reduce: version 3.3 06/02/2016, Copyright 1997-2016, J. Michael Word Processing file: --standard input-- Database of HETATM connections: "/home/srania/Amber/amber16/dat/reduce_wwPDB_het_dict.txt" VDW dot density = 16/A^2 Orientation penalty scale = 9999 (999900%) Eliminate contacts within 3 bonds. Ignore atoms with |occupancy| <= 0.01 during adjustments. Waters ignored if B-Factor >= 40 or |occupancy| < 0.66 Aromatic rings in amino acids accept hydrogen bonds. Building His ring NH Hydrogens. Flipping Asn, Gln and His groups. For each flip state, bumps where gap is more than 0.4A are indicated with '!'. Building or keeping OH & SH Hydrogens. Rotating existing OH & SH Hydrogens Rotating NH3 Hydrogens. Not processing Met methyls. Singles(size 121): A 1 VAL N : A 2 GLN : A 5 THR OG1 : A 19 LYS NZ : A 20 LYS NZ : A 23 TYR OH : A 25 THR OG1 : A 39 THR OG1 : A 44 TYR OH : A 50 THR OG1 : A 56 LYS NZ : A 57 GLN : A 58 SER OG : A 63 LYS NZ : A 65 THR OG1 : A 69 LYS NZ : A 71 LYS NZ : A 79 ASN : A 81 TYR OH : A 85 GLN : A 86 TYR OH : A 91 SER OG : A 92 TYR OH : A 93 GLN : A 96 ASN : A 97 SER OG : A 100 ASN : A 103 HIS : A 106 SER OG : A 107 GLN : A 113 TYR OH : A 119 THR OG1 : A 121 TYR OH : A 126 LYS NZ : A 127 ASN : A 129 HIS : A 134 SER OG : A 135 GLN : A 139 ASN : A 153 SER OG : A 154 SER OG : A 158 SER OG : A 159 ASN : A 162 SER OG : A 163 SER OG : A 169 GLN : A 171 TYR OH : A 175 HIS : A 183 GLN : A 192 ASN : A 206 CYS SG : A 210 THR OG1 : A 223 TYR OH : A 243 CYS SG : A 249 LYS NZ : A 255 SER OG : A 264 LYS NZ : A 267 LYS NZ : A 268 CYS SG : A 270 SER OG : A 273 GLN : A 275 ASN : A 276 ASN : A 281 GLN : A 285 ASN : A 293 THR OG1 : A 294 LYS NZ : A 296 TYR OH : A 301 THR OG1 : A 306 SER OG : A 307 THR OG1 : A 308 THR OG1 : A 317 TYR OH : A 320 ASN : A 332 CYS SG : A 334 LYS NZ : A 340 LYS NZ : A 346 GLN : A 348 HIS : A 356 HIS : A 357 GLN : A 358 GLN : A 359 CYS SG : A 360 LYS NZ : A 362 ASN : A 371 ASN : A 375 TYR OH : A 376 THR OG1 : A 377 LYS NZ : A 380 THR OG1 : A 381 LYS NZ : A 382 LYS NZ : A 388 ASN : A 392 SER OG : A 397 THR OG1 : A 400 ASN : A 402 TYR OH : A 403 LYS NZ : A 404 ASN : A 406 LYS NZ : A 420 CYS SG : A 422 SER OG : A 423 GLN : A 425 HIS : A 429 SER OG : A 440 THR OG1 : A 445 GLN : A 450 LYS NZ : A 452 LYS NZ : A 458 TYR OH : A 460 SER OG : A 464 THR OG1 : A 471 LYS NZ : A 476 GLN : A 477 TYR OH : A 480 THR OG1 : A 481 TYR OH : A 482 LYS NZ : A 485 ASN : A 487 HIS : A 488 LYS NZ Set 1 (size 2): A 152 GLN : A 444 HIS Set 2 (size 2): A 212 LYS NZ : A 337 ASN Set 3 (size 2): A 456 TYR OH : A 310 THR OG1 Set 4 (size 2): A 282 TYR OH : A 217 THR OG1 Set 5 (size 3): A 254 ASN : A 253 THR OG1 : A 252 SER OG Set 6 (size 2): A 262 LYS NZ : A 240 GLN Set 7 (size 2): A 203 ASN : A 200 ASN Set 8 (size 2): A 184 ASN : A 398 TYR OH Set 9 (size 3): A 179 LYS NZ : A 369 GLN : A 176 TYR OH Set 10 (size 4): A 145 LYS NZ : A 237 HIS : A 236 ASN : A 235 GLN Set 11 (size 2): A 132 CYS SG : A 131 SER OG Set 12 (size 2): A 160 HIS : A 125 THR OG1 Set 13 (size 2): A 80 SER OG : A 98 HIS Set 14 (size 2): A 14 SER OG : A 47 SER OG Set 15 (size 2): A 21 LYS NZ : A 411 TYR OH Set 16 (size 2): A 6 HIS : A 109 ASN Set 17 (size 2): A 3 SER OG : A 38 ASN orientation 1: A 1 VAL N :NH3+ -173: bump=-0.220, HB=0.000, total=-0.220 orientation 1: A 2 GLN : amide: bump=-0.313, HB=0.000, total=-0.313 orientation 2: A 5 THR OG1 : rot -168: bump=-0.012, HB=1.290, total=1.278 orientation 2: A 19 LYS NZ :NH3+ -172: bump=0.000, HB=0.000, total=0.000 orientation 1: A 20 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 3: A 23 TYR OH : rot 151: bump=0.000, HB=0.000, total=0.000 orientation 2: A 25 THR OG1 : rot 93: bump=0.000, HB=0.477, total=0.477 orientation 1: A 39 THR OG1 : rot 118: bump=-0.153, HB=1.335, total=1.182 orientation 10: A 44 TYR OH : rot -156: bump=-3.394, HB=0.273, total=-3.121, BADBUMP orientation 1: A 50 THR OG1 : rot 180: bump=-0.047, HB=0.000, total=-0.047 orientation 1: A 56 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 57 GLN : amide: bump=-2.635, HB=0.000, total=-2.635, BADBUMP orientation 3: A 58 SER OG : rot -36: bump=-0.441, HB=1.171, total=0.730 orientation 1: A 63 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 65 THR OG1 : rot 134: bump=-1.886, HB=1.406, total=-0.479, BADBUMP orientation 1: A 69 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 71 LYS NZ :NH3+ -176: bump=0.000, HB=0.291, total=0.291 orientation 1: A 79 ASN : amide: bump=-0.247, HB=1.137, total=0.890 orientation 8: A 81 TYR OH : rot -19: bump=-2.869, HB=1.334, total=-1.535, BADBUMP orientation 1: A 85 GLN : amide: bump=-2.666, HB=0.000, total=-2.666 orientation 1: A 86 TYR OH : rot 180: bump=-0.020, HB=0.000, total=-0.020 orientation 2: A 91 SER OG : rot 77: bump=-0.012, HB=0.210, total=0.198 orientation 12: A 92 TYR OH : rot -171: bump=0.000, HB=0.760, total=0.760 orientation 1: A 93 GLN : amide: bump=-4.404, HB=0.000, total=-4.404, BADBUMP orientation 1: A 96 ASN : amide: bump=-6.508, HB=0.079, total=-6.429, BADBUMP orientation 4: A 97 SER OG : rot -64: bump=-0.292, HB=1.031, total=0.738 orientation 1: A 100 ASN : amide: bump=-5.010, HB=0.000, total=-5.010, BADBUMP orientation 1: A 103 HIS : no HD1: bump=-2.515, HB=0.000, total=-2.515, BADBUMP orientation 1: A 106 SER OG : rot 180: bump=0.000, HB=0.021, total=0.021 orientation 1: A 107 GLN : amide: bump=-0.005, HB=0.000, total=-0.005 orientation 5: A 113 TYR OH : rot 32: bump=-0.094, HB=1.202, total=1.107 orientation 1: A 119 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 10: A 121 TYR OH : rot -136: bump=0.000, HB=0.205, total=0.205 orientation 2: A 126 LYS NZ :NH3+ -149: bump=0.000, HB=0.129, total=0.129 orientation 1: A 127 ASN : amide: bump=-1.876, HB=1.900, total=0.024 orientation 1: A 129 HIS : no HD1: bump=-0.153, HB=0.000, total=-0.153 orientation 1: A 134 SER OG : rot 170: bump=0.000, HB=0.061, total=0.061 orientation 1: A 135 GLN : amide: bump=-0.374, HB=0.010, total=-0.363 orientation 1: A 139 ASN : amide: bump=-4.158, HB=0.551, total=-3.607, BADBUMP orientation 2: A 153 SER OG : rot -104: bump=-0.534, HB=1.560, total=1.027 orientation 1: A 154 SER OG : rot 150: bump=0.000, HB=0.008, total=0.008 orientation 1: A 158 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 159 ASN : amide: bump=-0.545, HB=0.749, total=0.205 orientation 1: A 162 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 5: A 163 SER OG : rot -95: bump=-1.071, HB=1.248, total=0.177 orientation 1: A 169 GLN : amide: bump=-0.588, HB=0.300, total=-0.288 orientation 1: A 171 TYR OH : rot 180: bump=-0.032, HB=0.000, total=-0.032 orientation 1: A 175 HIS : no HD1: bump=0.000, HB=0.000, total=0.000 orientation 1: A 183 GLN : amide: bump=-4.448, HB=1.188, total=-3.260, BADBUMP orientation 1: A 192 ASN : amide: bump=-5.514, HB=0.484, total=-5.030, BADBUMP orientation 2: A 206 CYS SG : rot 20: bump=-1.480, HB=0.000, total=-1.480 orientation 1: A 210 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 223 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 243 CYS SG : rot 77: bump=-0.837, HB=0.034, total=-0.803 orientation 1: A 249 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 255 SER OG : rot 130: bump=0.000, HB=0.591, total=0.591 orientation 1: A 264 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 267 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 268 CYS SG : rot 170: bump=0.000, HB=0.000, total=0.000 orientation 1: A 270 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 273 GLN : amide: bump=0.000, HB=0.091, total=0.091 orientation 1: A 275 ASN : amide: bump=-1.046, HB=0.000, total=-1.046 orientation 1: A 276 ASN : amide: bump=-3.510, HB=0.000, total=-3.510, BADBUMP orientation 1: A 281 GLN : amide: bump=-0.384, HB=1.657, total=1.273 orientation 1: A 285 ASN : amide: bump=-8.353, HB=0.136, total=-8.217, BADBUMP orientation 2: A 293 THR OG1 : rot 79: bump=0.000, HB=0.173, total=0.173 orientation 1: A 294 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 12: A 296 TYR OH : rot -168: bump=0.000, HB=0.447, total=0.447 orientation 1: A 301 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 4: A 306 SER OG : rot -129: bump=-0.204, HB=0.386, total=0.182 orientation 1: A 307 THR OG1 : rot -110: bump=-1.022, HB=0.000, total=-1.022 orientation 3: A 308 THR OG1 : rot 130: bump=-0.019, HB=1.336, total=1.316 orientation 1: A 317 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 320 ASN : amide: bump=-1.081, HB=0.674, total=-0.407 orientation 1: A 332 CYS SG : rot 180: bump=-0.658, HB=0.000, total=-0.658 orientation 1: A 334 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 3: A 340 LYS NZ :NH3+ 159: bump=0.000, HB=1.152, total=1.152 orientation 1: A 346 GLN : amide: bump=-0.014, HB=1.569, total=1.555 orientation 1: A 348 HIS : no HD1: bump=-0.011, HB=0.000, total=-0.011 orientation 1: A 356 HIS : no HD1: bump=-0.525, HB=0.000, total=-0.525 orientation 1: A 357 GLN : amide: bump=0.000, HB=0.000, total=0.000 orientation 1: A 358 GLN : amide: bump=-1.786, HB=1.079, total=-0.707, BADBUMP orientation 1: A 359 CYS SG : rot 180: bump=-0.265, HB=0.000, total=-0.265 orientation 3: A 360 LYS NZ :NH3+ 155: bump=-0.043, HB=0.271, total=0.228 orientation 1: A 362 ASN : amide: bump=-3.102, HB=0.000, total=-3.102, BADBUMP orientation 1: A 371 ASN : amide: bump=-0.013, HB=0.000, total=-0.013 orientation 1: A 375 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 376 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 2: A 377 LYS NZ :NH3+ -153: bump=0.000, HB=0.362, total=0.362 orientation 1: A 380 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 381 LYS NZ :NH3+ 166: bump=-0.039, HB=0.857, total=0.817 orientation 1: A 382 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 388 ASN : amide: bump=-0.689, HB=0.669, total=-0.020 orientation 1: A 392 SER OG : rot 180: bump=0.000, HB=0.242, total=0.242 orientation 2: A 397 THR OG1 : rot 94: bump=0.000, HB=0.920, total=0.920 orientation 1: A 400 ASN : amide: bump=-0.095, HB=0.000, total=-0.095 orientation 1: A 402 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 403 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 404 ASN : amide: bump=-0.325, HB=0.000, total=-0.325 orientation 1: A 406 LYS NZ :NH3+ 174: bump=0.000, HB=0.023, total=0.023 orientation 1: A 420 CYS SG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 422 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 423 GLN : amide: bump=-0.296, HB=1.930, total=1.634 orientation 2: A 425 HIS : no HE2: bump=0.000, HB=0.033, total=0.033 orientation 5: A 429 SER OG : rot 73: bump=-0.332, HB=1.641, total=1.309 orientation 2: A 440 THR OG1 : rot 97: bump=-0.285, HB=1.655, total=1.370 orientation 1: A 445 GLN : amide: bump=-1.993, HB=0.000, total=-1.993 orientation 1: A 450 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 2: A 452 LYS NZ :NH3+ -163: bump=-0.414, HB=0.000, total=-0.414 orientation 5: A 458 TYR OH : rot 15: bump=-0.023, HB=0.000, total=-0.023 orientation 1: A 460 SER OG : rot 180: bump=-0.334, HB=0.057, total=-0.276 orientation 1: A 464 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 471 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 476 GLN : amide: bump=0.000, HB=0.000, total=0.000 orientation 1: A 477 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 2: A 480 THR OG1 : rot 54: bump=-0.009, HB=1.247, total=1.238 orientation 5: A 481 TYR OH : rot 23: bump=-0.086, HB=1.164, total=1.079 orientation 1: A 482 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 485 ASN : amide: bump=-2.226, HB=0.000, total=-2.226, BADBUMP orientation 1: A 487 HIS : no HD1: bump=-0.145, HB=0.000, total=-0.145 orientation 1: A 488 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 Processing set: A 152 GLN [2]: A 444 HIS [6] permutations: 12 Computing dot scores Num optimizations problems to be solved for this clique: 6 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: -7.266 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following high resolution, local optimization: -7.266 Processing set: A 212 LYS NZ [4]: A 337 ASN [2] permutations: 8 Computing dot scores Num optimizations problems to be solved for this clique: 3 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 0.162 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 0.162 > : 0.162 > : 0.162 > : 0.162 > : 0.162 > : 0.162 > : 0.162 > : 0.162 > : 0.162 > : 0.162 > : 0.162 > : 0.162 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 > : 0.187 Optimal score following high resolution, local optimization: 0.187 Processing set: A 456 TYR OH [13]: A 310 THR OG1 [5] permutations: 65 Computing dot scores Num optimizations problems to be solved for this clique: 1 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 0.422 > : 0.422 > : 0.422 > : 0.422 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 > : 0.478 Optimal score following high resolution, local optimization: 0.478 Processing set: A 282 TYR OH [12]: A 217 THR OG1 [3] permutations: 36 Computing dot scores Num optimizations problems to be solved for this clique: 1 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: -2.889 > : -2.889 > : -2.887 > : -2.887 > : -2.885 > : -2.885 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 > : -2.884 Optimal score following high resolution, local optimization: -2.884 Processing set: A 254 ASN [2]: A 253 THR OG1 [1]: A 252 SER OG [5] permutations: 10 Computing dot scores Num optimizations problems to be solved for this clique: 3 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: -0.369 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 > : -0.369 Optimal score following high resolution, local optimization: -0.369 Processing set: A 262 LYS NZ [4]: A 240 GLN [2] permutations: 8 Computing dot scores Num optimizations problems to be solved for this clique: 3 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 2.467 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 2.194 > : 2.194 > : 2.194 > : 2.194 > : 2.194 > : 2.271 > : 2.298 > : 2.298 > : 2.350 > : 2.350 > : 2.350 > : 2.382 > : 2.400 > : 2.411 > : 2.421 > : 2.432 > : 2.444 > : 2.453 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 > : 2.544 Optimal score following high resolution, local optimization: 2.544 Processing set: A 203 ASN [2]: A 200 ASN [2] permutations: 4 Computing dot scores Num optimizations problems to be solved for this clique: 4 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: -2.663 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following high resolution, local optimization: -2.663 Processing set: A 184 ASN [2]: A 398 TYR OH [13] permutations: 26 Computing dot scores Num optimizations problems to be solved for this clique: 3 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: -0.352 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : -0.352 > : -0.352 > : -0.352 > : -0.352 > : -0.352 > : -0.352 > : -0.352 > : -0.352 > : -0.352 > : -0.352 > : -0.352 > : -0.352 > : -0.352 > : -0.352 > : -0.352 > : -0.352 > : -0.352 > : -0.352 > : -0.352 > : -0.352 Optimal score following high resolution, local optimization: -0.352 Processing set: A 179 LYS NZ [4]: A 369 GLN [2]: A 176 TYR OH [15] permutations: 120 Computing dot scores Num optimizations problems to be solved for this clique: 3 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 1.092 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 0.530 > : 0.530 > : 0.530 > : 0.530 > : 0.530 > : 0.645 > : 0.645 > : 0.657 > : 0.657 > : 0.693 > : 0.762 > : 0.782 > : 0.782 > : 0.782 > : 0.782 > : 0.801 > : 0.955 > : 0.992 > : 1.009 > : 1.013 > : 1.014 > : 1.026 > : 1.071 > : 1.166 > : 1.290 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.388 > : 1.405 > : 1.405 > : 1.455 > : 1.455 > : 1.471 > : 1.471 > : 1.539 > : 1.539 > : 1.539 > : 1.539 > : 1.539 > : 1.539 > : 1.539 > : 1.539 > : 1.684 > : 1.684 > : 1.684 > : 1.684 > : 1.684 Optimal score following high resolution, local optimization: 1.684 Processing set: A 145 LYS NZ [4]: A 237 HIS [6]: A 236 ASN [2] : A 235 GLN [2] permutations: 96 Computing dot scores Num optimizations problems to be solved for this clique: 7 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: -4.925 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : -4.925 > : -4.920 > : -4.920 > : -4.917 > : -4.917 > : -4.916 > : -4.916 > : -4.916 > : -4.916 > : -4.916 > : -4.898 > : -4.898 > : -4.898 > : -4.898 > : -4.898 > : -4.898 > : -4.887 > : -4.887 > : -4.887 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 > : -4.839 Optimal score following high resolution, local optimization: -4.839 Processing set: A 132 CYS SG [3]: A 131 SER OG [2] permutations: 6 Computing dot scores Num optimizations problems to be solved for this clique: 1 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: -1.314 > : -1.314 > : -1.314 > : -1.314 > : -1.314 > : -1.314 > : -1.314 > : -1.311 > : -1.311 > : -1.311 > : -1.311 > : -1.311 > : -1.311 > : -1.311 > : -1.311 > : -1.311 > : -1.311 > : -1.311 > : -1.311 > : -1.311 > : -1.311 > : -1.311 > : -1.311 > : -1.302 > : -1.302 > : -1.295 > : -1.286 > : -1.286 > : -1.286 > : -1.284 > : -1.236 > : -1.236 > : -1.236 > : -1.236 > : -1.236 > : -1.236 > : -1.236 > : -1.236 > : -1.236 > : -1.236 > : -1.236 Optimal score following high resolution, local optimization: -1.236 Processing set: A 160 HIS [6]: A 125 THR OG1 [5] permutations: 30 Computing dot scores Num optimizations problems to be solved for this clique: 5 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 1.155 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 1.155 > : 1.155 > : 1.155 > : 1.155 > : 1.155 > : 1.155 > : 1.155 > : 1.155 > : 1.155 > : 1.155 > : 1.155 > : 1.155 > : 1.155 > : 1.155 > : 1.155 > : 1.155 > : 1.155 > : 1.155 > : 1.155 > : 1.155 Optimal score following high resolution, local optimization: 1.155 Processing set: A 80 SER OG [5]: A 98 HIS [6] permutations: 30 Computing dot scores Num optimizations problems to be solved for this clique: 5 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 2.177 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 2.177 > : 2.177 > : 2.196 > : 2.196 > : 2.196 > : 2.196 > : 2.196 > : 2.196 > : 2.196 > : 2.196 > : 2.196 > : 2.196 > : 2.196 > : 2.196 > : 2.196 > : 2.196 > : 2.196 > : 2.196 > : 2.196 > : 2.196 Optimal score following high resolution, local optimization: 2.196 Processing set: A 14 SER OG [1]: A 47 SER OG [1] permutations: 1 Computing dot scores Num optimizations problems to be solved for this clique: 1 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 > : 0.000 Optimal score following high resolution, local optimization: 0.000 Processing set: A 21 LYS NZ [4]: A 411 TYR OH [12] permutations: 48 Computing dot scores Num optimizations problems to be solved for this clique: 1 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 1.386 > : 0.116 > : 0.183 > : 0.183 > : 0.187 > : 0.254 > : 0.387 > : 0.447 > : 0.505 > : 0.586 > : 0.637 > : 0.718 > : 0.753 > : 0.781 > : 0.811 > : 0.841 > : 0.870 > : 0.945 > : 0.997 > : 1.066 > : 1.097 > : 1.130 > : 1.130 > : 1.135 > : 1.162 > : 1.162 > : 1.162 > : 1.162 > : 1.284 > : 1.305 > : 1.325 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 > : 1.386 Optimal score following high resolution, local optimization: 1.386 Processing set: A 6 HIS [6]: A 109 ASN [2] permutations: 12 Computing dot scores Num optimizations problems to be solved for this clique: 6 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 0.747 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following high resolution, local optimization: 0.747 Processing set: A 3 SER OG [3]: A 38 ASN [2] permutations: 6 Computing dot scores Num optimizations problems to be solved for this clique: 3 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: -0.001 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : -0.001 > : -0.001 > : -0.001 > : -0.001 > : -0.001 > : -0.001 > : -0.001 > : -0.001 > : -0.001 > : -0.001 > : -0.001 > : -0.001 > : -0.001 > : -0.001 > : -0.001 > : -0.001 > : -0.001 > : -0.001 > : -0.001 > : -0.001 Optimal score following high resolution, local optimization: -0.001 Found 0 hydrogens (0 hets) Standardized 0 hydrogens (0 hets) Added 3934 hydrogens (0 hets) Removed 0 hydrogens (0 hets) Adjusted 91 group(s) If you publish work which uses reduce, please cite: Word, et. al. (1999) J. Mol. Biol. 285, 1735-1747. For more information see http://kinemage.biochem.duke.edu