reduce: version 3.3 06/02/2016, Copyright 1997-2016, J. Michael Word Processing file: --standard input-- Database of HETATM connections: "/usr/local/bin/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. SKIPPED H( A 13 ASNHD21 ): A 13 ASN ND2 bonds- A 492 NAG C1 (H bumps) SKIPPED H( A 25 ASNHD21 ): A 25 ASN ND2 bonds- A 493 NAG C1 (H bumps) SKIPPED H( A 167 ASNHD21 ): A 167 ASN ND2 bonds- A 494 NAG C1 (H bumps) WARNING: atom H111 from SIA will be treated as hydrogen WARNING: atom H111 from SIA will be treated as hydrogen WARNING: atom H112 from SIA will be treated as hydrogen WARNING: atom H113 from SIA will be treated as hydrogen WARNING: atom H112 from SIA will be treated as hydrogen WARNING: atom H111 from SIA will be treated as hydrogen WARNING: atom H112 from SIA will be treated as hydrogen WARNING: atom H113 from SIA will be treated as hydrogen WARNING: atom H113 from SIA will be treated as hydrogen WARNING: atom H111 from SIA will be treated as hydrogen WARNING: atom H112 from SIA will be treated as hydrogen WARNING: atom H113 from SIA will be treated as hydrogen WARNING: atom H113 from SIA will be treated as hydrogen WARNING: atom H113 from SIA will be treated as hydrogen WARNING: atom H112 from SIA will be treated as hydrogen WARNING: atom H111 from SIA will be treated as hydrogen WARNING: atom H112 from SIA will be treated as hydrogen WARNING: atom H113 from SIA will be treated as hydrogen WARNING: atom H112 from SIA will be treated as hydrogen WARNING: atom H111 from SIA will be treated as hydrogen WARNING: atom H111 from SIA will be treated as hydrogen WARNING: atom H113 from SIA will be treated as hydrogen WARNING: atom H112 from SIA will be treated as hydrogen WARNING: atom H111 from SIA will be treated as hydrogen WARNING: atom H101 from EPE will be treated as hydrogen WARNING: atom H101 from EPE will be treated as hydrogen WARNING: atom H102 from EPE will be treated as hydrogen WARNING: atom H102 from EPE will be treated as hydrogen WARNING: atom H101 from EPE will be treated as hydrogen WARNING: atom H102 from EPE will be treated as hydrogen WARNING: atom H102 from EPE will be treated as hydrogen WARNING: atom H102 from EPE will be treated as hydrogen WARNING: atom H101 from EPE will be treated as hydrogen WARNING: atom H101 from EPE will be treated as hydrogen WARNING: atom H102 from EPE will be treated as hydrogen WARNING: atom H101 from EPE will be treated as hydrogen Singles(size 171): A 1 ASP N : A 4 GLN : A 9 TYR OH : A 10 HIS : A 12 ASN : A 14 SER OG : A 15 THR OG1 : A 17 GLN : A 20 THR OG1 : A 24 LYS NZ : A 27 THR OG1 : A 29 THR OG1 : A 30 HIS : A 32 GLN : A 37 LYS NZ : A 38 LYS NZ : A 39 HIS : A 40 ASN : A 42 LYS NZ : A 50 LYS NZ : A 58 SER OG : A 66 ASN : A 74 ASN : A 79 SER OG : A 80 TYR OH : A 84 LYS NZ : A 86 ASN : A 89 ASN : A 98 ASN : A 100 TYR OH : A 104 LYS NZ : A 105 HIS : A 111 ASN : A 112 HIS : A 117 GLN : A 121 LYS NZ : A 122 SER OG : A 123 SER OG : A 125 SER OG : A 126 SER OG : A 127 HIS : A 130 SER OG : A 135 SER OG : A 139 TYR OH : A 140 GLN : A 142 LYS NZ : A 143 SER OG : A 144 SER OG : A 155 LYS NZ : A 157 SER OG : A 158 THR OG1 : A 159 TYR OH : A 161 THR OG1 : A 163 LYS NZ : A 169 THR OG1 : A 171 GLN : A 182 HIS : A 184 ASN : A 190 THR OG1 : A 191 LYS NZ : A 195 ASN : A 197 THR OG1 : A 199 TYR OH : A 201 SER OG : A 205 SER OG : A 208 ASN : A 209 GLN : A 217 THR OG1 : A 219 SER OG : A 222 LYS NZ : A 233 THR OG1 : A 236 LYS NZ : A 238 ASN : A 245 SER OG : A 246 ASN : A 254 TYR OH : A 257 LYS NZ : A 260 LYS NZ : A 261 LYS NZ : A 265 THR OG1 : A 268 LYS NZ : A 269 SER OG : A 273 TYR OH : A 275 ASN : A 277 ASN : A 278 THR OG1 : A 279 LYS NZ : A 281 GLN : A 282 THR OG1 : A 289 SER OG : A 294 HIS : A 295 ASN : A 297 HIS : A 300 THR OG1 : A 306 LYS NZ : A 307 TYR OH : A 309 LYS NZ : A 310 SER OG : A 311 ASN : A 321 ASN : A 322 SER OG : A 492 NAG O3 : A 492 NAG O4 : A 492 NAG O6 : A 493 NAG O3 : A 493 NAG O4 : A 493 NAG O6 : A 494 NAG O3 : A 495 NAG O6 : A 496 BMA O2 : A 496 BMA O4 : A 497 BMA O2 : A 497 BMA O3 : A 497 BMA O4 : A 497 BMA O6 : A 498 MAN O2 : A 498 MAN O3 : A 498 MAN O6 : A 499 FUC O2 : A 499 FUC O3 : A 499 FUC O4 : A 500 SIA O4 : A 500 SIA O7 : A 501 GAL O2 : A 501 GAL O4 : A 502 NAG O1 : A 502 NAG O6 : B 339 GLN : B 348 TYR OH : B 350 HIS : B 351 SER OG : B 354 GLN : B 356 SER OG : B 358 TYR OH : B 362 LYS NZ : B 364 SER OG : B 365 THR OG1 : B 366 GLN : B 367 LYS NZ : B 373 THR OG1 : B 374 ASN : B 377 ASN : B 378 SER OG : B 382 LYS NZ : B 384 ASN : B 385 THR OG1 : B 386 GLN : B 395 ASN : B 396 ASN : B 403 ASN : B 405 ASN : B 406 LYS NZ : B 407 LYS NZ : B 417 THR OG1 : B 418 TYR OH : B 419 ASN : B 428 ASN : B 437 SER OG : B 440 LYS NZ : B 441 ASN : B 443 TYR OH : B 445 LYS NZ : B 449 GLN : B 455 LYS NZ : B 465 TYR OH : B 467 LYS NZ : B 475 SER OG : B 483 TYR OH : B 485 GLN : B 486 TYR OH : B 487 SER OG Set 1 (size 2): B 503 EPE O8 : B 459 ASN Set 2 (size 2): B 480 THR OG1 : B 478 ASN Set 3 (size 3): B 481 TYR OH : B 466 HIS : B 453 ASN Set 4 (size 3): B 438 ASN : B 435 HIS : B 346 TYR OH Set 5 (size 2): B 431 THR OG1 : B 375 LYS NZ Set 6 (size 2): B 470 ASN : B 352 ASN Set 7 (size 2): B 503 EPE O3S : B 349 HIS Set 8 (size 2): A 501 GAL O6 : A 502 NAG O3 Set 9 (size 2): A 498 MAN O4 : A 495 NAG O3 Set 10 (size 2): A 290 SER OG : A 288 ASN Set 11 (size 2): A 225 SER OG : A 220 LYS NZ Set 12 (size 2): A 206 THR OG1 : A 204 THR OG1 Set 13 (size 3): A 198 THR OG1 : A 189 GLN : A 248 ASN Set 14 (size 2): A 154 LYS NZ : A 194 GLN Set 15 (size 3): A 170 ASN : A 168 ASN : A 166 TYR OH Set 16 (size 2): A 165 SER OG : A 242 ASN Set 17 (size 3): A 148 ASN : A 256 TYR OH : A 115 LYS NZ Set 18 (size 2): A 500 SIA O1B : A 134 SER OG Set 19 (size 2): A 264 SER OG : A 108 SER OG Set 20 (size 5): A 193 TYR OH : A 500 SIA O9 : A 93 TYR OH : A 181 HIS : A 500 SIA O8 orientation 3: A 1 ASP N :NH3+ 130: bump=0.000, HB=0.050, total=0.050 orientation 1: A 4 GLN : amide: bump=-0.049, HB=0.615, total=0.566 orientation 11: A 9 TYR OH : rot -167: bump=0.000, HB=1.420, total=1.420 orientation 2: A 10 HIS : no HE2: bump=-0.064, HB=2.504, total=2.440 orientation 1: A 12 ASN : amide: bump=-0.731, HB=2.000, total=1.268 orientation 2: A 14 SER OG : rot -131: bump=0.000, HB=1.145, total=1.145 orientation 2: A 15 THR OG1 : rot -74: bump=0.000, HB=0.065, total=0.065 orientation 1: A 17 GLN : amide: bump=-0.431, HB=0.610, total=0.179 orientation 5: A 20 THR OG1 : rot -52: bump=-0.043, HB=1.587, total=1.544 orientation 1: A 24 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 5: A 27 THR OG1 : rot -72: bump=-1.221, HB=2.475, total=1.254 orientation 2: A 29 THR OG1 : rot 107: bump=-0.493, HB=0.956, total=0.463 orientation 1: A 30 HIS : no HD1: bump=-0.019, HB=0.000, total=-0.019 orientation 1: A 32 GLN : amide: bump=0.000, HB=1.071, total=1.071 orientation 3: A 37 LYS NZ :NH3+ 159: bump=-0.308, HB=0.883, total=0.575 orientation 1: A 38 LYS NZ :NH3+ 173: bump=-0.577, HB=0.003, total=-0.574 orientation 1: A 39 HIS : no HD1: bump=-0.051, HB=0.000, total=-0.051 orientation 1: A 40 ASN : amide: bump=-0.274, HB=1.625, total=1.352 orientation 1: A 42 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 50 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 2: A 58 SER OG : rot 159: bump=-1.246, HB=1.709, total=0.463 orientation 1: A 66 ASN : amide: bump=-0.684, HB=1.425, total=0.740 orientation 1: A 74 ASN : amide: bump=0.000, HB=0.000, total=0.000 orientation 4: A 79 SER OG : rot -120: bump=-0.019, HB=1.352, total=1.333 orientation 5: A 80 TYR OH : rot 22: bump=-0.029, HB=1.199, total=1.170 orientation 2: A 84 LYS NZ :NH3+ -171: bump=-0.024, HB=0.000, total=-0.024 orientation 1: A 86 ASN : amide: bump=-0.002, HB=0.000, total=-0.002 orientation 1: A 89 ASN : amide: bump=0.000, HB=0.000, total=0.000 orientation 1: A 98 ASN : amide: bump=0.000, HB=1.024, total=1.024 orientation 1: A 100 TYR OH : rot -177: bump=0.000, HB=2.039, total=2.039 orientation 2: A 104 LYS NZ :NH3+ -160: bump=0.000, HB=0.013, total=0.013 orientation 2: A 105 HIS : no HE2: bump=-0.515, HB=2.151, total=1.636 orientation 1: A 111 ASN : amide: bump=-0.382, HB=0.000, total=-0.382 orientation 2: A 112 HIS : no HE2: bump=-0.028, HB=0.351, total=0.323 orientation 1: A 117 GLN : amide: bump=-0.024, HB=0.273, total=0.249 orientation 1: A 121 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 122 SER OG : rot 180: bump=0.000, HB=0.005, total=0.005 orientation 2: A 123 SER OG : rot -75: bump=-0.188, HB=1.495, total=1.306 orientation 1: A 125 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 126 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 127 HIS : no HD1: bump=-0.438, HB=1.157, total=0.719 orientation 1: A 130 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 135 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 4: A 139 TYR OH : rot 53: bump=0.000, HB=0.575, total=0.575 orientation 1: A 140 GLN : amide: bump=0.000, HB=0.096, total=0.096 orientation 1: A 142 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 143 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 144 SER OG : rot 180: bump=-0.292, HB=0.741, total=0.449 orientation 4: A 155 LYS NZ :NH3+ -118: bump=0.000, HB=0.424, total=0.424 orientation 1: A 157 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 158 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 10: A 159 TYR OH : rot -155: bump=0.000, HB=1.185, total=1.185 orientation 1: A 161 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 163 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 169 THR OG1 : rot 180: bump=0.000, HB=0.034, total=0.034 orientation 1: A 171 GLN : amide: bump=0.000, HB=0.000, total=0.000 orientation 1: A 182 HIS : no HD1: bump=-0.148, HB=1.724, total=1.576 orientation 1: A 184 ASN : amide: bump=-4.066, HB=0.000, total=-4.066, BADBUMP orientation 1: A 190 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 191 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 195 ASN : amide: bump=-0.155, HB=1.942, total=1.787 orientation 1: A 197 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 10: A 199 TYR OH : rot -139: bump=-0.111, HB=1.385, total=1.274 orientation 1: A 201 SER OG : rot 180: bump=-1.386, HB=0.000, total=-1.386 orientation 2: A 205 SER OG : rot -81: bump=0.000, HB=0.322, total=0.322 orientation 1: A 208 ASN : amide: bump=0.000, HB=0.000, total=0.000 orientation 1: A 209 GLN : amide: bump=-0.001, HB=0.413, total=0.412 orientation 1: A 217 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 219 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 3: A 222 LYS NZ :NH3+ 133: bump=-1.548, HB=1.316, total=-0.232 orientation 1: A 233 THR OG1 : rot -137: bump=0.000, HB=0.763, total=0.763 orientation 3: A 236 LYS NZ :NH3+ 141: bump=0.000, HB=0.391, total=0.391 orientation 1: A 238 ASN : amide: bump=0.000, HB=0.000, total=0.000 orientation 2: A 245 SER OG : rot 54: bump=-0.310, HB=0.907, total=0.597 orientation 1: A 246 ASN : amide: bump=-0.405, HB=0.461, total=0.056 orientation 1: A 254 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 257 LYS NZ :NH3+ 175: bump=0.000, HB=0.011, total=0.011 orientation 1: A 260 LYS NZ :NH3+ 169: bump=-0.068, HB=1.660, total=1.592 orientation 3: A 261 LYS NZ :NH3+ 162: bump=-0.003, HB=0.000, total=-0.003 orientation 2: A 265 THR OG1 : rot 108: bump=-0.857, HB=1.169, total=0.312 orientation 2: A 268 LYS NZ :NH3+ -150: bump=0.000, HB=1.437, total=1.437 orientation 2: A 269 SER OG : rot 103: bump=0.000, HB=1.074, total=1.074 orientation 5: A 273 TYR OH : rot 41: bump=-0.066, HB=1.189, total=1.123 orientation 1: A 275 ASN : amide: bump=-0.052, HB=0.000, total=-0.052 orientation 1: A 277 ASN : amide: bump=-0.334, HB=0.000, total=-0.334 orientation 2: A 278 THR OG1 : rot 110: bump=-0.314, HB=0.189, total=-0.125 orientation 1: A 279 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 281 GLN : amide: bump=-0.291, HB=2.483, total=2.193 orientation 2: A 282 THR OG1 : rot -64: bump=0.000, HB=1.155, total=1.155 orientation 4: A 289 SER OG : rot -168: bump=-0.050, HB=1.278, total=1.228 orientation 1: A 294 HIS : no HD1: bump=-0.410, HB=1.093, total=0.683 orientation 1: A 295 ASN : amide: bump=-0.695, HB=0.638, total=-0.056 orientation 1: A 297 HIS : no HD1: bump=-0.554, HB=0.187, total=-0.367 orientation 3: A 300 THR OG1 : rot 81: bump=0.000, HB=2.198, total=2.198 orientation 1: A 306 LYS NZ :NH3+ 173: bump=-0.047, HB=0.589, total=0.542 orientation 1: A 307 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 309 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 2: A 310 SER OG : rot 100: bump=0.000, HB=1.049, total=1.049 orientation 1: A 311 ASN : amide: bump=0.000, HB=0.000, total=0.000 orientation 1: A 321 ASN : amide: bump=0.000, HB=1.035, total=1.035 orientation 1: A 322 SER OG : rot 180: bump=0.000, HB=0.025, total=0.025 orientation 2: A 492 NAG O3 : rot 146: bump=0.000, HB=0.006, total=0.006 orientation 1: A 492 NAG O4 : rot 160: bump=0.000, HB=0.005, total=0.005 orientation 1: A 492 NAG O6 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 2: A 493 NAG O3 : rot 144: bump=0.000, HB=0.005, total=0.005 orientation 1: A 493 NAG O4 : rot 150: bump=0.000, HB=0.001, total=0.001 orientation 1: A 493 NAG O6 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 3: A 494 NAG O3 : rot 122: bump=0.000, HB=0.745, total=0.745 orientation 1: A 495 NAG O6 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 3: A 496 BMA O2 : rot -33: bump=-0.006, HB=0.057, total=0.052 orientation 3: A 496 BMA O4 : rot 22: bump=-0.000, HB=0.266, total=0.266 orientation 1: A 497 BMA O2 : rot 146: bump=0.000, HB=0.113, total=0.113 orientation 1: A 497 BMA O3 : rot 180: bump=0.000, HB=0.115, total=0.115 orientation 1: A 497 BMA O4 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 3: A 497 BMA O6 : rot -33: bump=0.000, HB=0.248, total=0.248 orientation 1: A 498 MAN O2 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 498 MAN O3 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 2: A 498 MAN O6 : rot 27: bump=-0.005, HB=0.040, total=0.035 orientation 1: A 499 FUC O2 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 3: A 499 FUC O3 : rot -96: bump=0.000, HB=0.059, total=0.059 orientation 1: A 499 FUC O4 : rot 160: bump=0.000, HB=0.081, total=0.081 orientation 2: A 500 SIA O4 : rot -175: bump=-0.017, HB=1.088, total=1.071 orientation 1: A 500 SIA O7 : rot 80: bump=-0.010, HB=0.605, total=0.595 orientation 3: A 501 GAL O2 : rot -131: bump=0.000, HB=0.352, total=0.352 orientation 2: A 501 GAL O4 : rot -30: bump=0.000, HB=0.099, total=0.099 orientation 1: A 502 NAG O1 : rot 180: bump=-0.046, HB=0.000, total=-0.046 orientation 1: A 502 NAG O6 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: B 339 GLN : amide: bump=-0.145, HB=0.292, total=0.146 orientation 8: B 348 TYR OH : rot -15: bump=-0.820, HB=0.848, total=0.027 orientation 2: B 350 HIS : no HE2: bump=-0.029, HB=2.460, total=2.431 orientation 2: B 351 SER OG : rot -74: bump=0.000, HB=0.004, total=0.004 orientation 1: B 354 GLN : amide: bump=0.000, HB=0.441, total=0.441 orientation 1: B 356 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 4: B 358 TYR OH : rot 125: bump=0.000, HB=1.374, total=1.374 orientation 4: B 362 LYS NZ :NH3+ -136: bump=-0.024, HB=0.000, total=-0.024 orientation 4: B 364 SER OG : rot -61: bump=-0.400, HB=1.120, total=0.720 orientation 2: B 365 THR OG1 : rot 87: bump=0.000, HB=0.725, total=0.725 orientation 1: B 366 GLN : amide: bump=-0.190, HB=0.000, total=-0.190 orientation 1: B 367 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 4: B 373 THR OG1 : rot 67: bump=-0.034, HB=1.247, total=1.213 orientation 1: B 374 ASN : amide: bump=-0.004, HB=0.794, total=0.791 orientation 1: B 377 ASN : amide: bump=-0.115, HB=0.000, total=-0.115 orientation 1: B 378 SER OG : rot 76: bump=0.000, HB=1.884, total=1.884 orientation 1: B 382 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: B 384 ASN : amide: bump=-0.145, HB=0.000, total=-0.145 orientation 1: B 385 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: B 386 GLN : amide: bump=-0.259, HB=0.000, total=-0.259 orientation 1: B 395 ASN : amide: bump=-0.768, HB=0.197, total=-0.571 orientation 1: B 396 ASN : amide: bump=0.000, HB=0.804, total=0.804 orientation 1: B 403 ASN : amide: bump=0.000, HB=1.260, total=1.260 orientation 1: B 405 ASN : amide: bump=0.000, HB=1.868, total=1.868 orientation 3: B 406 LYS NZ :NH3+ 163: bump=-0.067, HB=1.308, total=1.241 orientation 1: B 407 LYS NZ :NH3+ -179: bump=-0.040, HB=1.330, total=1.289 orientation 2: B 417 THR OG1 : rot 80: bump=-0.054, HB=1.863, total=1.810 orientation 1: B 418 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: B 419 ASN : amide: bump=0.000, HB=0.000, total=0.000 orientation 1: B 428 ASN : amide: bump=-0.523, HB=2.678, total=2.155 orientation 3: B 437 SER OG : rot -118: bump=0.000, HB=1.146, total=1.146 orientation 2: B 440 LYS NZ :NH3+ -178: bump=0.000, HB=0.000, total=0.000 orientation 1: B 441 ASN : amide: bump=-0.015, HB=2.070, total=2.054 orientation 1: B 443 TYR OH : rot 179: bump=-0.583, HB=2.409, total=1.826 orientation 1: B 445 LYS NZ :NH3+ -176: bump=-0.010, HB=0.000, total=-0.010 orientation 1: B 449 GLN : amide: bump=-0.286, HB=0.550, total=0.265 orientation 1: B 455 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: B 465 TYR OH : rot 180: bump=-0.960, HB=0.000, total=-0.960 orientation 1: B 467 LYS NZ :NH3+ 163: bump=-0.044, HB=1.204, total=1.160 orientation 2: B 475 SER OG : rot -32: bump=-0.037, HB=1.294, total=1.257 orientation 10: B 483 TYR OH : rot -141: bump=-0.337, HB=1.508, total=1.171 orientation 1: B 485 GLN : amide: bump=-0.098, HB=0.000, total=-0.098 orientation 1: B 486 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: B 487 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 Processing set: B 503 EPE O8 [2]: B 459 ASN [2] permutations: 4 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: 0.281 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 0.281 > : 0.281 > : 0.281 > : 0.281 > : 0.281 > : 0.281 > : 0.281 > : 0.281 > : 0.281 > : 0.281 > : 0.281 > : 0.281 > : 0.281 > : 0.281 > : 0.281 > : 0.281 > : 0.281 > : 0.281 > : 0.281 > : 0.281 Optimal score following high resolution, local optimization: 0.281 Processing set: B 480 THR OG1 [5]: B 478 ASN [2] 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: 0.882 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 0.882 > : 0.928 > : 0.928 > : 0.928 > : 0.936 > : 0.936 > : 0.936 > : 0.936 > : 0.936 > : 0.936 > : 0.936 > : 0.936 > : 0.936 > : 0.936 > : 0.936 > : 0.936 > : 0.936 > : 0.936 > : 0.936 > : 0.936 Optimal score following high resolution, local optimization: 0.936 Processing set: B 481 TYR OH [15]: B 466 HIS [6]: B 453 ASN [2] permutations: 180 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: 3.232 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 3.232 > : 3.232 > : 3.232 > : 3.232 > : 3.232 > : 3.232 > : 3.232 > : 3.232 > : 3.232 > : 3.232 > : 3.232 > : 3.232 > : 3.232 > : 3.232 > : 3.232 > : 3.232 > : 3.232 > : 3.232 > : 3.232 > : 3.232 Optimal score following high resolution, local optimization: 3.232 Processing set: B 438 ASN [2]: B 435 HIS [6]: B 346 TYR OH [16] permutations: 192 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: 5.443 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 5.443 > : 5.454 > : 5.454 > : 5.465 > : 5.465 > : 5.465 > : 5.465 > : 5.465 > : 5.465 > : 5.465 > : 5.465 > : 5.465 > : 5.465 > : 5.465 > : 5.465 > : 5.465 > : 5.465 > : 5.465 > : 5.465 > : 5.465 Optimal score following high resolution, local optimization: 5.465 Processing set: B 431 THR OG1 [5]: B 375 LYS NZ [4] permutations: 20 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: 3.135 > : 3.135 > : 3.135 > : 3.135 > : 3.135 > : 3.135 > : 3.135 > : 3.135 > : 3.135 > : 3.135 > : 3.135 > : 3.135 > : 3.135 > : 3.135 > : 3.135 > : 3.135 > : 3.135 > : 3.135 > : 3.135 > : 3.135 > : 3.135 > : 3.135 > : 3.171 > : 3.171 > : 3.205 > : 3.205 > : 3.245 > : 3.245 > : 3.272 > : 3.272 > : 3.298 > : 3.298 > : 3.321 > : 3.321 > : 3.344 > : 3.344 > : 3.360 > : 3.360 > : 3.373 > : 3.373 > : 3.381 > : 3.381 > : 3.384 > : 3.384 > : 3.384 > : 3.384 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 > : 3.386 Optimal score following high resolution, local optimization: 3.386 Processing set: B 470 ASN [2]: B 352 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: 2.124 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: 2.124 Processing set: B 503 EPE O3S [16]: B 349 HIS [6] permutations: 96 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: 1.903 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 1.903 > : 1.917 > : 1.917 > : 1.924 > : 1.924 > : 1.929 > : 1.929 > : 1.929 > : 1.929 > : 1.929 > : 1.929 > : 1.929 > : 1.929 > : 1.929 > : 1.929 > : 1.929 > : 1.929 > : 1.929 > : 1.929 > : 1.929 Optimal score following high resolution, local optimization: 1.929 Processing set: A 501 GAL O6 [4]: A 502 NAG O3 [6] permutations: 24 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: 1.313 > : 1.313 > : 1.313 > : 1.314 > : 1.314 > : 1.314 > : 1.314 > : 1.314 > : 1.314 > : 1.314 > : 1.314 > : 1.314 > : 1.314 > : 1.314 > : 1.314 > : 1.314 > : 1.314 > : 1.314 > : 1.314 > : 1.314 > : 1.314 > : 1.314 > : 1.314 > : 1.332 > : 1.332 > : 1.332 > : 1.332 > : 1.332 > : 1.332 > : 1.332 > : 1.332 > : 1.332 > : 1.332 > : 1.332 > : 1.332 > : 1.332 > : 1.332 > : 1.332 > : 1.332 > : 1.332 > : 1.332 Optimal score following high resolution, local optimization: 1.332 Processing set: A 498 MAN O4 [2]: A 495 NAG O3 [4] permutations: 8 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: 1.005 > : 1.005 > : 1.005 > : 1.005 > : 1.005 > : 1.005 > : 1.005 > : 1.005 > : 1.005 > : 1.005 > : 1.005 > : 1.005 > : 1.005 > : 1.005 > : 1.005 > : 1.005 > : 1.005 > : 1.005 > : 1.005 > : 1.005 > : 1.005 > : 1.005 > : 1.010 > : 1.010 > : 1.010 > : 1.010 > : 1.010 > : 1.010 > : 1.010 > : 1.010 > : 1.010 > : 1.010 > : 1.048 > : 1.048 > : 1.048 > : 1.048 > : 1.048 > : 1.048 > : 1.048 > : 1.048 > : 1.048 Optimal score following high resolution, local optimization: 1.048 Processing set: A 290 SER OG [1]: A 288 ASN [2] permutations: 2 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: 0.000 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 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 225 SER OG [2]: A 220 LYS NZ [4] permutations: 8 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: 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.596 > : 0.612 > : 0.628 > : 0.643 > : 0.656 > : 0.666 > : 0.692 > : 0.699 > : 0.706 > : 0.713 > : 0.721 > : 0.728 > : 0.736 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 > : 0.740 Optimal score following high resolution, local optimization: 0.740 Processing set: A 206 THR OG1 [5]: A 204 THR OG1 [3] permutations: 15 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: 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 > : 3.472 Optimal score following high resolution, local optimization: 3.472 Processing set: A 198 THR OG1 [7]: A 189 GLN [2]: A 248 ASN [2] permutations: 28 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: 6.738 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 6.738 > : 6.738 > : 6.738 > : 6.738 > : 6.738 > : 6.738 > : 6.738 > : 6.738 > : 6.738 > : 6.738 > : 6.738 > : 6.738 > : 6.738 > : 6.738 > : 6.738 > : 6.738 > : 6.738 > : 6.738 > : 6.738 > : 6.738 Optimal score following high resolution, local optimization: 6.738 Processing set: A 154 LYS NZ [4]: A 194 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: -1.824 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : -2.451 > : -2.447 > : -2.440 > : -2.433 > : -2.426 > : -2.418 > : -2.407 > : -2.394 > : -2.379 > : -2.361 > : -2.341 > : -2.318 > : -2.293 > : -2.241 > : -2.214 > : -2.185 > : -2.154 > : -2.121 > : -2.089 > : -2.055 > : -2.024 > : -1.995 > : -1.967 > : -1.939 > : -1.912 > : -1.889 > : -1.869 > : -1.855 > : -1.843 > : -1.833 > : -1.824 > : -1.822 > : -1.822 > : -1.822 > : -1.822 > : -1.822 > : -1.822 > : -1.822 > : -1.822 > : -1.822 > : -1.822 > : -1.822 > : -1.822 > : -1.822 > : -1.822 > : -1.822 > : -1.822 > : -1.822 > : -1.822 > : -1.822 > : -1.822 > : -1.822 > : -1.822 > : -1.822 > : -1.822 > : -1.822 > : -1.822 > : -1.822 > : -1.822 > : -1.822 Optimal score following high resolution, local optimization: -1.822 Processing set: A 170 ASN [2]: A 168 ASN [2]: A 166 TYR OH [12] permutations: 48 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: 1.146 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 1.146 > : 1.146 > : 1.146 > : 1.146 > : 1.146 > : 1.146 > : 1.146 > : 1.146 > : 1.146 > : 1.146 > : 1.146 > : 1.146 > : 1.146 > : 1.146 > : 1.146 > : 1.146 > : 1.146 > : 1.146 > : 1.146 > : 1.146 Optimal score following high resolution, local optimization: 1.146 Processing set: A 165 SER OG [6]: A 242 ASN [2] permutations: 12 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: -0.240 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : -0.240 > : -0.200 > : -0.200 > : -0.131 > : -0.131 > : -0.101 > : -0.101 > : -0.087 > : -0.087 > : -0.067 > : -0.067 > : 0.001 > : 0.001 > : 0.049 > : 0.049 > : 0.049 > : 0.049 > : 0.049 > : 0.049 > : 0.049 Optimal score following high resolution, local optimization: 0.049 Processing set: A 148 ASN [2]: A 256 TYR OH [12]: A 115 LYS NZ [4] permutations: 96 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: 3.196 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 3.196 > : 3.196 > : 3.202 > : 3.202 > : 3.206 > : 3.206 > : 3.209 > : 3.209 > : 3.210 > : 3.210 > : 3.210 > : 3.210 > : 3.210 > : 3.210 > : 3.210 > : 3.210 > : 3.210 > : 3.210 > : 3.210 > : 3.210 > : 2.236 > : 2.273 > : 2.308 > : 2.342 > : 2.376 > : 2.413 > : 2.449 > : 2.489 > : 2.530 > : 2.572 > : 2.613 > : 2.654 > : 2.695 > : 2.736 > : 2.778 > : 2.818 > : 2.855 > : 2.890 > : 2.923 > : 2.954 > : 2.982 > : 3.011 > : 3.038 > : 3.066 > : 3.094 > : 3.119 > : 3.142 > : 3.162 > : 3.180 > : 3.195 > : 3.210 > : 3.223 > : 3.234 > : 3.242 > : 3.247 > : 3.249 > : 3.249 > : 3.249 > : 3.249 > : 3.249 > : 3.249 > : 3.249 > : 3.249 > : 3.249 > : 3.249 > : 3.249 > : 3.249 > : 3.249 > : 3.249 > : 3.249 > : 3.249 > : 3.249 > : 3.249 > : 3.249 > : 3.249 > : 3.249 > : 3.249 > : 3.249 > : 3.249 > : 3.249 Optimal score following high resolution, local optimization: 3.249 Processing set: A 500 SIA O1B [9]: A 134 SER OG [4] 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: 2.071 > : 2.071 > : 2.076 > : 2.076 > : 2.082 > : 2.082 > : 2.089 > : 2.089 > : 2.096 > : 2.096 > : 2.103 > : 2.103 > : 2.110 > : 2.110 > : 2.115 > : 2.115 > : 2.117 > : 2.117 > : 2.117 > : 2.117 > : 2.117 > : 2.117 > : 2.117 > : 2.117 > : 2.117 > : 2.117 > : 2.117 > : 2.117 > : 2.117 > : 2.117 > : 2.117 > : 2.117 > : 2.117 > : 2.117 > : 2.117 > : 2.117 > : 2.117 > : 2.117 > : 2.117 > : 2.117 > : 2.117 Optimal score following high resolution, local optimization: 2.117 Processing set: A 264 SER OG [3]: A 108 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: 2.607 > : 2.607 > : 2.607 > : 2.607 > : 2.607 > : 2.607 > : 2.607 > : 2.607 > : 2.607 > : 2.607 > : 2.607 > : 2.607 > : 2.607 > : 2.607 > : 2.607 > : 2.607 > : 2.607 > : 2.607 > : 2.607 > : 2.607 > : 2.607 > : 2.607 > : 2.607 > : 2.607 > : 2.607 > : 2.607 > : 2.607 > : 2.678 > : 2.678 > : 2.678 > : 2.678 > : 2.678 > : 2.678 > : 2.678 > : 2.678 > : 2.678 > : 2.678 > : 2.716 > : 2.716 > : 2.716 > : 2.716 Optimal score following high resolution, local optimization: 2.716 Processing set: A 193 TYR OH [11]: A 500 SIA O9 [8]: A 93 TYR OH [13] : A 181 HIS [6]: A 500 SIA O8 [7] permutations: 48048 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: 5.650 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 5.650 > : 5.675 > : 5.675 > : 5.698 > : 5.698 > : 5.721 > : 5.721 > : 5.819 > : 5.819 > : 5.819 > : 5.819 > : 5.819 > : 5.819 > : 5.819 > : 5.819 > : 5.819 > : 5.819 > : 5.819 > : 5.819 > : 5.819 > : 5.819 > : 5.819 > : 5.826 > : 5.826 > : 5.828 > : 5.828 > : 5.828 > : 5.828 > : 5.828 > : 5.828 > : 5.828 > : 5.828 > : 5.828 > : 5.828 > : 5.828 > : 5.828 > : 5.828 > : 5.828 > : 5.828 > : 5.828 > : 5.828 > : 5.834 > : 5.834 > : 5.838 > : 5.838 > : 5.839 > : 5.839 > : 5.841 > : 5.841 > : 5.843 > : 5.843 > : 5.845 > : 5.845 > : 5.847 > : 5.847 > : 5.849 > : 5.849 > : 5.852 > : 5.852 > : 5.853 > : 5.853 > : 5.853 > : 5.853 > : 5.853 > : 5.853 > : 5.853 > : 5.853 > : 5.853 > : 5.853 > : 5.853 > : 5.853 > : 5.853 > : 5.853 > : 5.853 > : 5.853 > : 5.853 > : 5.853 > : 5.853 > : 5.853 > : 5.853 Optimal score following high resolution, local optimization: 5.853 Found 0 hydrogens (0 hets) Standardized 0 hydrogens (0 hets) Added 3932 hydrogens (146 hets) Removed 0 hydrogens (0 hets) Adjusted 142 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