MODELLER 9v7, 2009/06/12, r6923 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2009 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, Linux plommebarlind.bccs.uib.no 2.6.18-194.32.1.el5 x86_64 Date and time of compilation : 2009/06/12 12:00:40 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2011/03/08 14:15:58 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v7}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v7}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234072 3158.273 3.084 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234600 3158.789 3.085 openf___224_> Open ${MODINSTALL9v7}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3283200 3206.250 3.131 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 ${MODINSTALL9v7}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3292440 3215.273 3.140 openf___224_> Open ${MODINSTALL9v7}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v7}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v7}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v7}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v7}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v7}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v7}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 io_data____W> Setting io.atom_files_directory to a colon-delimited string is deprecated, as it is not robust on Windows systems. Set it to a list of directories instead. For example: env.io.atom_files_directory = ['./', '../atom_files/'] openf___224_> Open ./2OB0.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 3450325 3369.458 3.290 read_mo_297_> Segments, residues, atoms: 1 154 1245 read_mo_298_> Segment: 1 1 A 154 A 1245 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3454762 3373.791 3.295 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 3545302 3462.209 3.381 openf___224_> Open ./2X7B.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 3711620 3624.629 3.540 read_pd_459W> Residue type COA not recognized. 'automodel' model building will treat this residue as a rigid body. To use real parameters, add the residue type to ${LIB}/restyp.lib, its topology to ${LIB}/top_*.lib, and suitable forcefield parameters to ${LIB}/par.lib. read_pd_459W> Residue type CL not recognized. 'automodel' model building will treat this residue as a rigid body. To use real parameters, add the residue type to ${LIB}/restyp.lib, its topology to ${LIB}/top_*.lib, and suitable forcefield parameters to ${LIB}/par.lib. read_mo_297_> Segments, residues, atoms: 1 158 1332 read_mo_298_> Segment: 1 11 A 202 A 1332 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3556154 3472.807 3.391 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 3650904 3565.336 3.482 ALIGN_CODES : 2OB0A 2X7BA Atom type for alignment (FIT_ATOMS) : CA FIT : T IMPROVE_ALIGNMENT : T WATER_IO, HETATM_IO, HYDROGEN_IO : F T F NO_TER : F OUTPUT : ALIGNMENT QUALITY FIT_ON_FIRST : F WRITE_FIT : F FIT_PDBNAM : T WRITE_WHOLE_PDB : T CURRENT_DIRECTORY : T Feature weights (FEATURE_WEIGHTS) : 1.0000 0.0000 0.0000 0.0000 1.0000 0.0000 NORMALIZE_PP_SCORES : F Gap initiation penalty (GAP_PENALTIES[1]) : -450.0000 Gap extension penalty (GAP_PENALTIES[2]) : -50.0000 Gap_function (align2d flag) : F 2-D Gap penalties : 3.50 3.50 3.50 0.20 4.00 6.50 2.00 0.00 GAP-GAP_SCORE : 0.0000 GAP-RESIDUE_SCORE : 0.0000 Perform gap-residue and gap-gap correction : T Residue type - residue type file (RR_FILE) : $(LIB)/as1.sim.mat OFF_DIAGONAL : 100 OVERHANG : 30 LOCAL_ALIGNMENT : F MATRIX_OFFSET : 0.0000 N_SUBOPT : 1 SUBOPT_OFFSET : 0.0000 Gap introduction penalty (GAP_PENALTIES_3D_1) : 0.0000 Gap extension penalty (GAP_PENALTIES_3D_2) : 3.0000 Max dist for equiv (2 * GAP_PENALTIES_3D_2) : 6.0000 ALIGN3D_TRF : F RMS_CUTOFF : 3.5 salign__276_> 'align_block' changed to 1. fndatmi_285W> Only 156 residues out of 158 contain atoms of type CA (This is usually caused by non-standard residues, such as ligands, or by PDB files with missing atoms.) openf___224_> Open $(LIB)/as1.sim.mat rdrrwgh_268_> Number of residue types: 20 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3651094 3565.521 3.482 SALIGN______> Matrix of pairwise protein distances for the initial tree: 2OB0A 2X7BA 2OB0A 0.000 0.361 2X7BA 0.361 0.000 SALIGN____> Matrix of pairwise equivalences: 2OB0A 2X7BA 2OB0A 0 133 2X7BA 0 0 SALIGN_____> adding the next group to the alignment; iteration 1 Current alignment total score: 58.85 pos_scr ... position-position dissimilarity from the dynamic programming matrix avr_avr ... distance between the two averages avr_dst ... for all aligned structures, average distance to the average structure std_dev ... for all aligned structures, standard deviation of distance to ave str group: 1 2 N pos_scr avr_ave avr_dst std_dev 2OB0A 2X7BA ------------------------------------------------------ 1 0.34 9.24 4.62 0.00 S 1 A D 11 A 2 0.00 0.00 0.00 0.00 K 2 A - 3 0.00 0.00 0.00 0.00 G 3 A - 4 0.00 0.00 0.00 0.00 S 4 A - 5 0.00 0.00 0.00 0.00 R 5 A - 6 0.28 1.12 0.56 0.00 I 6 A F 12 A 7 0.31 1.17 0.58 0.00 E 7 A T 13 A 8 0.06 1.83 0.91 0.00 * L 8 A L 14 A 9 0.35 2.89 1.44 0.00 G 9 A R 15 A 10 0.25 3.23 1.61 0.00 D 10 A N 16 A 11 0.24 2.57 1.29 0.00 V 11 A A 17 A 12 0.33 2.62 1.31 0.00 T 12 A R 18 A 13 0.45 2.87 1.43 0.00 P 13 A M 19 A 14 0.38 2.08 1.04 0.00 H 14 A D 20 A 15 0.25 2.32 1.16 0.00 N 15 A D 21 A 16 0.11 1.25 0.63 0.00 * I 16 A I 22 A 17 0.30 1.04 0.52 0.00 K 17 A D 23 A 18 0.09 0.98 0.49 0.00 * Q 18 A Q 24 A 19 0.19 0.92 0.46 0.00 L 19 A I 25 A 20 0.34 0.80 0.40 0.00 K 20 A I 26 A 21 0.19 0.82 0.41 0.00 R 21 A K 27 A 22 0.19 0.87 0.44 0.00 L 22 A I 28 A 23 0.11 0.88 0.44 0.00 * N 23 A N 29 A 24 0.28 0.89 0.45 0.00 Q 24 A R 30 A 25 0.19 1.09 0.54 0.00 V 25 A L 31 A 26 0.32 1.55 0.77 0.00 I 26 A T 32 A 27 0.24 1.49 0.74 0.00 F 27 A L 33 A 28 0.09 1.91 0.95 0.00 * P 28 A P 34 A 29 0.38 1.02 0.51 0.00 V 29 A E 35 A 30 0.28 1.27 0.63 0.00 S 30 A N 36 A 31 0.11 0.63 0.31 0.00 * Y 31 A Y 37 A 32 0.34 2.26 1.13 0.00 N 32 A P 38 A 33 0.35 3.52 1.76 0.00 D 33 A Y 39 A 34 0.34 3.22 1.61 0.00 K 34 A Y 40 A 35 0.06 0.86 0.43 0.00 * F 35 A F 41 A 36 0.20 2.06 1.03 0.00 Y 36 A F 42 A 37 0.32 2.44 1.22 0.00 K 37 A V 43 A 38 0.24 0.50 0.25 0.00 D 38 A E 44 A 39 0.41 2.70 1.35 0.00 V 39 A H 45 A 40 0.08 2.88 1.44 0.00 * L 40 A L 46 A 41 0.00 0.00 0.00 0.00 - K 47 A 42 0.22 3.41 1.71 0.00 * E 41 A E 48 A 43 0.37 2.15 1.07 0.00 V 42 A Y 49 A 44 0.07 1.84 0.92 0.00 * G 43 A G 50 A 45 0.41 1.59 0.79 0.00 E 44 A L 51 A 46 0.35 1.99 0.99 0.00 L 45 A A 52 A 47 0.37 1.39 0.70 0.00 A 46 A F 53 A 48 0.41 1.96 0.98 0.00 K 47 A F 54 A 49 0.21 1.81 0.90 0.00 L 48 A V 55 A 50 0.09 1.19 0.60 0.00 * A 49 A A 56 A 51 0.32 1.37 0.69 0.00 Y 50 A I 57 A 52 0.32 2.32 1.16 0.00 F 51 A V 58 A 53 0.25 3.53 1.76 0.00 N 52 A D 59 A 54 0.23 3.10 1.55 0.00 D 53 A N 60 A 55 0.35 3.11 1.55 0.00 I 54 A S 61 A 56 0.26 1.70 0.85 0.00 A 55 A V 62 A 57 0.10 1.01 0.51 0.00 * V 56 A V 63 A 58 0.06 0.84 0.42 0.00 * G 57 A G 64 A 59 0.34 0.72 0.36 0.00 A 58 A Y 65 A 60 0.18 0.58 0.29 0.00 V 59 A I 66 A 61 0.45 0.52 0.26 0.00 C 60 A M 67 A 62 0.48 0.32 0.16 0.00 C 61 A P 68 A 63 0.09 0.79 0.39 0.00 * R 62 A R 69 A 64 0.19 0.47 0.23 0.00 V 63 A I 70 A 65 0.25 1.02 0.51 0.00 D 64 A E 71 A 66 0.45 0.92 0.46 0.00 H 65 A W 72 A 67 0.36 1.57 0.78 0.00 S 66 A G 73 A 68 0.68 0.28 0.14 0.00 Q 67 A F 74 A 69 0.49 6.16 3.08 0.00 N 68 A S 75 A 70 0.00 0.00 0.00 0.00 - N 76 A 71 0.00 0.00 0.00 0.00 - I 77 A 72 0.00 0.00 0.00 0.00 - K 78 A 73 0.00 0.00 0.00 0.00 - Q 79 A 74 0.00 0.00 0.00 0.00 - L 80 A 75 0.00 0.00 0.00 0.00 - P 81 A 76 0.00 0.00 0.00 0.00 - S 82 A 77 0.00 0.00 0.00 0.00 - L 83 A 78 0.44 0.98 0.49 0.00 Q 69 A V 84 A 79 0.20 0.44 0.22 0.00 K 70 A R 85 A 80 0.21 0.27 0.13 0.00 R 71 A K 86 A 81 0.38 0.34 0.17 0.00 L 72 A G 87 A 82 0.31 0.31 0.16 0.00 Y 73 A H 88 A 83 0.17 0.36 0.18 0.00 I 74 A V 89 A 84 0.30 0.24 0.12 0.00 M 75 A V 90 A 85 0.21 0.63 0.32 0.00 T 76 A S 91 A 86 0.22 1.30 0.65 0.00 L 77 A I 92 A 87 0.26 1.72 0.86 0.00 G 78 A A 93 A 88 0.38 0.32 0.16 0.00 C 79 A V 94 A 89 0.06 1.27 0.64 0.00 * L 80 A L 95 A 90 0.26 1.95 0.98 0.00 A 81 A E 96 A 91 0.30 2.24 1.12 0.00 P 82 A E 97 A 92 0.05 1.29 0.65 0.00 * Y 83 A Y 98 A 93 0.07 0.95 0.48 0.00 * R 84 A R 99 A 94 0.07 0.65 0.32 0.00 * R 85 A R 100 A 95 0.30 0.26 0.13 0.00 L 86 A K 101 A 96 0.04 0.90 0.45 0.00 * G 87 A G 102 A 97 0.08 0.40 0.20 0.00 * I 88 A I 103 A 98 0.22 0.71 0.35 0.00 G 89 A A 104 A 99 0.07 1.40 0.70 0.00 * T 90 A T 105 A 100 0.25 1.23 0.62 0.00 K 91 A T 106 A 101 0.20 0.22 0.11 0.00 M 92 A L 107 A 102 0.06 0.82 0.41 0.00 * L 93 A L 108 A 103 0.29 1.22 0.61 0.00 N 94 A E 109 A 104 0.34 0.53 0.26 0.00 H 95 A A 110 A 105 0.31 1.26 0.63 0.00 V 96 A S 111 A 106 0.19 2.20 1.10 0.00 L 97 A M 112 A 107 0.26 1.85 0.92 0.00 N 98 A K 113 A 108 0.35 1.32 0.66 0.00 I 99 A S 114 A 109 0.45 3.48 1.74 0.00 C 100 A M 115 A 110 0.30 4.24 2.12 0.00 E 101 A K 116 A 111 0.30 2.93 1.47 0.00 K 102 A N 117 A 112 0.25 4.29 2.15 0.00 * D 103 A D 118 A 113 0.49 7.88 3.94 0.00 G 104 A Y 119 A 114 0.31 3.03 1.52 0.00 T 105 A N 120 A 115 0.35 2.07 1.03 0.00 F 106 A A 121 A 116 0.24 1.84 0.92 0.00 D 107 A E 122 A 117 0.31 0.17 0.09 0.00 N 108 A E 123 A 118 0.09 0.55 0.27 0.00 * I 109 A I 124 A 119 0.06 0.69 0.34 0.00 * Y 110 A Y 125 A 120 0.06 0.43 0.22 0.00 * L 111 A L 126 A 121 0.34 0.36 0.18 0.00 H 112 A E 127 A 122 0.08 0.75 0.38 0.00 * V 113 A V 128 A 123 0.29 0.50 0.25 0.00 Q 114 A R 129 A 124 0.17 0.35 0.17 0.00 I 115 A V 130 A 125 0.08 0.38 0.19 0.00 * S 116 A S 131 A 126 0.10 0.74 0.37 0.00 * N 117 A N 132 A 127 0.35 0.83 0.42 0.00 E 118 A Y 133 A 128 0.27 1.04 0.52 0.00 S 119 A P 134 A 129 0.08 0.81 0.41 0.00 * A 120 A A 135 A 130 0.08 0.93 0.47 0.00 * I 121 A I 136 A 131 0.27 0.90 0.45 0.00 D 122 A A 137 A 132 0.22 0.80 0.40 0.00 F 123 A L 138 A 133 0.05 0.80 0.40 0.00 * Y 124 A Y 139 A 134 0.31 0.69 0.34 0.00 R 125 A E 140 A 135 0.09 0.67 0.34 0.00 * K 126 A K 141 A 136 0.22 1.08 0.54 0.00 F 127 A L 142 A 137 0.27 0.92 0.46 0.00 G 128 A N 143 A 138 0.06 0.89 0.44 0.00 * F 129 A F 144 A 139 0.24 0.77 0.38 0.00 E 130 A K 145 A 140 0.35 0.71 0.36 0.00 I 131 A K 146 A 141 0.17 0.94 0.47 0.00 I 132 A V 147 A 142 0.25 1.06 0.53 0.00 E 133 A K 148 A 143 0.29 1.04 0.52 0.00 T 134 A V 149 A 144 0.33 0.73 0.37 0.00 K 135 A L 150 A 145 0.11 0.47 0.24 0.00 * K 136 A K 151 A 146 0.28 1.20 0.60 0.00 N 137 A G 152 A 147 0.08 0.85 0.43 0.00 * Y 138 A Y 153 A 148 0.12 0.96 0.48 0.00 * Y 139 A Y 154 A 149 0.38 2.09 1.04 0.00 K 140 A A 155 A 150 0.46 2.63 1.31 0.00 R 141 A D 156 A 151 0.46 5.68 2.84 0.00 I 142 A G 157 A 152 0.33 3.77 1.89 0.00 * E 143 A E 158 A 153 0.52 5.13 2.57 0.00 P 144 A D 159 A 154 0.25 6.37 3.18 0.00 * A 145 A A 160 A 155 0.00 0.00 0.00 0.00 D 146 A - 156 0.38 3.34 1.67 0.00 A 147 A Y 161 A 157 0.40 3.53 1.77 0.00 H 148 A L 162 A 158 0.33 2.84 1.42 0.00 V 149 A M 163 A 159 0.32 3.65 1.82 0.00 L 150 A A 164 A 160 0.31 3.19 1.59 0.00 Q 151 A R 165 A 161 0.31 3.79 1.89 0.00 K 152 A P 166 A 162 0.50 0.00 0.00 0.00 * N 153 A 163 0.50 0.00 0.00 0.00 * L 154 A ------------------------------------------------------ SALIGN______> Raw QUALITY_SCORE of the multiple alignment: 133.0 QUALITY_SCORE (percentage) : 86.4 Number of unique protein pairs : 1 QUALITY_SCORE_min : 133 RMS_CUTOFF : 3.5000 QS is the average number of structurally equivalent residue pairs. Two residues are equivalent when closer than RMS_CUTOFF upon pairwise least-squares superposition given current alignment. SALIGN______> Matrix of pairwise equivalences from individual pairwise alignments: 2OB0A 2X7BA 2OB0A 0 133 2X7BA 0 0 SALIGN______> Matrix of pairwise equivalences: 2OB0A 2X7BA 2OB0A 0 133 2X7BA 0 0 SALIGN______> Matrix of differences in pairwise equivalences inferred from the tree and individually: 2OB0A 2X7BA 2OB0A 0 0 2X7BA 0 0 SALIGN______> Matrix of %differences in pairwise equivalences inferred from the tree and individually: 2OB0A 2X7BA 2OB0A 0 0 2X7BA 0 0 ALIGN_CODES : 2OB0A 2X7BA Atom type for alignment (FIT_ATOMS) : CA FIT : T IMPROVE_ALIGNMENT : T WATER_IO, HETATM_IO, HYDROGEN_IO : F T F NO_TER : F OUTPUT : ALIGNMENT QUALITY FIT_ON_FIRST : F WRITE_FIT : F FIT_PDBNAM : T WRITE_WHOLE_PDB : T CURRENT_DIRECTORY : T Feature weights (FEATURE_WEIGHTS) : 1.0000 0.5000 1.0000 1.0000 1.0000 0.0000 NORMALIZE_PP_SCORES : F Gap initiation penalty (GAP_PENALTIES[1]) : -450.0000 Gap extension penalty (GAP_PENALTIES[2]) : -50.0000 Gap_function (align2d flag) : F 2-D Gap penalties : 3.50 3.50 3.50 0.20 4.00 6.50 2.00 0.00 GAP-GAP_SCORE : 0.0000 GAP-RESIDUE_SCORE : 0.0000 Perform gap-residue and gap-gap correction : T Residue type - residue type file (RR_FILE) : $(LIB)/as1.sim.mat OFF_DIAGONAL : 100 OVERHANG : 30 LOCAL_ALIGNMENT : F MATRIX_OFFSET : 0.0000 N_SUBOPT : 1 SUBOPT_OFFSET : 0.0000 Gap introduction penalty (GAP_PENALTIES_3D_1) : 0.0000 Gap extension penalty (GAP_PENALTIES_3D_2) : 3.0000 Max dist for equiv (2 * GAP_PENALTIES_3D_2) : 6.0000 ALIGN3D_TRF : F RMS_CUTOFF : 3.5 salign__276_> 'align_block' changed to 1. fndatmi_285W> Only 156 residues out of 158 contain atoms of type CA (This is usually caused by non-standard residues, such as ligands, or by PDB files with missing atoms.) mkapsa__637W> No residue topology library is in memory. Better radii would be used if topology.read() is called first. iup2crm_280W> No topology library in memory or assigning a BLK residue. Default CHARMM atom type assigned: N --> N This message is written only for the first such atom. iup2crm_280W> No topology library in memory or assigning a BLK residue. Default CHARMM atom type assigned: N --> N This message is written only for the first such atom. fndatmi_285W> Only 156 residues out of 158 contain atoms of type CA (This is usually caused by non-standard residues, such as ligands, or by PDB files with missing atoms.) openf___224_> Open $(LIB)/as1.sim.mat rdrrwgh_268_> Number of residue types: 20 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3651208 3565.633 3.482 rr_dist_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 1 144 144 1.5396 1.5396 0.0017 rr_dist_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 2 144 144 1.5396 1.5396 0.0000 SALIGN______> Matrix of pairwise protein distances for the initial tree: 2OB0A 2X7BA 2OB0A 0.000 0.411 2X7BA 0.411 0.000 SALIGN____> Matrix of pairwise equivalences: 2OB0A 2X7BA 2OB0A 0 142 2X7BA 0 0 SALIGN_____> adding the next group to the alignment; iteration 1 rr_dist_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 1 144 144 1.5396 1.5396 0.0017 rr_dist_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 2 144 144 1.5396 1.5396 0.0000 Current alignment total score: 67.32 pos_scr ... position-position dissimilarity from the dynamic programming matrix avr_avr ... distance between the two averages avr_dst ... for all aligned structures, average distance to the average structure std_dev ... for all aligned structures, standard deviation of distance to ave str group: 1 2 N pos_scr avr_ave avr_dst std_dev 2OB0A 2X7BA ------------------------------------------------------ 1 0.00 0.00 0.00 0.00 S 1 A - 2 0.00 0.00 0.00 0.00 K 2 A - 3 0.00 0.00 0.00 0.00 G 3 A - 4 0.00 0.00 0.00 0.00 S 4 A - 5 0.58 1.78 0.89 0.00 R 5 A D 11 A 6 0.49 1.30 0.65 0.00 I 6 A F 12 A 7 0.25 0.99 0.49 0.00 E 7 A T 13 A 8 0.20 1.56 0.78 0.00 * L 8 A L 14 A 9 0.43 2.53 1.26 0.00 G 9 A R 15 A 10 0.43 2.92 1.46 0.00 D 10 A N 16 A 11 0.36 2.31 1.16 0.00 V 11 A A 17 A 12 0.41 2.32 1.16 0.00 T 12 A R 18 A 13 0.49 2.64 1.32 0.00 P 13 A M 19 A 14 0.39 2.03 1.02 0.00 H 14 A D 20 A 15 0.58 2.19 1.10 0.00 N 15 A D 21 A 16 0.31 1.37 0.69 0.00 * I 16 A I 22 A 17 0.23 0.90 0.45 0.00 K 17 A D 23 A 18 0.15 1.00 0.50 0.00 * Q 18 A Q 24 A 19 0.20 1.00 0.50 0.00 L 19 A I 25 A 20 0.47 0.89 0.44 0.00 K 20 A I 26 A 21 0.18 0.85 0.42 0.00 R 21 A K 27 A 22 0.20 1.02 0.51 0.00 L 22 A I 28 A 23 0.16 0.98 0.49 0.00 * N 23 A N 29 A 24 0.23 0.90 0.45 0.00 Q 24 A R 30 A 25 0.20 0.99 0.50 0.00 V 25 A L 31 A 26 0.32 1.57 0.78 0.00 I 26 A T 32 A 27 0.26 1.39 0.70 0.00 F 27 A L 33 A 28 0.22 1.65 0.83 0.00 * P 28 A P 34 A 29 0.27 0.90 0.45 0.00 V 29 A E 35 A 30 0.23 0.92 0.46 0.00 S 30 A N 36 A 31 0.19 0.33 0.16 0.00 * Y 31 A Y 37 A 32 0.36 1.91 0.96 0.00 N 32 A P 38 A 33 0.52 3.27 1.63 0.00 D 33 A Y 39 A 34 0.48 2.96 1.48 0.00 K 34 A Y 40 A 35 0.22 0.74 0.37 0.00 * F 35 A F 41 A 36 0.32 2.04 1.02 0.00 Y 36 A F 42 A 37 0.50 2.27 1.14 0.00 K 37 A V 43 A 38 0.17 0.53 0.26 0.00 D 38 A E 44 A 39 0.48 2.72 1.36 0.00 V 39 A H 45 A 40 0.34 2.77 1.38 0.00 * L 40 A L 46 A 41 0.21 0.54 0.27 0.00 E 41 A K 47 A 42 0.00 0.00 0.00 0.00 - E 48 A 43 0.50 1.99 0.99 0.00 V 42 A Y 49 A 44 0.35 1.83 0.92 0.00 * G 43 A G 50 A 45 0.35 1.46 0.73 0.00 E 44 A L 51 A 46 0.59 1.87 0.93 0.00 L 45 A A 52 A 47 0.30 1.23 0.61 0.00 A 46 A F 53 A 48 0.38 1.75 0.88 0.00 K 47 A F 54 A 49 0.27 1.59 0.79 0.00 L 48 A V 55 A 50 0.15 0.99 0.50 0.00 * A 49 A A 56 A 51 0.51 1.26 0.63 0.00 Y 50 A I 57 A 52 0.41 2.43 1.21 0.00 F 51 A V 58 A 53 0.75 3.78 1.89 0.00 N 52 A D 59 A 54 0.47 3.29 1.64 0.00 D 53 A N 60 A 55 0.51 3.15 1.58 0.00 I 54 A S 61 A 56 0.29 1.62 0.81 0.00 A 55 A V 62 A 57 0.14 0.86 0.43 0.00 * V 56 A V 63 A 58 0.33 0.69 0.35 0.00 * G 57 A G 64 A 59 0.44 0.62 0.31 0.00 A 58 A Y 65 A 60 0.14 0.54 0.27 0.00 V 59 A I 66 A 61 0.26 0.52 0.26 0.00 C 60 A M 67 A 62 0.25 0.34 0.17 0.00 C 61 A P 68 A 63 0.12 0.69 0.35 0.00 * R 62 A R 69 A 64 0.36 0.50 0.25 0.00 V 63 A I 70 A 65 0.25 1.22 0.61 0.00 D 64 A E 71 A 66 0.33 1.21 0.61 0.00 H 65 A W 72 A 67 0.59 1.88 0.94 0.00 S 66 A G 73 A 68 0.37 0.58 0.29 0.00 Q 67 A F 74 A 69 0.00 0.00 0.00 0.00 - S 75 A 70 0.00 0.00 0.00 0.00 - N 76 A 71 0.00 0.00 0.00 0.00 - I 77 A 72 0.00 0.00 0.00 0.00 - K 78 A 73 0.00 0.00 0.00 0.00 - Q 79 A 74 0.00 0.00 0.00 0.00 - L 80 A 75 0.00 0.00 0.00 0.00 - P 81 A 76 0.00 0.00 0.00 0.00 - S 82 A 77 0.70 1.60 0.80 0.00 N 68 A L 83 A 78 0.57 1.41 0.70 0.00 Q 69 A V 84 A 79 0.18 0.81 0.40 0.00 K 70 A R 85 A 80 0.14 0.46 0.23 0.00 R 71 A K 86 A 81 0.20 0.25 0.13 0.00 L 72 A G 87 A 82 0.18 0.36 0.18 0.00 Y 73 A H 88 A 83 0.11 0.30 0.15 0.00 I 74 A V 89 A 84 0.17 0.32 0.16 0.00 M 75 A V 90 A 85 0.16 0.64 0.32 0.00 T 76 A S 91 A 86 0.46 1.24 0.62 0.00 L 77 A I 92 A 87 0.74 1.67 0.84 0.00 G 78 A A 93 A 88 0.42 0.24 0.12 0.00 C 79 A V 94 A 89 0.37 1.10 0.55 0.00 * L 80 A L 95 A 90 0.31 1.76 0.88 0.00 A 81 A E 96 A 91 0.36 2.08 1.04 0.00 P 82 A E 97 A 92 0.16 1.22 0.61 0.00 * Y 83 A Y 98 A 93 0.13 0.92 0.46 0.00 * R 84 A R 99 A 94 0.10 0.63 0.31 0.00 * R 85 A R 100 A 95 0.16 0.29 0.14 0.00 L 86 A K 101 A 96 0.10 0.75 0.37 0.00 * G 87 A G 102 A 97 0.07 0.29 0.15 0.00 * I 88 A I 103 A 98 0.18 0.72 0.36 0.00 G 89 A A 104 A 99 0.17 1.23 0.62 0.00 * T 90 A T 105 A 100 0.22 0.99 0.50 0.00 K 91 A T 106 A 101 0.10 0.10 0.05 0.00 M 92 A L 107 A 102 0.11 0.77 0.39 0.00 * L 93 A L 108 A 103 0.24 0.99 0.50 0.00 N 94 A E 109 A 104 0.18 0.23 0.11 0.00 H 95 A A 110 A 105 0.29 1.40 0.70 0.00 V 96 A S 111 A 106 0.33 2.17 1.09 0.00 L 97 A M 112 A 107 0.31 1.72 0.86 0.00 N 98 A K 113 A 108 0.54 1.46 0.73 0.00 I 99 A S 114 A 109 0.59 3.52 1.76 0.00 C 100 A M 115 A 110 0.60 4.19 2.10 0.00 E 101 A K 116 A 111 0.46 2.95 1.48 0.00 K 102 A N 117 A 112 0.74 4.62 2.31 0.00 * D 103 A D 118 A 113 1.22 8.04 4.02 0.00 G 104 A Y 119 A 114 0.50 3.25 1.63 0.00 T 105 A N 120 A 115 0.40 2.16 1.08 0.00 F 106 A A 121 A 116 0.36 2.25 1.12 0.00 D 107 A E 122 A 117 0.20 0.60 0.30 0.00 N 108 A E 123 A 118 0.07 0.31 0.15 0.00 * I 109 A I 124 A 119 0.31 0.58 0.29 0.00 * Y 110 A Y 125 A 120 0.07 0.43 0.21 0.00 * L 111 A L 126 A 121 0.19 0.34 0.17 0.00 H 112 A E 127 A 122 0.09 0.49 0.24 0.00 * V 113 A V 128 A 123 0.16 0.26 0.13 0.00 Q 114 A R 129 A 124 0.10 0.26 0.13 0.00 I 115 A V 130 A 125 0.06 0.18 0.09 0.00 * S 116 A S 131 A 126 0.09 0.41 0.21 0.00 * N 117 A N 132 A 127 0.22 0.60 0.30 0.00 E 118 A Y 133 A 128 0.22 0.85 0.43 0.00 S 119 A P 134 A 129 0.11 0.67 0.33 0.00 * A 120 A A 135 A 130 0.11 0.70 0.35 0.00 * I 121 A I 136 A 131 0.20 0.75 0.38 0.00 D 122 A A 137 A 132 0.18 0.77 0.38 0.00 F 123 A L 138 A 133 0.08 0.56 0.28 0.00 * Y 124 A Y 139 A 134 0.18 0.36 0.18 0.00 R 125 A E 140 A 135 0.10 0.57 0.29 0.00 * K 126 A K 141 A 136 0.20 0.92 0.46 0.00 F 127 A L 142 A 137 0.19 0.64 0.32 0.00 G 128 A N 143 A 138 0.08 0.52 0.26 0.00 * F 129 A F 144 A 139 0.13 0.24 0.12 0.00 E 130 A K 145 A 140 0.18 0.25 0.13 0.00 I 131 A K 146 A 141 0.12 0.40 0.20 0.00 I 132 A V 147 A 142 0.18 0.65 0.32 0.00 E 133 A K 148 A 143 0.19 0.57 0.28 0.00 T 134 A V 149 A 144 0.18 0.26 0.13 0.00 K 135 A L 150 A 145 0.08 0.29 0.15 0.00 * K 136 A K 151 A 146 0.24 1.09 0.54 0.00 N 137 A G 152 A 147 0.11 0.63 0.32 0.00 * Y 138 A Y 153 A 148 0.16 0.94 0.47 0.00 * Y 139 A Y 154 A 149 0.37 1.82 0.91 0.00 K 140 A A 155 A 150 0.54 3.06 1.53 0.00 R 141 A D 156 A 151 0.00 0.00 0.00 0.00 I 142 A - 152 0.00 0.00 0.00 0.00 E 143 A - 153 1.02 5.44 2.72 0.00 P 144 A G 157 A 154 0.33 1.40 0.70 0.00 A 145 A E 158 A 155 0.13 0.53 0.27 0.00 * D 146 A D 159 A 156 0.07 0.27 0.13 0.00 * A 147 A A 160 A 157 0.16 0.20 0.10 0.00 H 148 A Y 161 A 158 0.17 0.70 0.35 0.00 V 149 A L 162 A 159 0.19 0.93 0.47 0.00 L 150 A M 163 A 160 0.19 0.53 0.27 0.00 Q 151 A A 164 A 161 0.14 0.42 0.21 0.00 K 152 A R 165 A 162 0.19 0.39 0.19 0.00 N 153 A P 166 A 163 0.22 0.00 0.00 0.00 * L 154 A 164 0.00 0.00 0.00 0.00 - ------------------------------------------------------ SALIGN______> Raw QUALITY_SCORE of the multiple alignment: 142.0 QUALITY_SCORE (percentage) : 92.2 Number of unique protein pairs : 1 QUALITY_SCORE_min : 142 RMS_CUTOFF : 3.5000 QS is the average number of structurally equivalent residue pairs. Two residues are equivalent when closer than RMS_CUTOFF upon pairwise least-squares superposition given current alignment. SALIGN______> Matrix of pairwise equivalences from individual pairwise alignments: 2OB0A 2X7BA 2OB0A 0 142 2X7BA 0 0 SALIGN______> Matrix of pairwise equivalences: 2OB0A 2X7BA 2OB0A 0 142 2X7BA 0 0 SALIGN______> Matrix of differences in pairwise equivalences inferred from the tree and individually: 2OB0A 2X7BA 2OB0A 0 0 2X7BA 0 0 SALIGN______> Matrix of %differences in pairwise equivalences inferred from the tree and individually: 2OB0A 2X7BA 2OB0A 0 0 2X7BA 0 0 ALIGN_CODES : 2OB0A 2X7BA Atom type for alignment (FIT_ATOMS) : CA FIT : T IMPROVE_ALIGNMENT : T WATER_IO, HETATM_IO, HYDROGEN_IO : F T F NO_TER : F OUTPUT : ALIGNMENT QUALITY FIT_ON_FIRST : F WRITE_FIT : T FIT_PDBNAM : T WRITE_WHOLE_PDB : F CURRENT_DIRECTORY : T Feature weights (FEATURE_WEIGHTS) : 1.0000 1.0000 1.0000 1.0000 1.0000 0.0000 NORMALIZE_PP_SCORES : F Gap initiation penalty (GAP_PENALTIES[1]) : -450.0000 Gap extension penalty (GAP_PENALTIES[2]) : -50.0000 Gap_function (align2d flag) : F 2-D Gap penalties : 3.50 3.50 3.50 0.20 4.00 6.50 2.00 0.00 GAP-GAP_SCORE : 0.0000 GAP-RESIDUE_SCORE : 0.0000 Perform gap-residue and gap-gap correction : T Residue type - residue type file (RR_FILE) : $(LIB)/as1.sim.mat OFF_DIAGONAL : 100 OVERHANG : 30 LOCAL_ALIGNMENT : F MATRIX_OFFSET : 0.0000 N_SUBOPT : 1 SUBOPT_OFFSET : 0.0000 Gap introduction penalty (GAP_PENALTIES_3D_1) : 0.0000 Gap extension penalty (GAP_PENALTIES_3D_2) : 3.0000 Max dist for equiv (2 * GAP_PENALTIES_3D_2) : 6.0000 ALIGN3D_TRF : F RMS_CUTOFF : 3.5 salign__276_> 'align_block' changed to 1. fndatmi_285W> Only 156 residues out of 158 contain atoms of type CA (This is usually caused by non-standard residues, such as ligands, or by PDB files with missing atoms.) mkapsa__637W> No residue topology library is in memory. Better radii would be used if topology.read() is called first. openf___224_> Open $(LIB)/as1.sim.mat rdrrwgh_268_> Number of residue types: 20 rr_dist_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 1 145 145 1.5941 1.5941 0.0001 rr_dist_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 2 144 144 1.5396 1.5396 0.0000 rr_dist_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 3 144 144 1.5396 1.5396 0.0000 SALIGN______> Matrix of pairwise protein distances for the initial tree: 2OB0A 2X7BA 2OB0A 0.000 0.500 2X7BA 0.500 0.000 SALIGN____> Matrix of pairwise equivalences: 2OB0A 2X7BA 2OB0A 0 142 2X7BA 0 0 SALIGN_____> adding the next group to the alignment; iteration 1 rr_dist_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 1 145 145 1.5941 1.5941 0.0001 rr_dist_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 2 144 144 1.5396 1.5396 0.0000 rr_dist_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 3 144 144 1.5396 1.5396 0.0000 Current alignment total score: 82.07 pos_scr ... position-position dissimilarity from the dynamic programming matrix avr_avr ... distance between the two averages avr_dst ... for all aligned structures, average distance to the average structure std_dev ... for all aligned structures, standard deviation of distance to ave str group: 1 2 N pos_scr avr_ave avr_dst std_dev 2OB0A 2X7BA ------------------------------------------------------ 1 0.00 0.00 0.00 0.00 S 1 A - 2 0.00 0.00 0.00 0.00 K 2 A - 3 0.00 0.00 0.00 0.00 G 3 A - 4 0.00 0.00 0.00 0.00 S 4 A - 5 0.70 1.78 0.89 0.00 R 5 A D 11 A 6 0.57 1.30 0.65 0.00 I 6 A F 12 A 7 0.32 0.99 0.49 0.00 E 7 A T 13 A 8 0.34 1.56 0.78 0.00 * L 8 A L 14 A 9 0.64 2.53 1.26 0.00 G 9 A R 15 A 10 0.68 2.92 1.46 0.00 D 10 A N 16 A 11 0.56 2.31 1.16 0.00 V 11 A A 17 A 12 0.60 2.32 1.16 0.00 T 12 A R 18 A 13 0.71 2.64 1.32 0.00 P 13 A M 19 A 14 0.56 2.03 1.02 0.00 H 14 A D 20 A 15 0.74 2.19 1.10 0.00 N 15 A D 21 A 16 0.42 1.37 0.69 0.00 * I 16 A I 22 A 17 0.30 0.90 0.45 0.00 K 17 A D 23 A 18 0.24 1.00 0.50 0.00 * Q 18 A Q 24 A 19 0.28 1.00 0.50 0.00 L 19 A I 25 A 20 0.51 0.89 0.44 0.00 K 20 A I 26 A 21 0.25 0.85 0.42 0.00 R 21 A K 27 A 22 0.28 1.02 0.51 0.00 L 22 A I 28 A 23 0.24 0.98 0.49 0.00 * N 23 A N 29 A 24 0.29 0.90 0.45 0.00 Q 24 A R 30 A 25 0.28 0.99 0.50 0.00 V 25 A L 31 A 26 0.44 1.57 0.78 0.00 I 26 A T 32 A 27 0.37 1.39 0.70 0.00 F 27 A L 33 A 28 0.37 1.65 0.83 0.00 * P 28 A P 34 A 29 0.33 0.90 0.45 0.00 V 29 A E 35 A 30 0.30 0.92 0.46 0.00 S 30 A N 36 A 31 0.21 0.33 0.16 0.00 * Y 31 A Y 37 A 32 0.52 1.91 0.96 0.00 N 32 A P 38 A 33 0.79 3.27 1.63 0.00 D 33 A Y 39 A 34 0.73 2.96 1.48 0.00 K 34 A Y 40 A 35 0.27 0.74 0.37 0.00 * F 35 A F 41 A 36 0.49 2.04 1.02 0.00 Y 36 A F 42 A 37 0.68 2.27 1.14 0.00 K 37 A V 43 A 38 0.20 0.53 0.26 0.00 D 38 A E 44 A 39 0.71 2.72 1.36 0.00 V 39 A H 45 A 40 0.59 2.77 1.38 0.00 * L 40 A L 46 A 41 0.24 0.54 0.27 0.00 E 41 A K 47 A 42 0.00 0.00 0.00 0.00 - E 48 A 43 0.65 1.99 0.99 0.00 V 42 A Y 49 A 44 0.50 1.83 0.92 0.00 * G 43 A G 50 A 45 0.46 1.46 0.73 0.00 E 44 A L 51 A 46 0.71 1.87 0.93 0.00 L 45 A A 52 A 47 0.39 1.23 0.61 0.00 A 46 A F 53 A 48 0.51 1.75 0.88 0.00 K 47 A F 54 A 49 0.40 1.59 0.79 0.00 L 48 A V 55 A 50 0.24 0.99 0.50 0.00 * A 49 A A 56 A 51 0.58 1.26 0.63 0.00 Y 50 A I 57 A 52 0.61 2.43 1.21 0.00 F 51 A V 58 A 53 1.05 3.78 1.89 0.00 N 52 A D 59 A 54 0.75 3.29 1.64 0.00 D 53 A N 60 A 55 0.77 3.15 1.58 0.00 I 54 A S 61 A 56 0.43 1.62 0.81 0.00 A 55 A V 62 A 57 0.21 0.86 0.43 0.00 * V 56 A V 63 A 58 0.36 0.69 0.35 0.00 * G 57 A G 64 A 59 0.46 0.62 0.31 0.00 A 58 A Y 65 A 60 0.18 0.54 0.27 0.00 V 59 A I 66 A 61 0.28 0.52 0.26 0.00 C 60 A M 67 A 62 0.26 0.34 0.17 0.00 C 61 A P 68 A 63 0.18 0.69 0.35 0.00 * R 62 A R 69 A 64 0.37 0.50 0.25 0.00 V 63 A I 70 A 65 0.34 1.22 0.61 0.00 D 64 A E 71 A 66 0.42 1.21 0.61 0.00 H 65 A W 72 A 67 0.72 1.88 0.94 0.00 S 66 A G 73 A 68 0.39 0.58 0.29 0.00 Q 67 A F 74 A 69 0.00 0.00 0.00 0.00 - S 75 A 70 0.00 0.00 0.00 0.00 - N 76 A 71 0.00 0.00 0.00 0.00 - I 77 A 72 0.00 0.00 0.00 0.00 - K 78 A 73 0.00 0.00 0.00 0.00 - Q 79 A 74 0.00 0.00 0.00 0.00 - L 80 A 75 0.00 0.00 0.00 0.00 - P 81 A 76 0.00 0.00 0.00 0.00 - S 82 A 77 0.79 1.60 0.80 0.00 N 68 A L 83 A 78 0.66 1.41 0.70 0.00 Q 69 A V 84 A 79 0.24 0.81 0.40 0.00 K 70 A R 85 A 80 0.18 0.46 0.23 0.00 R 71 A K 86 A 81 0.20 0.25 0.13 0.00 L 72 A G 87 A 82 0.20 0.36 0.18 0.00 Y 73 A H 88 A 83 0.13 0.30 0.15 0.00 I 74 A V 89 A 84 0.18 0.32 0.16 0.00 M 75 A V 90 A 85 0.21 0.64 0.32 0.00 T 76 A S 91 A 86 0.54 1.24 0.62 0.00 L 77 A I 92 A 87 0.84 1.67 0.84 0.00 G 78 A A 93 A 88 0.40 0.24 0.12 0.00 C 79 A V 94 A 89 0.44 1.10 0.55 0.00 * L 80 A L 95 A 90 0.45 1.76 0.88 0.00 A 81 A E 96 A 91 0.53 2.08 1.04 0.00 P 82 A E 97 A 92 0.26 1.22 0.61 0.00 * Y 83 A Y 98 A 93 0.21 0.92 0.46 0.00 * R 84 A R 99 A 94 0.15 0.63 0.31 0.00 * R 85 A R 100 A 95 0.18 0.29 0.14 0.00 L 86 A K 101 A 96 0.17 0.75 0.37 0.00 * G 87 A G 102 A 97 0.09 0.29 0.15 0.00 * I 88 A I 103 A 98 0.23 0.72 0.36 0.00 G 89 A A 104 A 99 0.28 1.23 0.62 0.00 * T 90 A T 105 A 100 0.30 0.99 0.50 0.00 K 91 A T 106 A 101 0.10 0.10 0.05 0.00 M 92 A L 107 A 102 0.18 0.77 0.39 0.00 * L 93 A L 108 A 103 0.32 0.99 0.50 0.00 N 94 A E 109 A 104 0.18 0.23 0.11 0.00 H 95 A A 110 A 105 0.40 1.40 0.70 0.00 V 96 A S 111 A 106 0.51 2.17 1.09 0.00 L 97 A M 112 A 107 0.45 1.72 0.86 0.00 N 98 A K 113 A 108 0.63 1.46 0.73 0.00 I 99 A S 114 A 109 0.88 3.52 1.76 0.00 C 100 A M 115 A 110 0.96 4.19 2.10 0.00 E 101 A K 116 A 111 0.71 2.95 1.48 0.00 K 102 A N 117 A 112 1.12 4.62 2.31 0.00 * D 103 A D 118 A 113 1.91 8.04 4.02 0.00 G 104 A Y 119 A 114 0.77 3.25 1.63 0.00 T 105 A N 120 A 115 0.57 2.16 1.08 0.00 F 106 A A 121 A 116 0.54 2.25 1.12 0.00 D 107 A E 122 A 117 0.24 0.60 0.30 0.00 N 108 A E 123 A 118 0.10 0.31 0.15 0.00 * I 109 A I 124 A 119 0.34 0.58 0.29 0.00 * Y 110 A Y 125 A 120 0.11 0.43 0.21 0.00 * L 111 A L 126 A 121 0.20 0.34 0.17 0.00 H 112 A E 127 A 122 0.13 0.49 0.24 0.00 * V 113 A V 128 A 123 0.17 0.26 0.13 0.00 Q 114 A R 129 A 124 0.12 0.26 0.13 0.00 I 115 A V 130 A 125 0.07 0.18 0.09 0.00 * S 116 A S 131 A 126 0.12 0.41 0.21 0.00 * N 117 A N 132 A 127 0.26 0.60 0.30 0.00 E 118 A Y 133 A 128 0.28 0.85 0.43 0.00 S 119 A P 134 A 129 0.17 0.67 0.33 0.00 * A 120 A A 135 A 130 0.17 0.70 0.35 0.00 * I 121 A I 136 A 131 0.26 0.75 0.38 0.00 D 122 A A 137 A 132 0.24 0.77 0.38 0.00 F 123 A L 138 A 133 0.13 0.56 0.28 0.00 * Y 124 A Y 139 A 134 0.20 0.36 0.18 0.00 R 125 A E 140 A 135 0.15 0.57 0.29 0.00 * K 126 A K 141 A 136 0.27 0.92 0.46 0.00 F 127 A L 142 A 137 0.23 0.64 0.32 0.00 G 128 A N 143 A 138 0.13 0.52 0.26 0.00 * F 129 A F 144 A 139 0.14 0.24 0.12 0.00 E 130 A K 145 A 140 0.19 0.25 0.13 0.00 I 131 A K 146 A 141 0.15 0.40 0.20 0.00 I 132 A V 147 A 142 0.23 0.65 0.32 0.00 E 133 A K 148 A 143 0.23 0.57 0.28 0.00 T 134 A V 149 A 144 0.18 0.26 0.13 0.00 K 135 A L 150 A 145 0.10 0.29 0.15 0.00 * K 136 A K 151 A 146 0.33 1.09 0.54 0.00 N 137 A G 152 A 147 0.16 0.63 0.32 0.00 * Y 138 A Y 153 A 148 0.24 0.94 0.47 0.00 * Y 139 A Y 154 A 149 0.52 1.82 0.91 0.00 K 140 A A 155 A 150 0.80 3.06 1.53 0.00 R 141 A D 156 A 151 0.00 0.00 0.00 0.00 I 142 A - 152 0.00 0.00 0.00 0.00 E 143 A - 153 1.46 5.44 2.72 0.00 P 144 A G 157 A 154 0.43 1.40 0.70 0.00 A 145 A E 158 A 155 0.17 0.53 0.27 0.00 * D 146 A D 159 A 156 0.09 0.27 0.13 0.00 * A 147 A A 160 A 157 0.17 0.20 0.10 0.00 H 148 A Y 161 A 158 0.22 0.70 0.35 0.00 V 149 A L 162 A 159 0.27 0.93 0.47 0.00 L 150 A M 163 A 160 0.23 0.53 0.27 0.00 Q 151 A A 164 A 161 0.17 0.42 0.21 0.00 K 152 A R 165 A 162 0.21 0.39 0.19 0.00 N 153 A P 166 A 163 0.20 0.00 0.00 0.00 * L 154 A 164 0.00 0.00 0.00 0.00 - ------------------------------------------------------ openf___224_> Open 2OB0_fit.pdb wrpdb___568_> Residues, atoms, selected atoms: 154 1245 1245 openf___224_> Open 2X7B_fit.pdb wrpdb___568_> Residues, atoms, selected atoms: 158 1332 1332 SALIGN______> Raw QUALITY_SCORE of the multiple alignment: 142.0 QUALITY_SCORE (percentage) : 92.2 Number of unique protein pairs : 1 QUALITY_SCORE_min : 142 RMS_CUTOFF : 3.5000 QS is the average number of structurally equivalent residue pairs. Two residues are equivalent when closer than RMS_CUTOFF upon pairwise least-squares superposition given current alignment. SALIGN______> Matrix of pairwise equivalences from individual pairwise alignments: 2OB0A 2X7BA 2OB0A 0 142 2X7BA 0 0 SALIGN______> Matrix of pairwise equivalences: 2OB0A 2X7BA 2OB0A 0 142 2X7BA 0 0 SALIGN______> Matrix of differences in pairwise equivalences inferred from the tree and individually: 2OB0A 2X7BA 2OB0A 0 0 2X7BA 0 0 SALIGN______> Matrix of %differences in pairwise equivalences inferred from the tree and individually: 2OB0A 2X7BA 2OB0A 0 0 2X7BA 0 0 openf___224_> Open structures.pap openf___224_> Open structures.ali ALIGN_CODES : 2OB0A 2X7BA Atom type for alignment (FIT_ATOMS) : CA FIT : F IMPROVE_ALIGNMENT : F WATER_IO, HETATM_IO, HYDROGEN_IO : F T F NO_TER : F OUTPUT : QUALITY FIT_ON_FIRST : F WRITE_FIT : T FIT_PDBNAM : T WRITE_WHOLE_PDB : F CURRENT_DIRECTORY : T Feature weights (FEATURE_WEIGHTS) : 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 NORMALIZE_PP_SCORES : F Gap initiation penalty (GAP_PENALTIES[1]) : -450.0000 Gap extension penalty (GAP_PENALTIES[2]) : -50.0000 Gap_function (align2d flag) : F 2-D Gap penalties : 3.50 3.50 3.50 0.20 4.00 6.50 2.00 0.00 GAP-GAP_SCORE : 0.0000 GAP-RESIDUE_SCORE : 0.0000 Perform gap-residue and gap-gap correction : T Residue type - residue type file (RR_FILE) : $(LIB)/as1.sim.mat OFF_DIAGONAL : 100 OVERHANG : 30 LOCAL_ALIGNMENT : F MATRIX_OFFSET : 0.0000 N_SUBOPT : 1 SUBOPT_OFFSET : 0.0000 Gap introduction penalty (GAP_PENALTIES_3D_1) : 0.0000 Gap extension penalty (GAP_PENALTIES_3D_2) : 3.0000 Max dist for equiv (2 * GAP_PENALTIES_3D_2) : 6.0000 ALIGN3D_TRF : F RMS_CUTOFF : 1.0 salign__276_> 'align_block' changed to 1. fndatmi_285W> Only 156 residues out of 158 contain atoms of type CA (This is usually caused by non-standard residues, such as ligands, or by PDB files with missing atoms.) Current alignment total score: 0 pos_scr ... position-position dissimilarity from the dynamic programming matrix avr_avr ... distance between the two averages avr_dst ... for all aligned structures, average distance to the average structure std_dev ... for all aligned structures, standard deviation of distance to ave str group: 1 2 N pos_scr avr_ave avr_dst std_dev 2OB0A 2X7BA ------------------------------------------------------ 1 0.00 0.00 0.00 0.00 S 1 A - 2 0.00 0.00 0.00 0.00 K 2 A - 3 0.00 0.00 0.00 0.00 G 3 A - 4 0.00 0.00 0.00 0.00 S 4 A - 5 0.00 1.78 0.89 0.00 R 5 A D 11 A 6 0.00 1.30 0.65 0.00 I 6 A F 12 A 7 0.00 0.99 0.49 0.00 E 7 A T 13 A 8 0.00 1.56 0.78 0.00 * L 8 A L 14 A 9 0.00 2.53 1.26 0.00 G 9 A R 15 A 10 0.00 2.92 1.46 0.00 D 10 A N 16 A 11 0.00 2.31 1.16 0.00 V 11 A A 17 A 12 0.00 2.32 1.16 0.00 T 12 A R 18 A 13 0.00 2.64 1.32 0.00 P 13 A M 19 A 14 0.00 2.03 1.02 0.00 H 14 A D 20 A 15 0.00 2.19 1.10 0.00 N 15 A D 21 A 16 0.00 1.37 0.69 0.00 * I 16 A I 22 A 17 0.00 0.90 0.45 0.00 K 17 A D 23 A 18 0.00 1.00 0.50 0.00 * Q 18 A Q 24 A 19 0.00 1.00 0.50 0.00 L 19 A I 25 A 20 0.00 0.89 0.44 0.00 K 20 A I 26 A 21 0.00 0.85 0.42 0.00 R 21 A K 27 A 22 0.00 1.02 0.51 0.00 L 22 A I 28 A 23 0.00 0.98 0.49 0.00 * N 23 A N 29 A 24 0.00 0.90 0.45 0.00 Q 24 A R 30 A 25 0.00 0.99 0.50 0.00 V 25 A L 31 A 26 0.00 1.57 0.78 0.00 I 26 A T 32 A 27 0.00 1.39 0.70 0.00 F 27 A L 33 A 28 0.00 1.65 0.83 0.00 * P 28 A P 34 A 29 0.00 0.90 0.45 0.00 V 29 A E 35 A 30 0.00 0.92 0.46 0.00 S 30 A N 36 A 31 0.00 0.33 0.16 0.00 * Y 31 A Y 37 A 32 0.00 1.91 0.96 0.00 N 32 A P 38 A 33 0.00 3.27 1.63 0.00 D 33 A Y 39 A 34 0.00 2.96 1.48 0.00 K 34 A Y 40 A 35 0.00 0.74 0.37 0.00 * F 35 A F 41 A 36 0.00 2.04 1.02 0.00 Y 36 A F 42 A 37 0.00 2.27 1.14 0.00 K 37 A V 43 A 38 0.00 0.53 0.26 0.00 D 38 A E 44 A 39 0.00 2.72 1.36 0.00 V 39 A H 45 A 40 0.00 2.77 1.38 0.00 * L 40 A L 46 A 41 0.00 0.54 0.27 0.00 E 41 A K 47 A 42 0.00 0.00 0.00 0.00 - E 48 A 43 0.00 1.99 0.99 0.00 V 42 A Y 49 A 44 0.00 1.83 0.92 0.00 * G 43 A G 50 A 45 0.00 1.46 0.73 0.00 E 44 A L 51 A 46 0.00 1.87 0.93 0.00 L 45 A A 52 A 47 0.00 1.23 0.61 0.00 A 46 A F 53 A 48 0.00 1.75 0.88 0.00 K 47 A F 54 A 49 0.00 1.59 0.79 0.00 L 48 A V 55 A 50 0.00 0.99 0.50 0.00 * A 49 A A 56 A 51 0.00 1.26 0.63 0.00 Y 50 A I 57 A 52 0.00 2.43 1.21 0.00 F 51 A V 58 A 53 0.00 3.78 1.89 0.00 N 52 A D 59 A 54 0.00 3.29 1.64 0.00 D 53 A N 60 A 55 0.00 3.15 1.58 0.00 I 54 A S 61 A 56 0.00 1.62 0.81 0.00 A 55 A V 62 A 57 0.00 0.86 0.43 0.00 * V 56 A V 63 A 58 0.00 0.69 0.35 0.00 * G 57 A G 64 A 59 0.00 0.62 0.31 0.00 A 58 A Y 65 A 60 0.00 0.54 0.27 0.00 V 59 A I 66 A 61 0.00 0.52 0.26 0.00 C 60 A M 67 A 62 0.00 0.34 0.17 0.00 C 61 A P 68 A 63 0.00 0.69 0.35 0.00 * R 62 A R 69 A 64 0.00 0.50 0.25 0.00 V 63 A I 70 A 65 0.00 1.22 0.61 0.00 D 64 A E 71 A 66 0.00 1.21 0.61 0.00 H 65 A W 72 A 67 0.00 1.88 0.94 0.00 S 66 A G 73 A 68 0.00 0.58 0.29 0.00 Q 67 A F 74 A 69 0.00 0.00 0.00 0.00 - S 75 A 70 0.00 0.00 0.00 0.00 - N 76 A 71 0.00 0.00 0.00 0.00 - I 77 A 72 0.00 0.00 0.00 0.00 - K 78 A 73 0.00 0.00 0.00 0.00 - Q 79 A 74 0.00 0.00 0.00 0.00 - L 80 A 75 0.00 0.00 0.00 0.00 - P 81 A 76 0.00 0.00 0.00 0.00 - S 82 A 77 0.00 1.60 0.80 0.00 N 68 A L 83 A 78 0.00 1.41 0.70 0.00 Q 69 A V 84 A 79 0.00 0.81 0.40 0.00 K 70 A R 85 A 80 0.00 0.46 0.23 0.00 R 71 A K 86 A 81 0.00 0.25 0.13 0.00 L 72 A G 87 A 82 0.00 0.36 0.18 0.00 Y 73 A H 88 A 83 0.00 0.30 0.15 0.00 I 74 A V 89 A 84 0.00 0.32 0.16 0.00 M 75 A V 90 A 85 0.00 0.64 0.32 0.00 T 76 A S 91 A 86 0.00 1.24 0.62 0.00 L 77 A I 92 A 87 0.00 1.67 0.84 0.00 G 78 A A 93 A 88 0.00 0.24 0.12 0.00 C 79 A V 94 A 89 0.00 1.10 0.55 0.00 * L 80 A L 95 A 90 0.00 1.76 0.88 0.00 A 81 A E 96 A 91 0.00 2.08 1.04 0.00 P 82 A E 97 A 92 0.00 1.22 0.61 0.00 * Y 83 A Y 98 A 93 0.00 0.92 0.46 0.00 * R 84 A R 99 A 94 0.00 0.63 0.31 0.00 * R 85 A R 100 A 95 0.00 0.29 0.14 0.00 L 86 A K 101 A 96 0.00 0.75 0.37 0.00 * G 87 A G 102 A 97 0.00 0.29 0.15 0.00 * I 88 A I 103 A 98 0.00 0.72 0.36 0.00 G 89 A A 104 A 99 0.00 1.23 0.62 0.00 * T 90 A T 105 A 100 0.00 0.99 0.50 0.00 K 91 A T 106 A 101 0.00 0.10 0.05 0.00 M 92 A L 107 A 102 0.00 0.77 0.39 0.00 * L 93 A L 108 A 103 0.00 0.99 0.50 0.00 N 94 A E 109 A 104 0.00 0.23 0.11 0.00 H 95 A A 110 A 105 0.00 1.40 0.70 0.00 V 96 A S 111 A 106 0.00 2.17 1.09 0.00 L 97 A M 112 A 107 0.00 1.72 0.86 0.00 N 98 A K 113 A 108 0.00 1.46 0.73 0.00 I 99 A S 114 A 109 0.00 3.52 1.76 0.00 C 100 A M 115 A 110 0.00 4.19 2.10 0.00 E 101 A K 116 A 111 0.00 2.95 1.48 0.00 K 102 A N 117 A 112 0.00 4.62 2.31 0.00 * D 103 A D 118 A 113 0.00 8.04 4.02 0.00 G 104 A Y 119 A 114 0.00 3.25 1.63 0.00 T 105 A N 120 A 115 0.00 2.16 1.08 0.00 F 106 A A 121 A 116 0.00 2.25 1.12 0.00 D 107 A E 122 A 117 0.00 0.60 0.30 0.00 N 108 A E 123 A 118 0.00 0.31 0.15 0.00 * I 109 A I 124 A 119 0.00 0.58 0.29 0.00 * Y 110 A Y 125 A 120 0.00 0.43 0.21 0.00 * L 111 A L 126 A 121 0.00 0.34 0.17 0.00 H 112 A E 127 A 122 0.00 0.49 0.24 0.00 * V 113 A V 128 A 123 0.00 0.26 0.13 0.00 Q 114 A R 129 A 124 0.00 0.26 0.13 0.00 I 115 A V 130 A 125 0.00 0.18 0.09 0.00 * S 116 A S 131 A 126 0.00 0.41 0.21 0.00 * N 117 A N 132 A 127 0.00 0.60 0.30 0.00 E 118 A Y 133 A 128 0.00 0.85 0.43 0.00 S 119 A P 134 A 129 0.00 0.67 0.33 0.00 * A 120 A A 135 A 130 0.00 0.70 0.35 0.00 * I 121 A I 136 A 131 0.00 0.75 0.38 0.00 D 122 A A 137 A 132 0.00 0.77 0.38 0.00 F 123 A L 138 A 133 0.00 0.56 0.28 0.00 * Y 124 A Y 139 A 134 0.00 0.36 0.18 0.00 R 125 A E 140 A 135 0.00 0.57 0.29 0.00 * K 126 A K 141 A 136 0.00 0.92 0.46 0.00 F 127 A L 142 A 137 0.00 0.64 0.32 0.00 G 128 A N 143 A 138 0.00 0.52 0.26 0.00 * F 129 A F 144 A 139 0.00 0.24 0.12 0.00 E 130 A K 145 A 140 0.00 0.25 0.13 0.00 I 131 A K 146 A 141 0.00 0.40 0.20 0.00 I 132 A V 147 A 142 0.00 0.65 0.32 0.00 E 133 A K 148 A 143 0.00 0.57 0.28 0.00 T 134 A V 149 A 144 0.00 0.26 0.13 0.00 K 135 A L 150 A 145 0.00 0.29 0.15 0.00 * K 136 A K 151 A 146 0.00 1.09 0.54 0.00 N 137 A G 152 A 147 0.00 0.63 0.32 0.00 * Y 138 A Y 153 A 148 0.00 0.94 0.47 0.00 * Y 139 A Y 154 A 149 0.00 1.82 0.91 0.00 K 140 A A 155 A 150 0.00 3.06 1.53 0.00 R 141 A D 156 A 151 0.00 0.00 0.00 0.00 I 142 A - 152 0.00 0.00 0.00 0.00 E 143 A - 153 0.00 5.44 2.72 0.00 P 144 A G 157 A 154 0.00 1.40 0.70 0.00 A 145 A E 158 A 155 0.00 0.53 0.27 0.00 * D 146 A D 159 A 156 0.00 0.27 0.13 0.00 * A 147 A A 160 A 157 0.00 0.20 0.10 0.00 H 148 A Y 161 A 158 0.00 0.70 0.35 0.00 V 149 A L 162 A 159 0.00 0.93 0.47 0.00 L 150 A M 163 A 160 0.00 0.53 0.27 0.00 Q 151 A A 164 A 161 0.00 0.42 0.21 0.00 K 152 A R 165 A 162 0.00 0.39 0.19 0.00 N 153 A P 166 A 163 0.00 0.00 0.00 0.00 * L 154 A 164 0.00 0.00 0.00 0.00 - ------------------------------------------------------ openf___224_> Open 2OB0_fit.pdb wrpdb___568_> Residues, atoms, selected atoms: 154 1245 1245 openf___224_> Open 2X7B_fit.pdb wrpdb___568_> Residues, atoms, selected atoms: 158 1332 1332 openf___224_> Open 2X7B_fit.pdb openf___224_> Open 2X7B_fit.pdb SALIGN______> Raw QUALITY_SCORE of the multiple alignment: 80.0 QUALITY_SCORE (percentage) : 51.9 Number of unique protein pairs : 1 QUALITY_SCORE_min : 80 RMS_CUTOFF : 1.0000 QS is the average number of structurally equivalent residue pairs. Two residues are equivalent when closer than RMS_CUTOFF upon pairwise least-squares superposition given current alignment. SALIGN______> Matrix of pairwise equivalences: 2OB0A 2X7BA 2OB0A 0 80 2X7BA 0 0 Dynamically allocated memory at finish [B,KiB,MiB]: 3651208 3565.633 3.482 Starting time : 2011/03/08 14:15:58 Closing time : 2011/03/08 14:16:00 Total CPU time [seconds] : 0.75