2 3 51 49 K F 6.743 53 2 3 52 50 K R 6.779 64 2 3 62 61 T T 6.667 66 2 3 63 62 D D 6.250 68 2 3 65 64 C C 6.413 69 2 3 66 65 N N 7.281 70 2 3 67 66 H H 9.422 END OF TABLE check_ali___> Checking the sequence-structure alignment. Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- 18 2 17 20 G E 8.659 32 1 28 33 P P 9.643 32 2 31 36 P P 11.125 32 3 29 34 P P 8.504 45 1 41 44 C G 8.561 45 3 42 45 C G 8.793 END OF TABLE check_a_344_> << END OF COMMAND Starting time : 2016/04/05 22:42:04 Closing time : 2016/04/05 22:42:04 Total CPU time [seconds] : 0.19