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 22:42:19 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 fm07254_test.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]: 277902 271.389 0.265 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 506186 494.322 0.483 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 507310 495.420 0.484 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 508354 496.439 0.485 Read the alignment from file : fm07254_test.ali Total number of alignment positions: 433 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1rszA 282 1 1rszA_fit.p undefined 2 1sd2A 262 1 1sd2A_fit.p undefined ALIGN_CODES : 1rszA 1sd2A 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]) : -450.0000 Gap extension penalty (GAP_PENALTIES[2]) : -50.0000 Break-break bonus : 10000.0000 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 : 0 LOCAL_ALIGNMENT : F MATRIX_OFFSET : 0.0000 N_SUBOPT : 5 SUBOPT_OFFSET : 15.0000 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 $(LIB)/as1.sim.mat rdrrwgh_268_> Number of residue types: 20 SALIGN_____> adding the next group to the alignment; iteration 1 openf___224_> Open suboptimal_alignments.out i i1 i2 naln neqv oscore score sneqvN sneqv1 ------------------------------------------------------------------- 0 4 282 279 261 164.8 164.8 0.0 0 1 2 282 281 262 168.3 168.3 0.0 0 2 10 277 268 262 170.3 170.3 0.0 0 3 1 280 280 260 170.5 170.5 0.0 0 4 22 283 262 259 170.7 170.7 0.0 0 5 8 281 274 262 171.4 171.4 0.0 0 Current alignment total score: 171.4 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 1rszA 1sd2A ------------------------------------------------------ 1 0.00 0.00 0.00 0.00 N - 2 0.00 0.00 0.00 0.00 G - 3 0.00 0.00 0.00 0.00 Y - 4 0.00 0.00 0.00 0.00 T - 5 0.00 0.00 0.00 0.00 Y - 6 0.00 0.00 0.00 0.00 E - 7 0.00 0.00 0.00 0.00 D - 8 0.64 0.00 0.00 0.00 Y A 9 0.58 0.00 0.00 0.00 K V 10 0.48 0.00 0.00 0.00 N K 11 0.56 0.00 0.00 0.00 T I 12 0.42 0.00 0.00 0.00 A G 13 0.69 0.00 0.00 0.00 E I 14 0.74 0.00 0.00 0.00 W I 15 0.71 0.00 0.00 0.00 L G 16 0.71 0.00 0.00 0.00 L G 17 0.33 0.00 0.00 0.00 S T 18 0.65 0.00 0.00 0.00 H G 19 0.59 0.00 0.00 0.00 T L 20 0.52 0.00 0.00 0.00 K D 21 0.61 0.00 0.00 0.00 H D 22 0.67 0.00 0.00 0.00 R P 23 0.57 0.00 0.00 0.00 P E 24 0.75 0.00 0.00 0.00 Q I 25 0.35 0.00 0.00 0.00 V L 26 0.49 0.00 0.00 0.00 A E 27 0.76 0.00 0.00 0.00 I G 28 0.73 0.00 0.00 0.00 I R 29 0.76 0.00 0.00 0.00 C T 30 0.54 0.00 0.00 0.00 G E 31 0.49 0.00 0.00 0.00 S K 32 0.66 0.00 0.00 0.00 G Y 33 0.35 0.00 0.00 0.00 L V 34 0.51 0.00 0.00 0.00 G D 35 0.60 0.00 0.00 0.00 G T 36 0.66 0.00 0.00 0.00 L P 37 0.71 0.00 0.00 0.00 T F 38 0.51 0.00 0.00 0.00 D G 39 0.14 0.00 0.00 0.00 * K K 40 0.66 0.00 0.00 0.00 L P 41 0.33 0.00 0.00 0.00 T S 42 0.55 0.00 0.00 0.00 Q D 43 0.14 0.00 0.00 0.00 * A A 44 0.61 0.00 0.00 0.00 Q L 45 0.13 0.00 0.00 0.00 * I I 46 0.41 0.00 0.00 0.00 F L 47 0.51 0.00 0.00 0.00 D G 48 0.67 0.00 0.00 0.00 Y K 49 0.64 0.00 0.00 0.00 S I 50 0.45 0.00 0.00 0.00 E K 51 0.70 0.00 0.00 0.00 I N 52 0.64 0.00 0.00 0.00 P V 53 0.40 0.00 0.00 0.00 N D 54 0.78 0.00 0.00 0.00 F C 55 0.64 0.00 0.00 0.00 P V 56 0.60 0.00 0.00 0.00 R L 57 0.63 0.00 0.00 0.00 S L 58 0.46 0.00 0.00 0.00 T A 59 0.66 0.00 0.00 0.00 V R 60 0.71 0.00 0.00 0.00 P H 61 0.04 0.00 0.00 0.00 * G G 62 0.61 0.00 0.00 0.00 H R 63 0.52 0.00 0.00 0.00 A Q 64 0.65 0.00 0.00 0.00 G H 65 0.55 0.00 0.00 0.00 R T 66 0.35 0.00 0.00 0.00 L I 67 0.53 0.00 0.00 0.00 V M 68 0.75 0.00 0.00 0.00 F P 69 0.48 0.00 0.00 0.00 G S 70 0.73 0.00 0.00 0.00 F K 71 0.35 0.00 0.00 0.00 L V 72 0.18 0.00 0.00 0.00 * N N 73 0.66 0.00 0.00 0.00 G Y 74 0.54 0.00 0.00 0.00 R Q 75 0.14 0.00 0.00 0.00 * A A 76 0.86 0.00 0.00 0.00 C N 77 0.30 0.00 0.00 0.00 V I 78 0.68 0.00 0.00 0.00 M W 79 0.00 0.00 0.00 0.00 M - 80 0.00 0.00 0.00 0.00 Q - 81 0.00 0.00 0.00 0.00 G - 82 0.60 0.00 0.00 0.00 R A 83 0.41 0.00 0.00 0.00 F L 84 0.55 0.00 0.00 0.00 H K 85 0.73 0.00 0.00 0.00 M E 86 0.68 0.00 0.00 0.00 Y E 87 0.54 0.00 0.00 0.00 E G 88 0.80 0.00 0.00 0.00 G C 89 0.66 0.00 0.00 0.00 Y T 90 0.71 0.00 0.00 0.00 P H 91 0.35 0.00 0.00 0.00 L V 92 0.74 0.00 0.00 0.00 W I 93 0.58 0.00 0.00 0.00 K V 94 0.50 0.00 0.00 0.00 V T 95 0.12 0.00 0.00 0.00 * T T 96 0.61 0.00 0.00 0.00 F A 97 0.90 0.00 0.00 0.00 P C 98 0.67 0.00 0.00 0.00 V G 99 0.54 0.00 0.00 0.00 R S 100 0.35 0.00 0.00 0.00 V L 101 0.77 0.00 0.00 0.00 F R 102 0.63 0.00 0.00 0.00 H E 103 0.67 0.00 0.00 0.00 L E 104 0.35 0.00 0.00 0.00 L I 105 0.63 0.00 0.00 0.00 G Q 106 0.64 0.00 0.00 0.00 V P 107 0.51 0.00 0.00 0.00 D G 108 0.54 0.00 0.00 0.00 T D 109 0.35 0.00 0.00 0.00 L I 110 0.12 0.00 0.00 0.00 * V V 111 0.30 0.00 0.00 0.00 V I 112 0.56 0.00 0.00 0.00 T I 113 0.40 0.00 0.00 0.00 N D 114 0.52 0.00 0.00 0.00 A Q 115 0.61 0.00 0.00 0.00 A F 116 0.76 0.00 0.00 0.00 G I 117 0.51 0.00 0.00 0.00 G D 118 0.60 0.00 0.00 0.00 L R 119 0.48 0.00 0.00 0.00 N T 120 0.57 0.00 0.00 0.00 P T 121 0.67 0.00 0.00 0.00 K M 122 0.77 0.00 0.00 0.00 F R 123 0.57 0.00 0.00 0.00 E P 124 0.61 0.00 0.00 0.00 V Q 125 0.48 0.00 0.00 0.00 G S 126 0.78 0.00 0.00 0.00 D F 127 0.61 0.00 0.00 0.00 I Y 128 0.82 0.00 0.00 0.00 M D 129 0.71 0.00 0.00 0.00 L G 130 0.76 0.00 0.00 0.00 I G 131 0.66 0.00 0.00 0.00 R V 132 0.92 0.00 0.00 0.00 D C 133 0.13 0.00 0.00 0.00 * H H 134 0.13 0.00 0.00 0.00 * I I 135 0.60 0.00 0.00 0.00 N P 136 0.37 0.00 0.00 0.00 L M 137 0.49 0.00 0.00 0.00 P A 138 0.00 0.00 0.00 0.00 G - 139 0.00 0.00 0.00 0.00 F - 140 0.00 0.00 0.00 0.00 S - 141 0.00 0.00 0.00 0.00 G - 142 0.00 0.00 0.00 0.00 Q - 143 0.54 0.00 0.00 0.00 N E 144 0.07 0.00 0.00 0.00 * P P 145 0.41 0.00 0.00 0.00 L F 146 0.85 0.00 0.00 0.00 R C 147 0.60 0.00 0.00 0.00 G P 148 0.58 0.00 0.00 0.00 P K 149 0.48 0.00 0.00 0.00 N T 150 0.65 0.00 0.00 0.00 D R 151 0.14 0.00 0.00 0.00 * E E 152 0.66 0.00 0.00 0.00 R V 153 0.41 0.00 0.00 0.00 F L 154 0.76 0.00 0.00 0.00 G I 155 0.41 0.00 0.00 0.00 D E 156 0.55 0.00 0.00 0.00 R T 157 0.61 0.00 0.00 0.00 F A 158 0.58 0.00 0.00 0.00 P K 159 0.48 0.00 0.00 0.00 A K 160 0.37 0.00 0.00 0.00 M L 161 0.48 0.00 0.00 0.00 S G 162 0.74 0.00 0.00 0.00 D L 163 0.60 0.00 0.00 0.00 A R 164 0.84 0.00 0.00 0.00 Y C 165 0.61 0.00 0.00 0.00 D H 166 0.54 0.00 0.00 0.00 R S 167 0.47 0.00 0.00 0.00 T K 168 0.77 0.00 0.00 0.00 M G 169 0.55 0.00 0.00 0.00 R T 170 0.67 0.00 0.00 0.00 Q M 171 0.66 0.00 0.00 0.00 R V 172 0.46 0.00 0.00 0.00 A T 173 0.35 0.00 0.00 0.00 L I 174 0.53 0.00 0.00 0.00 S E 175 0.60 0.00 0.00 0.00 T G 176 0.88 0.00 0.00 0.00 W P 177 0.37 0.00 0.00 0.00 K R 178 0.75 0.00 0.00 0.00 Q F 179 0.71 0.00 0.00 0.00 M S 180 0.48 0.00 0.00 0.00 G S 181 0.58 0.00 0.00 0.00 E R 182 0.52 0.00 0.00 0.00 Q A 183 0.58 0.00 0.00 0.00 R E 184 0.53 0.00 0.00 0.00 E S 185 0.41 0.00 0.00 0.00 L F 186 0.67 0.00 0.00 0.00 Q M 187 0.74 0.00 0.00 0.00 E F 188 0.60 0.00 0.00 0.00 G R 189 0.12 0.00 0.00 0.00 * T T 190 0.52 0.00 0.00 0.00 Y W 191 0.00 0.00 0.00 0.00 V - 192 0.00 0.00 0.00 0.00 M - 193 0.00 0.00 0.00 0.00 V - 194 0.00 0.00 0.00 0.00 A - 195 0.04 0.00 0.00 0.00 * G G 196 0.49 0.00 0.00 0.00 P A 197 0.46 0.00 0.00 0.00 S D 198 0.54 0.00 0.00 0.00 F V 199 0.69 0.00 0.00 0.00 E I 200 0.48 0.00 0.00 0.00 T N 201 0.53 0.00 0.00 0.00 V M 202 0.46 0.00 0.00 0.00 A T 203 0.53 0.00 0.00 0.00 E T 204 0.72 0.00 0.00 0.00 C V 205 0.67 0.00 0.00 0.00 R P 206 0.62 0.00 0.00 0.00 V E 207 0.35 0.00 0.00 0.00 L V 208 0.61 0.00 0.00 0.00 Q V 209 0.58 0.00 0.00 0.00 K L 210 0.53 0.00 0.00 0.00 L A 211 0.56 0.00 0.00 0.00 G K 212 0.49 0.00 0.00 0.00 A E 213 0.50 0.00 0.00 0.00 D A 214 0.42 0.00 0.00 0.00 A G 215 0.30 0.00 0.00 0.00 V I 216 0.80 0.00 0.00 0.00 G C 217 0.69 0.00 0.00 0.00 M Y 218 0.40 0.00 0.00 0.00 S A 219 0.33 0.00 0.00 0.00 T S 220 0.30 0.00 0.00 0.00 V I 221 0.49 0.00 0.00 0.00 P A 222 0.73 0.00 0.00 0.00 E M 223 0.43 0.00 0.00 0.00 V A 224 0.56 0.00 0.00 0.00 I T 225 0.66 0.00 0.00 0.00 V D 226 0.64 0.00 0.00 0.00 A Y 227 0.65 0.00 0.00 0.00 R D 228 0.92 0.00 0.00 0.00 H C 229 1.00 0.00 0.00 0.00 C W 230 0.42 0.00 0.00 0.00 G A 231 0.35 0.00 0.00 0.00 L V 232 0.54 0.00 0.00 0.00 R S 233 0.12 0.00 0.00 0.00 * V V 234 0.78 0.00 0.00 0.00 F D 235 0.60 0.00 0.00 0.00 G R 236 0.54 0.00 0.00 0.00 F V 237 0.63 0.00 0.00 0.00 S L 238 0.58 0.00 0.00 0.00 L K 239 0.56 0.00 0.00 0.00 I T 240 0.59 0.00 0.00 0.00 T L 241 0.48 0.00 0.00 0.00 N K 242 0.45 0.00 0.00 0.00 K E 243 0.67 0.00 0.00 0.00 V N 244 0.57 0.00 0.00 0.00 I A 245 0.75 0.00 0.00 0.00 M N 246 0.52 0.00 0.00 0.00 D K 247 0.64 0.00 0.00 0.00 Y A 248 0.45 0.00 0.00 0.00 E K 249 0.11 0.00 0.00 0.00 * S S 250 0.09 0.00 0.00 0.00 * L L 251 0.67 0.00 0.00 0.00 E L 252 0.58 0.00 0.00 0.00 K L 253 0.46 0.00 0.00 0.00 A T 254 0.48 0.00 0.00 0.00 N T 255 0.78 0.00 0.00 0.00 H I 256 0.57 0.00 0.00 0.00 E P 257 0.43 0.00 0.00 0.00 E Q 258 0.30 0.00 0.00 0.00 V I 259 0.71 0.00 0.00 0.00 L G 260 0.40 0.00 0.00 0.00 A S 261 0.46 0.00 0.00 0.00 A T 262 0.54 0.00 0.00 0.00 G E 263 0.79 0.00 0.00 0.00 K W 264 0.54 0.00 0.00 0.00 Q S 265 0.49 0.00 0.00 0.00 A E 266 0.46 0.00 0.00 0.00 A T 267 0.61 0.00 0.00 0.00 Q L 268 0.55 0.00 0.00 0.00 K H 269 0.67 0.00 0.00 0.00 L N 270 0.67 0.00 0.00 0.00 E L 271 0.44 0.00 0.00 0.00 Q K 272 0.72 0.00 0.00 0.00 F N 273 0.53 0.00 0.00 0.00 V M 274 0.40 0.00 0.00 0.00 S A 275 0.75 0.00 0.00 0.00 I Q 276 0.41 0.00 0.00 0.00 L F 277 0.71 0.00 0.00 0.00 M S 278 0.43 0.00 0.00 0.00 A V 279 0.63 0.00 0.00 0.00 S L 280 0.35 0.00 0.00 0.00 I L 281 0.07 0.00 0.00 0.00 * P P 282 0.00 0.00 0.00 0.00 L - ------------------------------------------------------ openf___224_> Open fm07254_out0.ali openf___224_> Open fm07254_out1.ali openf___224_> Open fm07254_out2.ali openf___224_> Open fm07254_out3.ali openf___224_> Open fm07254_out4.ali openf___224_> Open fm07254_out5.ali Dynamically allocated memory at finish [B,KiB,MiB]: 508354 496.439 0.485 Starting time : 2016/04/05 22:42:19 Closing time : 2016/04/05 22:42:20 Total CPU time [seconds] : 0.81