Starting phenix.real_space_refine on Thu Aug 6 06:14:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uv7_64527/08_2026/9uv7_64527.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uv7_64527/08_2026/9uv7_64527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uv7_64527/08_2026/9uv7_64527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uv7_64527/08_2026/9uv7_64527.map" model { file = "/net/cci-nas-00/data/ceres_data/9uv7_64527/08_2026/9uv7_64527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uv7_64527/08_2026/9uv7_64527.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 77 5.16 5 C 8703 2.51 5 N 2251 2.21 5 O 2453 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13484 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3263 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 16, 'TRANS': 421} Chain breaks: 2 Chain: "A" Number of atoms: 3263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3263 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 16, 'TRANS': 421} Chain breaks: 2 Chain: "C" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 758 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "D" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 758 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "E" Number of atoms: 2739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2739 Classifications: {'peptide': 367} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 347} Chain breaks: 1 Chain: "F" Number of atoms: 2703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2703 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 19, 'TRANS': 341} Chain breaks: 1 Time building chain proxies: 2.18, per 1000 atoms: 0.16 Number of scatterers: 13484 At special positions: 0 Unit cell: (92.66, 135.3, 105.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 77 16.00 O 2453 8.00 N 2251 7.00 C 8703 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 611.3 milliseconds 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3288 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 6 sheets defined 58.9% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'B' and resid 4 through 24 removed outlier: 3.780A pdb=" N LEU B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 50 Processing helix chain 'B' and resid 56 through 76 Processing helix chain 'B' and resid 82 through 108 removed outlier: 3.705A pdb=" N ASN B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 148 removed outlier: 3.901A pdb=" N LEU B 122 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 180 Processing helix chain 'B' and resid 183 through 208 Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'B' and resid 213 through 237 removed outlier: 3.751A pdb=" N SER B 219 " --> pdb=" O PRO B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 262 Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'B' and resid 297 through 305 Processing helix chain 'B' and resid 315 through 320 removed outlier: 3.592A pdb=" N ALA B 320 " --> pdb=" O GLY B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 336 Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.704A pdb=" N VAL B 357 " --> pdb=" O GLY B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 367 No H-bonds generated for 'chain 'B' and resid 365 through 367' Processing helix chain 'B' and resid 372 through 376 Processing helix chain 'B' and resid 377 through 380 removed outlier: 4.185A pdb=" N ALA B 380 " --> pdb=" O ASP B 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 377 through 380' Processing helix chain 'B' and resid 413 through 417 Processing helix chain 'B' and resid 436 through 441 removed outlier: 3.529A pdb=" N LYS B 441 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 461 removed outlier: 3.632A pdb=" N ALA B 457 " --> pdb=" O ALA B 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 24 removed outlier: 3.617A pdb=" N LEU A 24 " --> pdb=" O SER A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 48 removed outlier: 4.840A pdb=" N GLY A 37 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 77 removed outlier: 3.506A pdb=" N LEU A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 107 Processing helix chain 'A' and resid 114 through 147 removed outlier: 3.858A pdb=" N VAL A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 181 Processing helix chain 'A' and resid 183 through 208 Processing helix chain 'A' and resid 213 through 237 removed outlier: 3.527A pdb=" N SER A 219 " --> pdb=" O PRO A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 263 removed outlier: 3.716A pdb=" N ILE A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 295 through 306 Processing helix chain 'A' and resid 314 through 320 removed outlier: 3.652A pdb=" N ALA A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 336 Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.623A pdb=" N VAL A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 436 through 441 Processing helix chain 'A' and resid 450 through 459 Processing helix chain 'C' and resid 413 through 420 removed outlier: 6.715A pdb=" N SER C 418 " --> pdb=" O TRP C 415 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA C 420 " --> pdb=" O ALA C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 443 Processing helix chain 'C' and resid 451 through 461 Processing helix chain 'C' and resid 463 through 470 removed outlier: 4.022A pdb=" N GLY C 467 " --> pdb=" O ILE C 463 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 475 removed outlier: 4.341A pdb=" N GLY C 475 " --> pdb=" O ILE C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 504 removed outlier: 3.507A pdb=" N ASN C 492 " --> pdb=" O ILE C 488 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR C 498 " --> pdb=" O PHE C 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 426 through 443 Processing helix chain 'D' and resid 450 through 462 Processing helix chain 'D' and resid 464 through 469 Processing helix chain 'D' and resid 475 through 496 removed outlier: 3.573A pdb=" N ASN D 492 " --> pdb=" O ILE D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 504 Processing helix chain 'E' and resid 1019 through 1028 Processing helix chain 'E' and resid 1040 through 1044 removed outlier: 3.643A pdb=" N SER E1044 " --> pdb=" O GLN E1041 " (cutoff:3.500A) Processing helix chain 'E' and resid 1046 through 1054 Processing helix chain 'E' and resid 1059 through 1064 removed outlier: 3.783A pdb=" N VAL E1063 " --> pdb=" O GLY E1060 " (cutoff:3.500A) Processing helix chain 'E' and resid 1098 through 1105 removed outlier: 3.800A pdb=" N GLN E1103 " --> pdb=" O PRO E1099 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU E1105 " --> pdb=" O LEU E1101 " (cutoff:3.500A) Processing helix chain 'E' and resid 1116 through 1118 No H-bonds generated for 'chain 'E' and resid 1116 through 1118' Processing helix chain 'E' and resid 1121 through 1125 Processing helix chain 'E' and resid 1128 through 1149 removed outlier: 3.692A pdb=" N SER E1132 " --> pdb=" O ASP E1128 " (cutoff:3.500A) Processing helix chain 'E' and resid 1174 through 1188 removed outlier: 4.604A pdb=" N ALA E1179 " --> pdb=" O VAL E1175 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA E1180 " --> pdb=" O ALA E1176 " (cutoff:3.500A) Processing helix chain 'E' and resid 1201 through 1207 Processing helix chain 'E' and resid 1226 through 1231 removed outlier: 3.519A pdb=" N MET E1230 " --> pdb=" O TYR E1226 " (cutoff:3.500A) Processing helix chain 'E' and resid 1231 through 1247 removed outlier: 3.586A pdb=" N ILE E1235 " --> pdb=" O SER E1231 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS E1247 " --> pdb=" O ALA E1243 " (cutoff:3.500A) Processing helix chain 'E' and resid 1268 through 1273 removed outlier: 3.556A pdb=" N VAL E1272 " --> pdb=" O THR E1268 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP E1273 " --> pdb=" O ARG E1269 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1268 through 1273' Processing helix chain 'E' and resid 1285 through 1289 removed outlier: 3.745A pdb=" N GLY E1289 " --> pdb=" O ALA E1286 " (cutoff:3.500A) Processing helix chain 'E' and resid 1314 through 1319 Processing helix chain 'E' and resid 1320 through 1339 Processing helix chain 'E' and resid 1353 through 1358 removed outlier: 3.614A pdb=" N VAL E1358 " --> pdb=" O VAL E1354 " (cutoff:3.500A) Processing helix chain 'F' and resid 1019 through 1028 removed outlier: 3.907A pdb=" N GLN F1025 " --> pdb=" O LYS F1021 " (cutoff:3.500A) Processing helix chain 'F' and resid 1038 through 1044 removed outlier: 4.292A pdb=" N LEU F1042 " --> pdb=" O GLY F1038 " (cutoff:3.500A) Processing helix chain 'F' and resid 1046 through 1053 Processing helix chain 'F' and resid 1061 through 1066 removed outlier: 3.568A pdb=" N SER F1066 " --> pdb=" O VAL F1063 " (cutoff:3.500A) Processing helix chain 'F' and resid 1077 through 1083 removed outlier: 3.605A pdb=" N LEU F1083 " --> pdb=" O ILE F1080 " (cutoff:3.500A) Processing helix chain 'F' and resid 1098 through 1107 removed outlier: 4.399A pdb=" N MET F1102 " --> pdb=" O ASN F1098 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN F1103 " --> pdb=" O PRO F1099 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU F1107 " --> pdb=" O GLN F1103 " (cutoff:3.500A) Processing helix chain 'F' and resid 1121 through 1125 Processing helix chain 'F' and resid 1128 through 1149 Processing helix chain 'F' and resid 1174 through 1187 Processing helix chain 'F' and resid 1201 through 1208 Processing helix chain 'F' and resid 1237 through 1242 removed outlier: 4.093A pdb=" N PHE F1242 " --> pdb=" O GLU F1238 " (cutoff:3.500A) Processing helix chain 'F' and resid 1244 through 1249 removed outlier: 3.595A pdb=" N GLU F1248 " --> pdb=" O ALA F1244 " (cutoff:3.500A) Processing helix chain 'F' and resid 1268 through 1275 Processing helix chain 'F' and resid 1319 through 1340 removed outlier: 3.936A pdb=" N TYR F1327 " --> pdb=" O SER F1323 " (cutoff:3.500A) Processing helix chain 'F' and resid 1352 through 1359 removed outlier: 3.655A pdb=" N ARG F1356 " --> pdb=" O ASP F1352 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 369 through 371 removed outlier: 6.495A pdb=" N VAL B 385 " --> pdb=" O ILE B 421 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N PHE B 423 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL B 387 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL B 420 " --> pdb=" O HIS B 445 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU B 447 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL B 422 " --> pdb=" O LEU B 447 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 369 through 371 removed outlier: 6.496A pdb=" N SER A 308 " --> pdb=" O THR A 384 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU A 386 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE A 310 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE A 388 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N THR A 312 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL A 385 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N PHE A 423 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL A 387 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A 420 " --> pdb=" O HIS A 445 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LEU A 447 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 422 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 1056 through 1058 removed outlier: 7.960A pdb=" N VAL E1033 " --> pdb=" O GLU E1056 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N VAL E1058 " --> pdb=" O VAL E1033 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL E1035 " --> pdb=" O VAL E1058 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU E1036 " --> pdb=" O ILE E1005 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE E1068 " --> pdb=" O ARG E1002 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU E1070 " --> pdb=" O GLY E1004 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE E1092 " --> pdb=" O LYS E1071 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ASN E1073 " --> pdb=" O PHE E1092 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU E1089 " --> pdb=" O MET E1113 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA E1114 " --> pdb=" O THR E1359 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N THR E1359 " --> pdb=" O ALA E1114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 1210 through 1211 removed outlier: 7.000A pdb=" N VAL E1191 " --> pdb=" O GLU E1210 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL E1168 " --> pdb=" O ARG E1192 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N PHE E1194 " --> pdb=" O VAL E1168 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL E1170 " --> pdb=" O PHE E1194 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYS E1167 " --> pdb=" O ILE E1251 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL E1253 " --> pdb=" O LYS E1167 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N MET E1169 " --> pdb=" O VAL E1253 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 1033 through 1035 removed outlier: 6.520A pdb=" N GLY F1004 " --> pdb=" O LEU F1070 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU F1089 " --> pdb=" O MET F1113 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 1210 through 1211 removed outlier: 6.884A pdb=" N VAL F1191 " --> pdb=" O GLU F1210 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL F1168 " --> pdb=" O ARG F1192 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N PHE F1194 " --> pdb=" O VAL F1168 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N VAL F1170 " --> pdb=" O PHE F1194 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N MET F1169 " --> pdb=" O VAL F1253 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE F1252 " --> pdb=" O VAL F1282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 724 hydrogen bonds defined for protein. 2082 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.93 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.17: 1 1.17 - 1.33: 3187 1.33 - 1.50: 4631 1.50 - 1.66: 5769 1.66 - 1.83: 145 Bond restraints: 13733 Sorted by residual: bond pdb=" CG PRO E1262 " pdb=" CD PRO E1262 " ideal model delta sigma weight residual 1.503 1.001 0.502 3.40e-02 8.65e+02 2.18e+02 bond pdb=" N PRO E1262 " pdb=" CD PRO E1262 " ideal model delta sigma weight residual 1.473 1.658 -0.185 1.40e-02 5.10e+03 1.75e+02 bond pdb=" C LYS E1261 " pdb=" N PRO E1262 " ideal model delta sigma weight residual 1.334 1.558 -0.224 2.34e-02 1.83e+03 9.15e+01 bond pdb=" N PRO E1262 " pdb=" CA PRO E1262 " ideal model delta sigma weight residual 1.469 1.388 0.080 1.28e-02 6.10e+03 3.95e+01 bond pdb=" CG1 ILE F1069 " pdb=" CD1 ILE F1069 " ideal model delta sigma weight residual 1.513 1.329 0.184 3.90e-02 6.57e+02 2.21e+01 ... (remaining 13728 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.97: 18615 5.97 - 11.95: 37 11.95 - 17.92: 4 17.92 - 23.90: 0 23.90 - 29.87: 2 Bond angle restraints: 18658 Sorted by residual: angle pdb=" CA PRO E1262 " pdb=" N PRO E1262 " pdb=" CD PRO E1262 " ideal model delta sigma weight residual 112.00 84.29 27.71 1.40e+00 5.10e-01 3.92e+02 angle pdb=" CA PRO F1264 " pdb=" N PRO F1264 " pdb=" CD PRO F1264 " ideal model delta sigma weight residual 112.00 96.42 15.58 1.40e+00 5.10e-01 1.24e+02 angle pdb=" N PRO E1262 " pdb=" CD PRO E1262 " pdb=" CG PRO E1262 " ideal model delta sigma weight residual 103.20 89.65 13.55 1.50e+00 4.44e-01 8.16e+01 angle pdb=" CA PRO E1262 " pdb=" CB PRO E1262 " pdb=" CG PRO E1262 " ideal model delta sigma weight residual 104.50 89.83 14.67 1.90e+00 2.77e-01 5.96e+01 angle pdb=" C LYS E1261 " pdb=" N PRO E1262 " pdb=" CD PRO E1262 " ideal model delta sigma weight residual 125.00 154.87 -29.87 4.10e+00 5.95e-02 5.31e+01 ... (remaining 18653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 6888 17.61 - 35.22: 957 35.22 - 52.83: 241 52.83 - 70.44: 56 70.44 - 88.05: 14 Dihedral angle restraints: 8156 sinusoidal: 3051 harmonic: 5105 Sorted by residual: dihedral pdb=" CA TRP F1368 " pdb=" C TRP F1368 " pdb=" N PRO F1369 " pdb=" CA PRO F1369 " ideal model delta harmonic sigma weight residual -180.00 -131.61 -48.39 0 5.00e+00 4.00e-02 9.37e+01 dihedral pdb=" CA THR A 81 " pdb=" C THR A 81 " pdb=" N GLU A 82 " pdb=" CA GLU A 82 " ideal model delta harmonic sigma weight residual 180.00 142.86 37.14 0 5.00e+00 4.00e-02 5.52e+01 dihedral pdb=" CA LYS E1261 " pdb=" C LYS E1261 " pdb=" N PRO E1262 " pdb=" CA PRO E1262 " ideal model delta harmonic sigma weight residual -180.00 -152.42 -27.58 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 8153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1836 0.058 - 0.117: 374 0.117 - 0.175: 33 0.175 - 0.234: 3 0.234 - 0.292: 2 Chirality restraints: 2248 Sorted by residual: chirality pdb=" CB ILE F1069 " pdb=" CA ILE F1069 " pdb=" CG1 ILE F1069 " pdb=" CG2 ILE F1069 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB VAL E1112 " pdb=" CA VAL E1112 " pdb=" CG1 VAL E1112 " pdb=" CG2 VAL E1112 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB VAL A 347 " pdb=" CA VAL A 347 " pdb=" CG1 VAL A 347 " pdb=" CG2 VAL A 347 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.61e-01 ... (remaining 2245 not shown) Planarity restraints: 2361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA F1263 " 0.091 5.00e-02 4.00e+02 1.26e-01 2.52e+01 pdb=" N PRO F1264 " -0.216 5.00e-02 4.00e+02 pdb=" CA PRO F1264 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO F1264 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP F1368 " -0.072 5.00e-02 4.00e+02 1.11e-01 1.97e+01 pdb=" N PRO F1369 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO F1369 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO F1369 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E1261 " -0.075 5.00e-02 4.00e+02 9.76e-02 1.53e+01 pdb=" N PRO E1262 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO E1262 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E1262 " -0.065 5.00e-02 4.00e+02 ... (remaining 2358 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 1 2.04 - 2.76: 2456 2.76 - 3.47: 20696 3.47 - 4.19: 34427 4.19 - 4.90: 60927 Nonbonded interactions: 118507 Sorted by model distance: nonbonded pdb=" O LYS D 508 " pdb=" O ASN D 509 " model vdw 1.330 3.040 nonbonded pdb=" O ASP F1349 " pdb=" OD1 ASP F1349 " model vdw 2.047 3.040 nonbonded pdb=" OG1 THR E1154 " pdb=" O LEU E1187 " model vdw 2.104 3.040 nonbonded pdb=" O GLU F1270 " pdb=" OG SER F1274 " model vdw 2.127 3.040 nonbonded pdb=" O THR A 135 " pdb=" OG SER A 139 " model vdw 2.131 3.040 ... (remaining 118502 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 1001 through 1214 or resid 1224 or resid 1231 through 1374 \ )) selection = (chain 'F' and resid 1001 through 1374) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.500 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.502 13733 Z= 0.324 Angle : 0.878 29.873 18658 Z= 0.484 Chirality : 0.046 0.292 2248 Planarity : 0.007 0.126 2361 Dihedral : 17.706 88.054 4868 Min Nonbonded Distance : 1.330 Molprobity Statistics. All-atom Clashscore : 22.70 Ramachandran Plot: Outliers : 1.29 % Allowed : 7.82 % Favored : 90.89 % Rotamer: Outliers : 1.47 % Allowed : 30.34 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.20), residues: 1778 helix: 0.21 (0.17), residues: 931 sheet: -1.03 (0.46), residues: 134 loop : -1.95 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 73 TYR 0.012 0.002 TYR A 315 PHE 0.019 0.002 PHE B 178 TRP 0.016 0.001 TRP C 415 HIS 0.008 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00803 / 0.32 (13733) covalent geometry : angle 0.87807 / 0.48 (18658) hydrogen bonds : bond 0.15391 / 10.08 ( 724) hydrogen bonds : angle 6.29520 / 4.61 ( 2082) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 7 residues processed: 216 average time/residue: 0.0929 time to fit residues: 30.2623 Evaluate side-chains 194 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 187 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain E residue 1275 MET Chi-restraints excluded: chain E residue 1315 LEU Chi-restraints excluded: chain E residue 1318 ARG Chi-restraints excluded: chain F residue 1207 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 HIS A 264 ASN ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN ** E1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1305 ASN F1156 GLN F1330 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.135179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.102756 restraints weight = 21873.625| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.66 r_work: 0.3006 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13733 Z= 0.177 Angle : 0.692 10.389 18658 Z= 0.356 Chirality : 0.046 0.281 2248 Planarity : 0.006 0.107 2361 Dihedral : 5.677 47.437 1889 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 1.07 % Allowed : 7.03 % Favored : 91.90 % Rotamer: Outliers : 3.99 % Allowed : 26.63 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.20), residues: 1778 helix: 0.47 (0.17), residues: 958 sheet: -1.15 (0.45), residues: 139 loop : -1.86 (0.25), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 334 TYR 0.013 0.002 TYR F1294 PHE 0.028 0.001 PHE F1149 TRP 0.016 0.001 TRP C 415 HIS 0.004 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (13733) covalent geometry : angle 0.69197 / 0.36 (18658) hydrogen bonds : bond 0.04608 / 3.08 ( 724) hydrogen bonds : angle 4.79225 / 3.47 ( 2082) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 203 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 HIS cc_start: 0.8080 (OUTLIER) cc_final: 0.7841 (t70) REVERT: B 448 PHE cc_start: 0.7712 (m-10) cc_final: 0.7436 (m-10) REVERT: A 338 ILE cc_start: 0.6775 (OUTLIER) cc_final: 0.6354 (tt) REVERT: C 500 THR cc_start: 0.9060 (m) cc_final: 0.8800 (m) REVERT: E 1125 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7652 (pm20) REVERT: E 1149 PHE cc_start: 0.6226 (OUTLIER) cc_final: 0.5743 (t80) REVERT: F 1202 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8173 (mp0) outliers start: 57 outliers final: 24 residues processed: 243 average time/residue: 0.0878 time to fit residues: 33.4007 Evaluate side-chains 222 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain E residue 1023 VAL Chi-restraints excluded: chain E residue 1111 THR Chi-restraints excluded: chain E residue 1125 GLN Chi-restraints excluded: chain E residue 1149 PHE Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1235 ILE Chi-restraints excluded: chain E residue 1296 VAL Chi-restraints excluded: chain E residue 1305 ASN Chi-restraints excluded: chain E residue 1315 LEU Chi-restraints excluded: chain F residue 1110 VAL Chi-restraints excluded: chain F residue 1202 GLU Chi-restraints excluded: chain F residue 1281 ILE Chi-restraints excluded: chain F residue 1307 VAL Chi-restraints excluded: chain F residue 1360 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 31 optimal weight: 0.8980 chunk 171 optimal weight: 7.9990 chunk 2 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 32 optimal weight: 0.0980 chunk 47 optimal weight: 0.4980 chunk 74 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN ** E1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1147 HIS E1305 ASN E1322 GLN F1333 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.138111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.104150 restraints weight = 21703.841| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.68 r_work: 0.3055 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13733 Z= 0.149 Angle : 0.643 9.609 18658 Z= 0.329 Chirality : 0.044 0.211 2248 Planarity : 0.006 0.101 2361 Dihedral : 5.107 45.967 1875 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.90 % Allowed : 6.75 % Favored : 92.35 % Rotamer: Outliers : 4.70 % Allowed : 26.00 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.20), residues: 1778 helix: 0.73 (0.17), residues: 952 sheet: -1.09 (0.45), residues: 139 loop : -1.74 (0.25), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1362 TYR 0.015 0.001 TYR E1312 PHE 0.024 0.001 PHE F1149 TRP 0.016 0.001 TRP C 415 HIS 0.004 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (13733) covalent geometry : angle 0.64307 / 0.33 (18658) hydrogen bonds : bond 0.04102 / 2.75 ( 724) hydrogen bonds : angle 4.49079 / 3.24 ( 2082) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 203 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8191 (mt) REVERT: A 189 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8576 (mt) REVERT: A 331 GLU cc_start: 0.7338 (mp0) cc_final: 0.7115 (mp0) REVERT: A 338 ILE cc_start: 0.6903 (OUTLIER) cc_final: 0.6444 (tt) REVERT: C 500 THR cc_start: 0.9068 (m) cc_final: 0.8808 (m) REVERT: E 1033 VAL cc_start: 0.6510 (p) cc_final: 0.6208 (m) REVERT: E 1067 GLU cc_start: 0.6110 (pt0) cc_final: 0.5730 (pm20) REVERT: E 1149 PHE cc_start: 0.6283 (OUTLIER) cc_final: 0.5857 (t80) REVERT: F 1144 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6763 (mm-30) REVERT: F 1169 MET cc_start: 0.6188 (tmm) cc_final: 0.5876 (tmm) REVERT: F 1275 MET cc_start: 0.7055 (ppp) cc_final: 0.6735 (tmm) outliers start: 67 outliers final: 31 residues processed: 248 average time/residue: 0.0848 time to fit residues: 32.7765 Evaluate side-chains 227 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain D residue 415 TRP Chi-restraints excluded: chain E residue 1023 VAL Chi-restraints excluded: chain E residue 1111 THR Chi-restraints excluded: chain E residue 1149 PHE Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1200 VAL Chi-restraints excluded: chain E residue 1212 LEU Chi-restraints excluded: chain E residue 1235 ILE Chi-restraints excluded: chain E residue 1296 VAL Chi-restraints excluded: chain F residue 1142 ILE Chi-restraints excluded: chain F residue 1144 GLU Chi-restraints excluded: chain F residue 1204 VAL Chi-restraints excluded: chain F residue 1281 ILE Chi-restraints excluded: chain F residue 1307 VAL Chi-restraints excluded: chain F residue 1331 LEU Chi-restraints excluded: chain F residue 1360 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 75 optimal weight: 0.0270 chunk 74 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN E1147 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.138304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.106151 restraints weight = 21594.539| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.55 r_work: 0.2930 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13733 Z= 0.148 Angle : 0.637 9.545 18658 Z= 0.325 Chirality : 0.044 0.239 2248 Planarity : 0.005 0.096 2361 Dihedral : 4.949 44.512 1873 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.90 % Allowed : 7.14 % Favored : 91.96 % Rotamer: Outliers : 4.41 % Allowed : 26.00 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.21), residues: 1778 helix: 0.89 (0.17), residues: 952 sheet: -1.20 (0.47), residues: 134 loop : -1.51 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E1356 TYR 0.010 0.001 TYR B 366 PHE 0.020 0.001 PHE F1149 TRP 0.014 0.001 TRP C 415 HIS 0.005 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (13733) covalent geometry : angle 0.63742 / 0.33 (18658) hydrogen bonds : bond 0.03893 / 2.62 ( 724) hydrogen bonds : angle 4.36688 / 3.15 ( 2082) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 202 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 ASP cc_start: 0.7063 (p0) cc_final: 0.6786 (p0) REVERT: A 189 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8624 (mt) REVERT: A 331 GLU cc_start: 0.7273 (mp0) cc_final: 0.7010 (mp0) REVERT: A 338 ILE cc_start: 0.6885 (OUTLIER) cc_final: 0.6451 (tt) REVERT: E 1033 VAL cc_start: 0.6217 (p) cc_final: 0.6008 (m) REVERT: E 1149 PHE cc_start: 0.6379 (OUTLIER) cc_final: 0.6019 (t80) REVERT: E 1291 ASN cc_start: 0.5545 (m110) cc_final: 0.5183 (t0) REVERT: F 1169 MET cc_start: 0.6337 (tmm) cc_final: 0.5613 (tmm) outliers start: 63 outliers final: 39 residues processed: 244 average time/residue: 0.0901 time to fit residues: 34.3834 Evaluate side-chains 233 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 191 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain D residue 415 TRP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 1023 VAL Chi-restraints excluded: chain E residue 1083 LEU Chi-restraints excluded: chain E residue 1093 ILE Chi-restraints excluded: chain E residue 1111 THR Chi-restraints excluded: chain E residue 1149 PHE Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1200 VAL Chi-restraints excluded: chain E residue 1212 LEU Chi-restraints excluded: chain E residue 1235 ILE Chi-restraints excluded: chain E residue 1296 VAL Chi-restraints excluded: chain F residue 1073 ASN Chi-restraints excluded: chain F residue 1142 ILE Chi-restraints excluded: chain F residue 1153 PHE Chi-restraints excluded: chain F residue 1204 VAL Chi-restraints excluded: chain F residue 1281 ILE Chi-restraints excluded: chain F residue 1307 VAL Chi-restraints excluded: chain F residue 1360 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 32 optimal weight: 0.8980 chunk 132 optimal weight: 20.0000 chunk 49 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 109 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN E1147 HIS E1185 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.139146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.106311 restraints weight = 21556.294| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.72 r_work: 0.2901 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13733 Z= 0.179 Angle : 0.658 12.288 18658 Z= 0.333 Chirality : 0.045 0.261 2248 Planarity : 0.005 0.092 2361 Dihedral : 4.977 43.415 1873 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.37 % Favored : 91.84 % Rotamer: Outliers : 4.98 % Allowed : 25.79 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.21), residues: 1778 helix: 0.83 (0.17), residues: 952 sheet: -0.92 (0.50), residues: 129 loop : -1.44 (0.25), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 502 TYR 0.013 0.002 TYR B 366 PHE 0.018 0.001 PHE F1149 TRP 0.025 0.001 TRP C 415 HIS 0.005 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (13733) covalent geometry : angle 0.65833 / 0.33 (18658) hydrogen bonds : bond 0.03998 / 2.71 ( 724) hydrogen bonds : angle 4.44151 / 3.21 ( 2082) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 187 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 ASP cc_start: 0.7147 (p0) cc_final: 0.6792 (p0) REVERT: A 189 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8615 (mt) REVERT: A 331 GLU cc_start: 0.7193 (mp0) cc_final: 0.6930 (mp0) REVERT: A 338 ILE cc_start: 0.6892 (OUTLIER) cc_final: 0.6464 (tt) REVERT: C 500 THR cc_start: 0.9073 (m) cc_final: 0.8804 (m) REVERT: E 1033 VAL cc_start: 0.6304 (p) cc_final: 0.6078 (m) REVERT: E 1103 GLN cc_start: 0.3165 (OUTLIER) cc_final: 0.2170 (mp10) REVERT: E 1133 MET cc_start: 0.8392 (mmm) cc_final: 0.8188 (mmt) REVERT: E 1149 PHE cc_start: 0.6251 (OUTLIER) cc_final: 0.5866 (t80) REVERT: E 1334 LEU cc_start: 0.7538 (tt) cc_final: 0.7307 (tp) REVERT: F 1169 MET cc_start: 0.6154 (tmm) cc_final: 0.5428 (tmm) outliers start: 71 outliers final: 47 residues processed: 237 average time/residue: 0.0844 time to fit residues: 31.3165 Evaluate side-chains 239 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 188 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain D residue 415 TRP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain E residue 1023 VAL Chi-restraints excluded: chain E residue 1083 LEU Chi-restraints excluded: chain E residue 1093 ILE Chi-restraints excluded: chain E residue 1103 GLN Chi-restraints excluded: chain E residue 1142 ILE Chi-restraints excluded: chain E residue 1149 PHE Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1169 MET Chi-restraints excluded: chain E residue 1200 VAL Chi-restraints excluded: chain E residue 1212 LEU Chi-restraints excluded: chain E residue 1214 LEU Chi-restraints excluded: chain E residue 1235 ILE Chi-restraints excluded: chain E residue 1296 VAL Chi-restraints excluded: chain F residue 1073 ASN Chi-restraints excluded: chain F residue 1112 VAL Chi-restraints excluded: chain F residue 1142 ILE Chi-restraints excluded: chain F residue 1153 PHE Chi-restraints excluded: chain F residue 1204 VAL Chi-restraints excluded: chain F residue 1207 MET Chi-restraints excluded: chain F residue 1281 ILE Chi-restraints excluded: chain F residue 1307 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 79 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 144 optimal weight: 0.0570 chunk 153 optimal weight: 9.9990 chunk 136 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 131 optimal weight: 0.0980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 HIS A 187 GLN ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1147 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.140210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.107322 restraints weight = 21231.724| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.41 r_work: 0.2970 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13733 Z= 0.133 Angle : 0.631 10.131 18658 Z= 0.318 Chirality : 0.044 0.286 2248 Planarity : 0.005 0.099 2361 Dihedral : 4.903 48.597 1871 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.67 % Allowed : 6.81 % Favored : 92.52 % Rotamer: Outliers : 4.34 % Allowed : 26.21 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.21), residues: 1778 helix: 1.01 (0.17), residues: 948 sheet: -0.71 (0.48), residues: 139 loop : -1.47 (0.25), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E1356 TYR 0.011 0.001 TYR F1139 PHE 0.017 0.001 PHE F1149 TRP 0.043 0.002 TRP F1368 HIS 0.003 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (13733) covalent geometry : angle 0.63068 / 0.32 (18658) hydrogen bonds : bond 0.03767 / 2.54 ( 724) hydrogen bonds : angle 4.34704 / 3.14 ( 2082) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 199 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 ASP cc_start: 0.7084 (p0) cc_final: 0.6822 (p0) REVERT: A 189 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8579 (mt) REVERT: A 331 GLU cc_start: 0.7062 (mp0) cc_final: 0.6811 (mp0) REVERT: A 338 ILE cc_start: 0.6940 (OUTLIER) cc_final: 0.6492 (tt) REVERT: C 490 SER cc_start: 0.8785 (p) cc_final: 0.8574 (m) REVERT: C 492 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.8492 (m-40) REVERT: E 1149 PHE cc_start: 0.6329 (OUTLIER) cc_final: 0.5912 (t80) REVERT: F 1169 MET cc_start: 0.6144 (tmm) cc_final: 0.5362 (tmm) REVERT: F 1234 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7751 (m-80) outliers start: 62 outliers final: 45 residues processed: 242 average time/residue: 0.0793 time to fit residues: 30.3095 Evaluate side-chains 242 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 192 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain D residue 415 TRP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain E residue 1023 VAL Chi-restraints excluded: chain E residue 1083 LEU Chi-restraints excluded: chain E residue 1093 ILE Chi-restraints excluded: chain E residue 1142 ILE Chi-restraints excluded: chain E residue 1149 PHE Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1169 MET Chi-restraints excluded: chain E residue 1200 VAL Chi-restraints excluded: chain E residue 1212 LEU Chi-restraints excluded: chain E residue 1214 LEU Chi-restraints excluded: chain E residue 1235 ILE Chi-restraints excluded: chain E residue 1296 VAL Chi-restraints excluded: chain F residue 1073 ASN Chi-restraints excluded: chain F residue 1112 VAL Chi-restraints excluded: chain F residue 1142 ILE Chi-restraints excluded: chain F residue 1153 PHE Chi-restraints excluded: chain F residue 1190 ILE Chi-restraints excluded: chain F residue 1204 VAL Chi-restraints excluded: chain F residue 1207 MET Chi-restraints excluded: chain F residue 1234 PHE Chi-restraints excluded: chain F residue 1281 ILE Chi-restraints excluded: chain F residue 1307 VAL Chi-restraints excluded: chain F residue 1360 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 31 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 139 optimal weight: 10.0000 chunk 172 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 38 optimal weight: 0.0770 chunk 98 optimal weight: 0.5980 chunk 156 optimal weight: 0.0050 overall best weight: 0.3952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 GLN ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.140893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.105202 restraints weight = 21336.370| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.37 r_work: 0.2947 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13733 Z= 0.131 Angle : 0.626 11.143 18658 Z= 0.316 Chirality : 0.043 0.256 2248 Planarity : 0.005 0.092 2361 Dihedral : 4.817 46.517 1871 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.62 % Allowed : 6.58 % Favored : 92.80 % Rotamer: Outliers : 4.41 % Allowed : 25.93 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.21), residues: 1778 helix: 1.14 (0.17), residues: 942 sheet: -0.72 (0.48), residues: 143 loop : -1.45 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E1356 TYR 0.013 0.001 TYR F1139 PHE 0.018 0.001 PHE F1350 TRP 0.027 0.001 TRP F1368 HIS 0.004 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (13733) covalent geometry : angle 0.62573 / 0.32 (18658) hydrogen bonds : bond 0.03664 / 2.47 ( 724) hydrogen bonds : angle 4.27609 / 3.09 ( 2082) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 198 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.9113 (tpt) cc_final: 0.8421 (tpt) REVERT: A 182 ASP cc_start: 0.7025 (p0) cc_final: 0.6782 (p0) REVERT: A 184 VAL cc_start: 0.8842 (t) cc_final: 0.8635 (p) REVERT: A 189 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8565 (mt) REVERT: A 331 GLU cc_start: 0.7086 (mp0) cc_final: 0.6822 (mp0) REVERT: A 338 ILE cc_start: 0.6992 (OUTLIER) cc_final: 0.6534 (tt) REVERT: C 490 SER cc_start: 0.8788 (p) cc_final: 0.8534 (m) REVERT: C 492 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8467 (m-40) REVERT: E 1103 GLN cc_start: 0.2867 (OUTLIER) cc_final: 0.1947 (mp10) REVERT: E 1149 PHE cc_start: 0.6176 (OUTLIER) cc_final: 0.5777 (t80) REVERT: E 1271 MET cc_start: 0.7677 (mmt) cc_final: 0.7455 (mmt) REVERT: E 1349 ASP cc_start: 0.7299 (m-30) cc_final: 0.6921 (p0) REVERT: F 1169 MET cc_start: 0.5948 (tmm) cc_final: 0.5121 (tmm) REVERT: F 1234 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.8028 (m-80) outliers start: 63 outliers final: 49 residues processed: 242 average time/residue: 0.0902 time to fit residues: 33.8439 Evaluate side-chains 244 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 189 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain D residue 415 TRP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain E residue 1023 VAL Chi-restraints excluded: chain E residue 1083 LEU Chi-restraints excluded: chain E residue 1093 ILE Chi-restraints excluded: chain E residue 1103 GLN Chi-restraints excluded: chain E residue 1113 MET Chi-restraints excluded: chain E residue 1142 ILE Chi-restraints excluded: chain E residue 1149 PHE Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1169 MET Chi-restraints excluded: chain E residue 1200 VAL Chi-restraints excluded: chain E residue 1212 LEU Chi-restraints excluded: chain E residue 1214 LEU Chi-restraints excluded: chain E residue 1235 ILE Chi-restraints excluded: chain E residue 1272 VAL Chi-restraints excluded: chain E residue 1296 VAL Chi-restraints excluded: chain F residue 1073 ASN Chi-restraints excluded: chain F residue 1112 VAL Chi-restraints excluded: chain F residue 1142 ILE Chi-restraints excluded: chain F residue 1153 PHE Chi-restraints excluded: chain F residue 1190 ILE Chi-restraints excluded: chain F residue 1204 VAL Chi-restraints excluded: chain F residue 1207 MET Chi-restraints excluded: chain F residue 1234 PHE Chi-restraints excluded: chain F residue 1281 ILE Chi-restraints excluded: chain F residue 1307 VAL Chi-restraints excluded: chain F residue 1360 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 164 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 155 optimal weight: 0.0870 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.140283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.105589 restraints weight = 21244.620| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.71 r_work: 0.2900 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13733 Z= 0.149 Angle : 0.648 10.528 18658 Z= 0.324 Chirality : 0.044 0.228 2248 Planarity : 0.005 0.085 2361 Dihedral : 4.829 43.980 1871 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.69 % Favored : 92.74 % Rotamer: Outliers : 4.41 % Allowed : 26.28 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.21), residues: 1778 helix: 1.04 (0.17), residues: 953 sheet: -0.71 (0.48), residues: 143 loop : -1.36 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 334 TYR 0.014 0.002 TYR F1139 PHE 0.016 0.001 PHE F1149 TRP 0.026 0.001 TRP C 415 HIS 0.004 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (13733) covalent geometry : angle 0.64803 / 0.32 (18658) hydrogen bonds : bond 0.03767 / 2.53 ( 724) hydrogen bonds : angle 4.30889 / 3.12 ( 2082) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 197 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.9116 (tpt) cc_final: 0.8586 (tpt) REVERT: A 182 ASP cc_start: 0.7159 (p0) cc_final: 0.6907 (p0) REVERT: A 184 VAL cc_start: 0.8844 (t) cc_final: 0.8635 (p) REVERT: A 331 GLU cc_start: 0.7120 (mp0) cc_final: 0.6815 (mp0) REVERT: A 338 ILE cc_start: 0.6938 (OUTLIER) cc_final: 0.6495 (tt) REVERT: C 490 SER cc_start: 0.8809 (p) cc_final: 0.8553 (m) REVERT: D 422 LYS cc_start: 0.7909 (tptt) cc_final: 0.7587 (tptt) REVERT: E 1103 GLN cc_start: 0.2686 (OUTLIER) cc_final: 0.1840 (mp10) REVERT: E 1149 PHE cc_start: 0.6194 (OUTLIER) cc_final: 0.5841 (t80) REVERT: E 1202 GLU cc_start: 0.8151 (tp30) cc_final: 0.7920 (tp30) REVERT: E 1349 ASP cc_start: 0.7271 (m-30) cc_final: 0.6899 (p0) REVERT: F 1169 MET cc_start: 0.6025 (tmm) cc_final: 0.5200 (tmm) REVERT: F 1234 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.8211 (m-80) outliers start: 63 outliers final: 47 residues processed: 246 average time/residue: 0.0901 time to fit residues: 34.7666 Evaluate side-chains 242 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 191 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain D residue 415 TRP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain E residue 1083 LEU Chi-restraints excluded: chain E residue 1093 ILE Chi-restraints excluded: chain E residue 1103 GLN Chi-restraints excluded: chain E residue 1142 ILE Chi-restraints excluded: chain E residue 1149 PHE Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1169 MET Chi-restraints excluded: chain E residue 1200 VAL Chi-restraints excluded: chain E residue 1212 LEU Chi-restraints excluded: chain E residue 1214 LEU Chi-restraints excluded: chain E residue 1235 ILE Chi-restraints excluded: chain E residue 1272 VAL Chi-restraints excluded: chain E residue 1296 VAL Chi-restraints excluded: chain F residue 1023 VAL Chi-restraints excluded: chain F residue 1073 ASN Chi-restraints excluded: chain F residue 1112 VAL Chi-restraints excluded: chain F residue 1142 ILE Chi-restraints excluded: chain F residue 1153 PHE Chi-restraints excluded: chain F residue 1190 ILE Chi-restraints excluded: chain F residue 1204 VAL Chi-restraints excluded: chain F residue 1207 MET Chi-restraints excluded: chain F residue 1234 PHE Chi-restraints excluded: chain F residue 1281 ILE Chi-restraints excluded: chain F residue 1307 VAL Chi-restraints excluded: chain F residue 1360 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 25 optimal weight: 0.9990 chunk 134 optimal weight: 0.0020 chunk 125 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 HIS ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.140516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.103919 restraints weight = 21433.834| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.18 r_work: 0.2914 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13733 Z= 0.147 Angle : 0.649 12.726 18658 Z= 0.324 Chirality : 0.044 0.207 2248 Planarity : 0.005 0.081 2361 Dihedral : 4.818 43.074 1871 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.81 % Favored : 92.63 % Rotamer: Outliers : 4.13 % Allowed : 27.05 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.21), residues: 1778 helix: 1.11 (0.17), residues: 949 sheet: -0.66 (0.48), residues: 143 loop : -1.29 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 334 TYR 0.015 0.001 TYR F1139 PHE 0.021 0.001 PHE F1350 TRP 0.022 0.001 TRP C 415 HIS 0.004 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (13733) covalent geometry : angle 0.64899 / 0.32 (18658) hydrogen bonds : bond 0.03733 / 2.51 ( 724) hydrogen bonds : angle 4.30706 / 3.11 ( 2082) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 192 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.9153 (tpt) cc_final: 0.8650 (tpt) REVERT: A 182 ASP cc_start: 0.7547 (p0) cc_final: 0.7308 (p0) REVERT: A 184 VAL cc_start: 0.8869 (t) cc_final: 0.8656 (p) REVERT: A 331 GLU cc_start: 0.7376 (mp0) cc_final: 0.7094 (mp0) REVERT: A 338 ILE cc_start: 0.7021 (OUTLIER) cc_final: 0.6551 (tt) REVERT: C 490 SER cc_start: 0.8907 (p) cc_final: 0.8629 (m) REVERT: C 492 ASN cc_start: 0.8806 (OUTLIER) cc_final: 0.8563 (m-40) REVERT: D 422 LYS cc_start: 0.8123 (tptt) cc_final: 0.7789 (tptp) REVERT: E 1033 VAL cc_start: 0.6211 (p) cc_final: 0.5972 (m) REVERT: E 1092 PHE cc_start: 0.7662 (OUTLIER) cc_final: 0.7096 (m-80) REVERT: E 1103 GLN cc_start: 0.2999 (OUTLIER) cc_final: 0.2019 (mp10) REVERT: E 1135 ASN cc_start: 0.7795 (t0) cc_final: 0.7517 (t0) REVERT: E 1149 PHE cc_start: 0.6245 (OUTLIER) cc_final: 0.5867 (t80) REVERT: E 1202 GLU cc_start: 0.8270 (tp30) cc_final: 0.8011 (tp30) REVERT: E 1271 MET cc_start: 0.7939 (mmt) cc_final: 0.7449 (mtp) REVERT: E 1349 ASP cc_start: 0.7306 (m-30) cc_final: 0.6946 (p0) REVERT: F 1169 MET cc_start: 0.6033 (tmm) cc_final: 0.5327 (tmm) REVERT: F 1234 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.8233 (m-80) outliers start: 59 outliers final: 48 residues processed: 238 average time/residue: 0.0780 time to fit residues: 29.0044 Evaluate side-chains 240 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 186 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain D residue 415 TRP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain E residue 1083 LEU Chi-restraints excluded: chain E residue 1092 PHE Chi-restraints excluded: chain E residue 1093 ILE Chi-restraints excluded: chain E residue 1103 GLN Chi-restraints excluded: chain E residue 1142 ILE Chi-restraints excluded: chain E residue 1149 PHE Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1169 MET Chi-restraints excluded: chain E residue 1200 VAL Chi-restraints excluded: chain E residue 1212 LEU Chi-restraints excluded: chain E residue 1214 LEU Chi-restraints excluded: chain E residue 1235 ILE Chi-restraints excluded: chain E residue 1296 VAL Chi-restraints excluded: chain E residue 1358 VAL Chi-restraints excluded: chain F residue 1023 VAL Chi-restraints excluded: chain F residue 1073 ASN Chi-restraints excluded: chain F residue 1112 VAL Chi-restraints excluded: chain F residue 1142 ILE Chi-restraints excluded: chain F residue 1153 PHE Chi-restraints excluded: chain F residue 1158 THR Chi-restraints excluded: chain F residue 1190 ILE Chi-restraints excluded: chain F residue 1204 VAL Chi-restraints excluded: chain F residue 1207 MET Chi-restraints excluded: chain F residue 1234 PHE Chi-restraints excluded: chain F residue 1281 ILE Chi-restraints excluded: chain F residue 1307 VAL Chi-restraints excluded: chain F residue 1360 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 50 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 139 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 102 optimal weight: 0.5980 chunk 36 optimal weight: 0.3980 chunk 163 optimal weight: 6.9990 chunk 27 optimal weight: 0.0470 chunk 44 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.141090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.106213 restraints weight = 21202.150| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.84 r_work: 0.2926 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13733 Z= 0.136 Angle : 0.648 12.910 18658 Z= 0.324 Chirality : 0.044 0.206 2248 Planarity : 0.005 0.078 2361 Dihedral : 4.749 41.364 1871 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.02 % Favored : 93.42 % Rotamer: Outliers : 4.06 % Allowed : 27.19 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.21), residues: 1778 helix: 1.15 (0.17), residues: 953 sheet: -0.61 (0.48), residues: 143 loop : -1.27 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1197 TYR 0.013 0.001 TYR F1139 PHE 0.017 0.001 PHE E1194 TRP 0.023 0.001 TRP C 415 HIS 0.005 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (13733) covalent geometry : angle 0.64830 / 0.32 (18658) hydrogen bonds : bond 0.03647 / 2.45 ( 724) hydrogen bonds : angle 4.24904 / 3.07 ( 2082) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 194 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 ASP cc_start: 0.7136 (p0) cc_final: 0.6894 (p0) REVERT: A 184 VAL cc_start: 0.8847 (t) cc_final: 0.8643 (p) REVERT: A 331 GLU cc_start: 0.7084 (mp0) cc_final: 0.6780 (mp0) REVERT: A 338 ILE cc_start: 0.6926 (OUTLIER) cc_final: 0.6488 (tt) REVERT: C 492 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8478 (m-40) REVERT: D 422 LYS cc_start: 0.7779 (tptt) cc_final: 0.7453 (tptp) REVERT: E 1033 VAL cc_start: 0.6051 (p) cc_final: 0.5823 (m) REVERT: E 1092 PHE cc_start: 0.7707 (OUTLIER) cc_final: 0.7164 (m-10) REVERT: E 1103 GLN cc_start: 0.2847 (OUTLIER) cc_final: 0.1920 (mp10) REVERT: E 1135 ASN cc_start: 0.7699 (t0) cc_final: 0.7445 (t0) REVERT: E 1149 PHE cc_start: 0.6184 (OUTLIER) cc_final: 0.5820 (t80) REVERT: E 1271 MET cc_start: 0.7877 (mmt) cc_final: 0.7403 (mtp) REVERT: E 1349 ASP cc_start: 0.7237 (m-30) cc_final: 0.6901 (p0) REVERT: F 1169 MET cc_start: 0.5924 (tmm) cc_final: 0.5222 (tmm) REVERT: F 1234 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.8240 (m-80) outliers start: 58 outliers final: 49 residues processed: 236 average time/residue: 0.0815 time to fit residues: 29.9653 Evaluate side-chains 244 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 189 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain D residue 415 TRP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain E residue 1083 LEU Chi-restraints excluded: chain E residue 1092 PHE Chi-restraints excluded: chain E residue 1093 ILE Chi-restraints excluded: chain E residue 1103 GLN Chi-restraints excluded: chain E residue 1142 ILE Chi-restraints excluded: chain E residue 1149 PHE Chi-restraints excluded: chain E residue 1153 PHE Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1169 MET Chi-restraints excluded: chain E residue 1212 LEU Chi-restraints excluded: chain E residue 1214 LEU Chi-restraints excluded: chain E residue 1235 ILE Chi-restraints excluded: chain E residue 1272 VAL Chi-restraints excluded: chain E residue 1296 VAL Chi-restraints excluded: chain E residue 1358 VAL Chi-restraints excluded: chain F residue 1023 VAL Chi-restraints excluded: chain F residue 1073 ASN Chi-restraints excluded: chain F residue 1112 VAL Chi-restraints excluded: chain F residue 1142 ILE Chi-restraints excluded: chain F residue 1153 PHE Chi-restraints excluded: chain F residue 1156 GLN Chi-restraints excluded: chain F residue 1190 ILE Chi-restraints excluded: chain F residue 1204 VAL Chi-restraints excluded: chain F residue 1234 PHE Chi-restraints excluded: chain F residue 1281 ILE Chi-restraints excluded: chain F residue 1307 VAL Chi-restraints excluded: chain F residue 1360 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 141 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 31 optimal weight: 0.2980 chunk 35 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 115 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 HIS ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.140552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.105414 restraints weight = 21357.732| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.70 r_work: 0.2901 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13733 Z= 0.159 Angle : 0.668 15.311 18658 Z= 0.333 Chirality : 0.044 0.206 2248 Planarity : 0.005 0.076 2361 Dihedral : 4.776 41.466 1871 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.64 % Favored : 92.80 % Rotamer: Outliers : 3.92 % Allowed : 27.47 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.21), residues: 1778 helix: 1.11 (0.17), residues: 951 sheet: -0.62 (0.48), residues: 143 loop : -1.28 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 334 TYR 0.015 0.002 TYR F1139 PHE 0.020 0.001 PHE F1350 TRP 0.019 0.001 TRP C 415 HIS 0.005 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (13733) covalent geometry : angle 0.66779 / 0.33 (18658) hydrogen bonds : bond 0.03705 / 2.48 ( 724) hydrogen bonds : angle 4.27468 / 3.09 ( 2082) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2567.60 seconds wall clock time: 44 minutes 49.36 seconds (2689.36 seconds total)