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 22:42:16 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 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191562 187.072 0.183 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192090 187.588 0.183 openf___224_> Open ${MODINSTALL9v16}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240690 235.049 0.230 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 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253990 248.037 0.242 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 align2d_in.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 256152 250.148 0.244 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 257602 251.564 0.246 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 260502 254.396 0.248 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 266302 260.061 0.254 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 382986 374.010 0.365 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 383978 374.979 0.366 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 384774 375.756 0.367 Read the alignment from file : align2d_in.ali Total number of alignment positions: 265 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1bmlB 249 1 1bml 2 seq 200 1 seq ALIGN_CODES : 1bmlB seq Atom type for alignment (FIT_ATOMS) : CA FIT : T IMPROVE_ALIGNMENT : T WATER_IO, HETATM_IO, HYDROGEN_IO : F F F NO_TER : F OUTPUT : 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 0.0000 0.0000 NORMALIZE_PP_SCORES : F Gap initiation penalty (GAP_PENALTIES[1]) : -100.0000 Gap extension penalty (GAP_PENALTIES[2]) : 0.0000 Break-break bonus : 10000.0000 Gap_function (align2d flag) : T 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 : 0 LOCAL_ALIGNMENT : F MATRIX_OFFSET : 0.0000 N_SUBOPT : 0 SUBOPT_OFFSET : 0.0000 Gap introduction penalty (GAP_PENALTIES_3D_1) : 0.0000 Gap extension penalty (GAP_PENALTIES_3D_2) : 1.7500 Max dist for equiv (2 * GAP_PENALTIES_3D_2) : 3.5000 ALIGN3D_TRF : F RMS_CUTOFF : 3.5 salign__276_> 'align_block' changed to 1. openf___224_> Open ../atom_files/pdb1bml.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 461199 450.390 0.440 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 461199 450.390 0.440 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 461370 450.557 0.440 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 462220 451.387 0.441 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 463478 452.615 0.442 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 465382 454.475 0.444 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 465382 454.475 0.444 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 465472 454.562 0.444 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 468328 457.352 0.447 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 468328 457.352 0.447 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 468463 457.483 0.447 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 472747 461.667 0.451 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 472747 461.667 0.451 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 472945 461.860 0.451 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 479371 468.136 0.457 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 479371 468.136 0.457 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 479668 468.426 0.457 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 489290 477.822 0.467 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 489290 477.822 0.467 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 489740 478.262 0.467 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 504190 492.373 0.481 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 504190 492.373 0.481 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 504865 493.032 0.481 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 526523 514.183 0.502 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 526523 514.183 0.502 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 527531 515.167 0.503 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 526739 514.394 0.502 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. openf___224_> Open $(LIB)/as1.sim.mat rdrrwgh_268_> Number of residue types: 20 SALIGN_____> adding the next group to the alignment; iteration 1 Current alignment total score: 103 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 1bmlB seq ------------------------------------------------------ 1 0.00 0.00 0.00 0.00 A - 2 0.00 0.00 0.00 0.00 A - 3 0.00 0.00 0.00 0.00 P - 4 0.00 0.00 0.00 0.00 S - 5 0.00 0.00 0.00 0.00 F - 6 0.00 0.00 0.00 0.00 D - 7 0.00 0.00 0.00 0.00 C - 8 0.00 0.00 0.00 0.00 G - 9 0.00 0.00 0.00 0.00 K - 10 0.00 0.00 0.00 0.00 P - 11 0.00 0.00 0.00 0.00 Q - 12 0.00 0.00 0.00 0.00 V - 13 0.00 0.00 0.00 0.00 E - 14 0.00 0.00 0.00 0.00 P - 15 0.00 0.00 0.00 0.00 K - 16 0.00 0.00 0.00 0.00 K - 17 0.00 0.00 0.00 0.00 C - 18 0.00 0.00 0.00 0.00 P - 19 0.58 0.00 0.00 0.00 G A 20 0.44 0.00 0.00 0.00 R N 21 0.70 0.00 0.00 0.00 V I 22 0.88 0.00 0.00 0.00 * V V 23 0.96 0.00 0.00 0.00 * G G 24 0.96 0.00 0.00 0.00 * G G 25 0.17 0.00 0.00 0.00 C I 26 0.38 0.00 0.00 0.00 V E 27 0.36 0.00 0.00 0.00 A Y 28 0.00 0.00 0.00 0.00 H - 29 0.00 0.00 0.00 0.00 P - 30 0.00 0.00 0.00 0.00 H - 31 0.89 0.00 0.00 0.00 * S S 32 0.26 0.00 0.00 0.00 W I 33 0.40 0.00 0.00 0.00 P N 34 0.00 0.00 0.00 0.00 W - 35 0.44 0.00 0.00 0.00 Q N 36 0.57 0.00 0.00 0.00 V A 37 0.89 0.00 0.00 0.00 * S S 38 0.91 0.00 0.00 0.00 * L L 39 0.15 0.00 0.00 0.00 R C 40 0.67 0.00 0.00 0.00 T S 41 0.00 0.00 0.00 0.00 R - 42 0.46 0.00 0.00 0.00 F V 43 0.96 0.00 0.00 0.00 * G G 44 0.40 0.00 0.00 0.00 M F 45 0.37 0.00 0.00 0.00 H S 46 0.46 0.00 0.00 0.00 F V 47 0.24 0.00 0.00 0.00 C T 48 0.40 0.00 0.00 0.00 G R 49 0.96 0.00 0.00 0.00 * G G 50 0.54 0.00 0.00 0.00 T A 51 0.41 0.00 0.00 0.00 L T 52 0.32 0.00 0.00 0.00 I K 53 0.52 0.00 0.00 0.00 S G 54 0.00 0.00 0.00 0.00 P - 55 0.00 0.00 0.00 0.00 E - 56 0.00 0.00 0.00 0.00 W - 57 0.46 0.00 0.00 0.00 V F 58 0.65 0.00 0.00 0.00 L V 59 0.88 0.00 0.00 0.00 * T T 60 0.86 0.00 0.00 0.00 * A A 61 0.58 0.00 0.00 0.00 A G 62 0.87 0.00 0.00 0.00 * H H 63 1.00 0.00 0.00 0.00 * C C 64 0.29 0.00 0.00 0.00 L G 65 0.47 0.00 0.00 0.00 E T 66 0.42 0.00 0.00 0.00 K V 67 0.58 0.00 0.00 0.00 S N 68 0.00 0.00 0.00 0.00 P - 69 0.00 0.00 0.00 0.00 R - 70 0.00 0.00 0.00 0.00 P - 71 0.00 0.00 0.00 0.00 S - 72 0.60 0.00 0.00 0.00 S A 73 0.34 0.00 0.00 0.00 Y T 74 0.52 0.00 0.00 0.00 K A 75 0.34 0.00 0.00 0.00 V R 76 0.87 0.00 0.00 0.00 * I I 77 0.29 0.00 0.00 0.00 L G 78 0.96 0.00 0.00 0.00 * G G 79 0.86 0.00 0.00 0.00 * A A 80 0.00 0.00 0.00 0.00 H - 81 0.00 0.00 0.00 0.00 Q - 82 0.00 0.00 0.00 0.00 E - 83 0.00 0.00 0.00 0.00 V - 84 0.00 0.00 0.00 0.00 N - 85 0.00 0.00 0.00 0.00 L - 86 0.00 0.00 0.00 0.00 E - 87 0.00 0.00 0.00 0.00 P - 88 0.00 0.00 0.00 0.00 H - 89 0.88 0.00 0.00 0.00 * V V 90 0.39 0.00 0.00 0.00 Q V 91 0.46 0.00 0.00 0.00 E G 92 0.44 0.00 0.00 0.00 I T 93 0.26 0.00 0.00 0.00 E F 94 0.57 0.00 0.00 0.00 V A 95 0.60 0.00 0.00 0.00 S A 96 0.87 0.00 0.00 0.00 * R R 97 0.65 0.00 0.00 0.00 L V 98 0.90 0.00 0.00 0.00 * F F 99 0.34 0.00 0.00 0.00 L P 100 0.46 0.00 0.00 0.00 E G 101 0.00 0.00 0.00 0.00 P - 102 0.00 0.00 0.00 0.00 T - 103 0.00 0.00 0.00 0.00 R - 104 0.52 0.00 0.00 0.00 K N 105 0.89 0.00 0.00 0.00 * D D 106 0.27 0.00 0.00 0.00 I R 107 0.86 0.00 0.00 0.00 * A A 108 0.35 0.00 0.00 0.00 L W 109 0.65 0.00 0.00 0.00 L V 110 0.51 0.00 0.00 0.00 K S 111 0.91 0.00 0.00 0.00 * L L 112 0.67 0.00 0.00 0.00 S T 113 0.89 0.00 0.00 0.00 * S S 114 0.51 0.00 0.00 0.00 P A 115 0.48 0.00 0.00 0.00 A Q 116 0.50 0.00 0.00 0.00 V T 117 0.64 0.00 0.00 0.00 I L 118 0.41 0.00 0.00 0.00 T L 119 0.45 0.00 0.00 0.00 D P 120 0.63 0.00 0.00 0.00 K R 121 0.88 0.00 0.00 0.00 * V V 122 0.43 0.00 0.00 0.00 I A 123 0.40 0.00 0.00 0.00 P N 124 0.58 0.00 0.00 0.00 A G 125 0.22 0.00 0.00 0.00 C S 126 0.37 0.00 0.00 0.00 L S 127 0.48 0.00 0.00 0.00 P S 128 0.89 0.00 0.00 0.00 * S S 129 0.00 0.00 0.00 0.00 P - 130 0.00 0.00 0.00 0.00 N - 131 0.63 0.00 0.00 0.00 Y F 132 0.88 0.00 0.00 0.00 * V V 133 0.00 0.00 0.00 0.00 - T 134 0.88 0.00 0.00 0.00 * V V 135 0.40 0.00 0.00 0.00 A R 136 0.49 0.00 0.00 0.00 D G 137 0.46 0.00 0.00 0.00 R S 138 0.88 0.00 0.00 0.00 * T T 139 0.86 0.00 0.00 0.00 * E E 140 0.32 0.00 0.00 0.00 C A 141 0.40 0.00 0.00 0.00 F A 142 0.70 0.00 0.00 0.00 I V 143 0.00 0.00 0.00 0.00 T - 144 0.96 0.00 0.00 0.00 * G G 145 0.23 0.00 0.00 0.00 W A 146 0.58 0.00 0.00 0.00 G A 147 0.38 0.00 0.00 0.00 E V 148 0.24 0.00 0.00 0.00 T C 149 0.00 0.00 0.00 0.00 Q - 150 0.00 0.00 0.00 0.00 G - 151 0.00 0.00 0.00 0.00 T - 152 0.00 0.00 0.00 0.00 F - 153 0.40 0.00 0.00 0.00 G R 154 0.60 0.00 0.00 0.00 A S 155 0.96 0.00 0.00 0.00 * G G 156 0.40 0.00 0.00 0.00 L R 157 0.41 0.00 0.00 0.00 L T 158 0.53 0.00 0.00 0.00 K T 159 0.46 0.00 0.00 0.00 E G 160 0.36 0.00 0.00 0.00 A Y 161 0.87 0.00 0.00 0.00 * Q Q 162 0.20 0.00 0.00 0.00 L C 163 0.40 0.00 0.00 0.00 P G 164 0.50 0.00 0.00 0.00 V T 165 0.87 0.00 0.00 0.00 * I I 166 0.47 0.00 0.00 0.00 E T 167 0.47 0.00 0.00 0.00 N A 168 0.86 0.00 0.00 0.00 * K K 169 0.33 0.00 0.00 0.00 V N 170 0.28 0.00 0.00 0.00 C V 171 0.52 0.00 0.00 0.00 N T 172 0.40 0.00 0.00 0.00 R A 173 0.00 0.00 0.00 0.00 Y - 174 0.46 0.00 0.00 0.00 E N 175 0.63 0.00 0.00 0.00 F Y 176 0.47 0.00 0.00 0.00 L A 177 0.46 0.00 0.00 0.00 N E 178 0.96 0.00 0.00 0.00 * G G 179 0.40 0.00 0.00 0.00 R A 180 0.88 0.00 0.00 0.00 * V V 181 0.46 0.00 0.00 0.00 Q R 182 0.00 0.00 0.00 0.00 S - 183 0.45 0.00 0.00 0.00 T R 184 0.46 0.00 0.00 0.00 E G 185 0.91 0.00 0.00 0.00 * L L 186 0.24 0.00 0.00 0.00 C T 187 0.48 0.00 0.00 0.00 A Q 188 0.96 0.00 0.00 0.00 * G G 189 0.00 0.00 0.00 0.00 H - 190 0.00 0.00 0.00 0.00 L - 191 0.00 0.00 0.00 0.00 A - 192 0.00 0.00 0.00 0.00 G - 193 0.00 0.00 0.00 0.00 G - 194 0.00 0.00 0.00 0.00 T - 195 0.60 0.00 0.00 0.00 D N 196 0.60 0.00 0.00 0.00 S A 197 1.00 0.00 0.00 0.00 * C C 198 0.00 0.00 0.00 0.00 - M 199 0.00 0.00 0.00 0.00 - G 200 0.46 0.00 0.00 0.00 Q R 201 0.96 0.00 0.00 0.00 * G G 202 0.89 0.00 0.00 0.00 * D D 203 0.60 0.00 0.00 0.00 A S 204 0.96 0.00 0.00 0.00 * G G 205 0.96 0.00 0.00 0.00 * G G 206 0.48 0.00 0.00 0.00 P S 207 0.35 0.00 0.00 0.00 L W 208 0.70 0.00 0.00 0.00 V I 209 0.24 0.00 0.00 0.00 C T 210 0.30 0.00 0.00 0.00 F S 211 0.51 0.00 0.00 0.00 E A 212 0.00 0.00 0.00 0.00 - G 213 0.56 0.00 0.00 0.00 K Q 214 0.50 0.00 0.00 0.00 D A 215 0.56 0.00 0.00 0.00 K Q 216 0.34 0.00 0.00 0.00 Y G 217 0.70 0.00 0.00 0.00 I V 218 0.63 0.00 0.00 0.00 L M 219 0.47 0.00 0.00 0.00 Q S 220 0.96 0.00 0.00 0.00 * G G 221 0.00 0.00 0.00 0.00 - G 222 0.00 0.00 0.00 0.00 - N 223 0.88 0.00 0.00 0.00 * V V 224 0.44 0.00 0.00 0.00 T Q 225 0.89 0.00 0.00 0.00 * S S 226 0.19 0.00 0.00 0.00 W N 227 0.96 0.00 0.00 0.00 * G G 228 0.33 0.00 0.00 0.00 L N 229 0.48 0.00 0.00 0.00 G N 230 1.00 0.00 0.00 0.00 * C C 231 0.58 0.00 0.00 0.00 A G 232 0.27 0.00 0.00 0.00 R I 233 0.93 0.00 0.00 0.00 * P P 234 0.00 0.00 0.00 0.00 - A 235 0.00 0.00 0.00 0.00 - S 236 0.44 0.00 0.00 0.00 N Q 237 0.63 0.00 0.00 0.00 K R 238 0.48 0.00 0.00 0.00 P S 239 0.52 0.00 0.00 0.00 G S 240 0.65 0.00 0.00 0.00 V L 241 0.63 0.00 0.00 0.00 Y F 242 0.38 0.00 0.00 0.00 V E 243 0.87 0.00 0.00 0.00 * R R 244 0.65 0.00 0.00 0.00 V L 245 0.47 0.00 0.00 0.00 S Q 246 0.33 0.00 0.00 0.00 R P 247 0.50 0.00 0.00 0.00 F I 248 0.65 0.00 0.00 0.00 V L 249 0.67 0.00 0.00 0.00 T S 250 0.15 0.00 0.00 0.00 W Q 251 0.39 0.00 0.00 0.00 I Y 252 0.46 0.00 0.00 0.00 E G 253 0.29 0.00 0.00 0.00 G L 254 0.40 0.00 0.00 0.00 V S 255 0.63 0.00 0.00 0.00 M L 256 0.34 0.00 0.00 0.00 R V 257 0.52 0.00 0.00 0.00 N T ------------------------------------------------------ openf___224_> Open align2d.ali openf___224_> Open align2d.pap Dynamically allocated memory at finish [B,KiB,MiB]: 526739 514.394 0.502 Starting time : 2016/04/05 22:42:16 Closing time : 2016/04/05 22:42:17 Total CPU time [seconds] : 0.53