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 22:41:54 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 ../atom_files/pdb1fas.ent read_mo_297_> Segments, residues, atoms: 1 61 468 read_mo_298_> Segment: 1 1 A 61 A 468 openf___224_> Open ../atom_files/pdb2ctx.ent read_mo_297_> Segments, residues, atoms: 1 71 518 read_mo_298_> Segment: 1 1 A 71 A 518 align___276_> 'align_block' changed to 1. openf___224_> Open $(LIB)/as1.sim.mat rdrrwgh_268_> Number of residue types: 20 Pairwise dynamic programming alignment (ALIGN): Residue-residue metric : $(LIB)/as1.sim.mat Diagonal : 100 Overhang : 0 Local alignment : F MATRIX_OFFSET (local aln): 0.0000 N_SUBOPT : 0 SUBOPT_OFFSET : 0.0000 Alignment block : 1 Gap introduction penalty : -600.0000 Gap extension penalty : -400.0000 Break-break bonus : 10000.0000 Length of alignment : 71 Score : 26716.0000 openf___224_> Open toxin-seq.ali inialig_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 1 32 32 2.2868 2.2868 0.9429 inialig_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 2 42 42 2.4575 2.4575 0.0289 inialig_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 3 45 46 2.2939 2.3606 0.0255 inialig_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 4 46 47 2.0828 2.1417 0.0210 inialig_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 5 50 51 1.8530 1.9235 0.0175 inialig_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 6 51 51 1.7372 1.7372 0.0375 inialig_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 7 51 51 1.7279 1.7279 0.0205 inialig_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 8 51 51 1.7279 1.7279 0.0007 inialig_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 9 51 51 1.7279 1.7279 0.0000 Least-squares dynamic programming alignment: FIT_ATOMS atoms for alignment : CA Numb of residues/atoms in STR1 : 61 468 Numb of residues/atoms in STR2 : 71 518 Maximal distance for equivalence : 4.0000 Gap introduction penalty : 0.0000 Gap extension penalty : 2.0000 Alignment score : 137.3289 Numb of aligned residues : 51 Numb of aligned atoms : 51 51 Numb of aligned atom-atom distanc: 1263 1275 RMS after superposition : 1.7279 1.7279 DRMS : 1.2507 1.3111 # Sequence alignment of the structurally conserved regions # [average distance and standard deviation are with respect # to the framework (i.e., average structure)] # # N av ds st dv 1fas 2ctx # =============================== 1 1.157 0.000 T 1 I 1 2 0.461 0.000 M 2 R 2 3 0.281 0.000 * C 3 C 3 4 0.461 0.000 Y 4 F 4 5 0.660 0.000 S 5 I 5 6 0.669 0.000 H 6 T 6 7 1.718 0.000 T 7 P 7 # =============================== 8 1.199 0.000 T 9 I 9 # =============================== 9 1.623 0.000 A 12 T 10 # =============================== 10 0.402 0.000 L 14 K 12 11 1.470 0.000 T 15 D 13 12 1.037 0.000 N 16 C 14 # =============================== 13 1.551 0.000 C 17 G 17 # =============================== 14 0.444 0.000 N 20 H 18 15 0.278 0.000 S 21 V 19 16 0.429 0.000 * C 22 C 20 17 0.358 0.000 * Y 23 Y 21 18 0.542 0.000 R 24 T 22 19 0.575 0.000 * K 25 K 23 20 0.793 0.000 S 26 T 24 21 0.567 0.000 R 27 W 25 # =============================== 22 1.804 0.000 H 29 C 26 # =============================== 23 1.262 0.000 P 30 C 30 # =============================== 24 1.427 0.000 P 31 G 34 25 0.216 0.000 * K 32 K 35 26 0.823 0.000 M 33 R 36 27 0.570 0.000 * V 34 V 37 # =============================== 28 1.046 0.000 G 36 D 38 29 0.855 0.000 R 37 L 39 30 0.848 0.000 * G 38 G 40 31 0.939 0.000 * C 39 C 41 32 0.961 0.000 G 40 A 42 # =============================== 33 1.014 0.000 * C 41 C 45 34 0.732 0.000 * P 42 P 46 35 0.788 0.000 P 43 T 47 36 1.033 0.000 G 44 V 48 # =============================== 37 1.223 0.000 D 45 T 50 38 0.697 0.000 D 46 G 51 # =============================== 39 0.584 0.000 L 48 V 52 40 0.558 0.000 E 49 D 53 41 0.593 0.000 V 50 I 54 42 0.317 0.000 K 51 Q 55 43 0.276 0.000 * C 52 C 56 44 0.224 0.000 * C 53 C 57 45 0.353 0.000 T 54 S 58 46 0.642 0.000 S 55 T 59 # =============================== 47 0.642 0.000 * D 57 D 60 48 0.493 0.000 K 58 N 61 49 0.216 0.000 * C 59 C 62 50 0.437 0.000 * N 60 N 63 51 0.416 0.000 Y 61 P 64 # =============================== openf___224_> Open toxin-str.ali openf___224_> Open toxin-seq.ali Read the alignment from file : toxin-seq.ali Total number of alignment positions: 71 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1fas 61 1 1fas MOL_ID 1; MOLECULE FASCICULIN 1; CHAIN A; ENGINEERED YES 2 2ctx 71 1 2ctx MOL_ID 1; MOLECULE ALPHA-COBRATOXIN; CHAIN A; ENGINEERED YES openf___224_> Open toxin-str.ali Read the alignment from file : toxin-str.ali Total number of alignment positions: 81 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1fas 61 1 1fas MOL_ID 1; MOLECULE FASCICULIN 1; CHAIN A; ENGINEERED YES 2 2ctx 71 1 2ctx MOL_ID 1; MOLECULE ALPHA-COBRATOXIN; CHAIN A; ENGINEERED YES COMPARE_ALIGNMENTS: Evaluate an alignment of a sequence. ALIGNMENT (A) of residues in SEQ1 with residues of SEQ2 is evaluated with respect to ALIGNMENT2 (A2). ALL ... all residue pairs CORE ... res. pairs in segms of at least 3aa in A2 NON-CORE ... ALL - CORE Delta ... from correct position pseudo core ... core defined based on A, not A2 ALL CORE NON-CORE ------------------------------------------------------------ All res-res -> res-res pairs (A->A2): 51 44 7 Correct res-res -> res-res pairs (A->A2): 16 16 0 All res-res -> res-gap pairs (A->A2): 10 0 10 All res-gap -> res-res pairs (A->A2): 0 0 0 ALL CORE NON-CORE --------------- --------------- --------------- Delta Number % Number % Number % 0 16 31.4 16 36.4 0 0.0 1 10 19.6 7 15.9 3 42.9 2 5 9.8 5 11.4 0 0.0 3 5 9.8 3 6.8 2 28.6 4 1 2.0 0 0.0 1 14.3 5 2 3.9 2 4.5 0 0.0 6 6 11.8 6 13.6 0 0.0 7 6 11.8 5 11.4 1 14.3 8 0 0.0 0 0.0 0 0.0 9 0 0.0 0 0.0 0 0.0 10 0 0.0 0 0.0 0 0.0 total number of res-res pairs in core regions (A2) : 44 total number of res-res->res-res pairs (core regions): 44 number of correct res-res pairs in core regions : 16 number of res-res pairs in pseudo-core regions (A) : 61 number of incorrect pairs in core regions : 28 Starting time : 2016/04/05 22:41:54 Closing time : 2016/04/05 22:41:55 Total CPU time [seconds] : 0.19