Starting phenix.real_space_refine on Thu Aug 6 05:24:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uva_64529/08_2026/9uva_64529.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uva_64529/08_2026/9uva_64529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uva_64529/08_2026/9uva_64529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uva_64529/08_2026/9uva_64529.map" model { file = "/net/cci-nas-00/data/ceres_data/9uva_64529/08_2026/9uva_64529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uva_64529/08_2026/9uva_64529.cif" } resolution = 3.73 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= -0.000 sd= 0.010 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 74 5.16 5 C 8508 2.51 5 N 2200 2.21 5 O 2395 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 13177 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2943 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 383} Chain breaks: 3 Chain: "A" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3304 Classifications: {'peptide': 444} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 427} Chain breaks: 1 Chain: "C" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 730 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} 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: 2.76, per 1000 atoms: 0.21 Number of scatterers: 13177 At special positions: 0 Unit cell: (125.46, 97.58, 139.4, 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 74 16.00 O 2395 8.00 N 2200 7.00 C 8508 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: 1.02 Conformation dependent library (CDL) restraints added in 451.8 milliseconds 3478 Ramachandran restraints generated. 1739 Oldfield, 0 Emsley, 1739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3212 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 8 sheets defined 58.0% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'B' and resid 4 through 23 Processing helix chain 'B' and resid 29 through 50 removed outlier: 3.751A pdb=" N GLY B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 78 Processing helix chain 'B' and resid 82 through 108 Processing helix chain 'B' and resid 114 through 148 removed outlier: 3.680A pdb=" N CYS B 147 " --> pdb=" O PHE B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 181 Processing helix chain 'B' and resid 183 through 209 Processing helix chain 'B' and resid 213 through 237 Processing helix chain 'B' and resid 238 through 263 Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'B' and resid 295 through 306 Processing helix chain 'B' and resid 325 through 337 removed outlier: 3.534A pdb=" N GLY B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 462 removed outlier: 3.598A pdb=" N SER B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 24 Processing helix chain 'A' and resid 25 through 28 removed outlier: 7.206A pdb=" N GLU A 28 " --> pdb=" O SER A 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 25 through 28' Processing helix chain 'A' and resid 29 through 48 removed outlier: 4.193A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A 47 " --> pdb=" O ILE A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 78 removed outlier: 4.096A pdb=" N ALA A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 108 Processing helix chain 'A' and resid 114 through 147 removed outlier: 4.043A pdb=" N VAL A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 181 Processing helix chain 'A' and resid 183 through 209 Processing helix chain 'A' and resid 213 through 237 Processing helix chain 'A' and resid 238 through 263 removed outlier: 3.934A pdb=" N ILE A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 272 Processing helix chain 'A' and resid 297 through 305 removed outlier: 4.024A pdb=" N GLU A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 334 removed outlier: 3.931A pdb=" N VAL A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 Processing helix chain 'A' and resid 375 through 379 removed outlier: 4.002A pdb=" N PHE A 379 " --> pdb=" O ASN A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 removed outlier: 4.011A pdb=" N PHE A 439 " --> pdb=" O ASN A 436 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 440 " --> pdb=" O PRO A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 458 removed outlier: 3.870A pdb=" N ALA A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 417 removed outlier: 3.613A pdb=" N ALA C 417 " --> pdb=" O GLY C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 442 removed outlier: 3.503A pdb=" N TYR C 440 " --> pdb=" O VAL C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 450 Processing helix chain 'C' and resid 451 through 462 Processing helix chain 'C' and resid 464 through 471 Processing helix chain 'C' and resid 476 through 505 Processing helix chain 'D' and resid 411 through 417 removed outlier: 4.248A pdb=" N ALA D 417 " --> pdb=" O GLY D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 442 Processing helix chain 'D' and resid 446 through 461 Proline residue: D 452 - end of helix Processing helix chain 'D' and resid 464 through 472 Processing helix chain 'D' and resid 475 through 505 removed outlier: 4.875A pdb=" N THR D 498 " --> pdb=" O PHE D 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 1019 through 1030 removed outlier: 3.687A pdb=" N GLY E1030 " --> pdb=" O LEU E1026 " (cutoff:3.500A) Processing helix chain 'E' and resid 1046 through 1054 removed outlier: 3.509A pdb=" N PHE E1050 " --> pdb=" O ASP E1046 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL E1051 " --> pdb=" O ASP E1047 " (cutoff:3.500A) Processing helix chain 'E' and resid 1059 through 1064 removed outlier: 3.751A pdb=" N VAL E1063 " --> pdb=" O GLY E1060 " (cutoff:3.500A) Processing helix chain 'E' and resid 1098 through 1107 removed outlier: 3.843A pdb=" N MET E1102 " --> pdb=" O ASN E1098 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN E1103 " --> pdb=" O PRO E1099 " (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: 3.702A pdb=" N SER E1132 " --> pdb=" O ASP E1128 " (cutoff:3.500A) Processing helix chain 'E' and resid 1174 through 1188 removed outlier: 4.557A pdb=" N ALA E1179 " --> pdb=" O VAL E1175 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA E1180 " --> pdb=" O ALA E1176 " (cutoff:3.500A) Processing helix chain 'E' and resid 1201 through 1206 Processing helix chain 'E' and resid 1226 through 1231 Processing helix chain 'E' and resid 1231 through 1247 removed outlier: 3.551A pdb=" N ILE E1235 " --> pdb=" O SER E1231 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS E1247 " --> pdb=" O ALA E1243 " (cutoff:3.500A) Processing helix chain 'E' and resid 1268 through 1275 removed outlier: 3.536A pdb=" N VAL E1272 " --> pdb=" O THR E1268 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP E1273 " --> pdb=" O ARG E1269 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N MET E1275 " --> pdb=" O MET E1271 " (cutoff:3.500A) Processing helix chain 'E' and resid 1285 through 1289 removed outlier: 3.808A 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 1321 through 1339 removed outlier: 3.503A pdb=" N CYS E1339 " --> pdb=" O LEU E1335 " (cutoff:3.500A) Processing helix chain 'E' and resid 1353 through 1359 removed outlier: 3.511A pdb=" N VAL E1358 " --> pdb=" O VAL E1354 " (cutoff:3.500A) Processing helix chain 'F' and resid 1019 through 1030 removed outlier: 3.521A pdb=" N GLN F1025 " --> pdb=" O LYS F1021 " (cutoff:3.500A) Processing helix chain 'F' and resid 1038 through 1043 removed outlier: 4.333A 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 Processing helix chain 'F' and resid 1077 through 1083 removed outlier: 3.789A pdb=" N LEU F1083 " --> pdb=" O ILE F1080 " (cutoff:3.500A) Processing helix chain 'F' and resid 1098 through 1107 removed outlier: 3.770A pdb=" N MET F1102 " --> pdb=" O ASN F1098 " (cutoff:3.500A) removed outlier: 3.726A 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 removed outlier: 3.536A pdb=" N GLN F1205 " --> pdb=" O LYS F1201 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET F1207 " --> pdb=" O GLN F1203 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY F1208 " --> pdb=" O VAL F1204 " (cutoff:3.500A) Processing helix chain 'F' and resid 1244 through 1249 removed outlier: 3.619A pdb=" N GLU F1248 " --> pdb=" O ALA F1244 " (cutoff:3.500A) Processing helix chain 'F' and resid 1268 through 1275 removed outlier: 3.637A pdb=" N VAL F1272 " --> pdb=" O THR F1268 " (cutoff:3.500A) Processing helix chain 'F' and resid 1319 through 1340 removed outlier: 3.824A pdb=" N TYR F1327 " --> pdb=" O SER F1323 " (cutoff:3.500A) Processing helix chain 'F' and resid 1352 through 1359 removed outlier: 3.621A pdb=" N ARG F1356 " --> pdb=" O ASP F1352 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 292 through 293 removed outlier: 8.364A pdb=" N ARG B 292 " --> pdb=" O MET B 446 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B 420 " --> pdb=" O HIS B 445 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 340 through 341 removed outlier: 3.679A pdb=" N LEU B 386 " --> pdb=" O ILE B 310 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 339 through 342 removed outlier: 3.710A pdb=" N ARG A 341 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N THR A 384 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 310 " --> pdb=" O THR A 384 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 386 " --> pdb=" O ILE A 310 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 1056 through 1058 removed outlier: 8.076A pdb=" N VAL E1033 " --> pdb=" O GLU E1056 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N VAL E1058 " --> pdb=" O VAL E1033 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL E1035 " --> pdb=" O VAL E1058 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE E1005 " --> pdb=" O ALA E1034 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU E1036 " --> pdb=" O ILE E1005 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ARG E1002 " --> pdb=" O ILE E1068 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N LEU E1070 " --> pdb=" O ARG E1002 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N GLY E1004 " --> pdb=" O LEU E1070 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N VAL E1072 " --> pdb=" O GLY E1004 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE E1092 " --> pdb=" O LYS E1071 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASN E1073 " --> pdb=" O PHE E1092 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 1209 through 1211 removed outlier: 6.776A pdb=" N VAL E1191 " --> pdb=" O GLU E1210 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL E1168 " --> pdb=" O ARG E1192 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N PHE E1194 " --> pdb=" O VAL E1168 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL E1170 " --> pdb=" O PHE E1194 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS E1167 " --> pdb=" O ILE E1251 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N VAL E1253 " --> pdb=" O LYS E1167 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N MET E1169 " --> pdb=" O VAL E1253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 1361 through 1362 Processing sheet with id=AA7, first strand: chain 'F' and resid 1003 through 1004 removed outlier: 6.439A pdb=" N GLY F1004 " --> pdb=" O LEU F1070 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET F1113 " --> pdb=" O LEU F1089 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER F1091 " --> pdb=" O MET F1113 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 1210 through 1211 removed outlier: 5.717A pdb=" N VAL F1168 " --> pdb=" O ARG F1192 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N PHE F1194 " --> pdb=" O VAL F1168 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N VAL F1170 " --> pdb=" O PHE F1194 " (cutoff:3.500A) removed outlier: 5.985A 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) 723 hydrogen bonds defined for protein. 2097 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: 1.72 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3487 1.33 - 1.45: 2252 1.45 - 1.58: 7540 1.58 - 1.70: 1 1.70 - 1.82: 138 Bond restraints: 13418 Sorted by residual: bond pdb=" C MET B 214 " pdb=" N PRO B 215 " ideal model delta sigma weight residual 1.335 1.364 -0.029 1.30e-02 5.92e+03 4.92e+00 bond pdb=" CG1 ILE C 493 " pdb=" CD1 ILE C 493 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.70e+00 bond pdb=" CG MET C 503 " pdb=" SD MET C 503 " ideal model delta sigma weight residual 1.803 1.752 0.051 2.50e-02 1.60e+03 4.20e+00 bond pdb=" SD MET A 214 " pdb=" CE MET A 214 " ideal model delta sigma weight residual 1.791 1.741 0.050 2.50e-02 1.60e+03 3.99e+00 bond pdb=" CA ASP B 400 " pdb=" C ASP B 400 " ideal model delta sigma weight residual 1.523 1.546 -0.023 1.34e-02 5.57e+03 2.97e+00 ... (remaining 13413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 17848 2.93 - 5.86: 327 5.86 - 8.79: 41 8.79 - 11.71: 10 11.71 - 14.64: 5 Bond angle restraints: 18231 Sorted by residual: angle pdb=" C SER B 152 " pdb=" N LYS B 153 " pdb=" CA LYS B 153 " ideal model delta sigma weight residual 120.65 132.17 -11.52 1.36e+00 5.41e-01 7.17e+01 angle pdb=" N PRO A 402 " pdb=" CA PRO A 402 " pdb=" C PRO A 402 " ideal model delta sigma weight residual 112.47 125.60 -13.13 2.06e+00 2.36e-01 4.06e+01 angle pdb=" CA SER A 208 " pdb=" C SER A 208 " pdb=" N ILE A 209 " ideal model delta sigma weight residual 117.96 126.92 -8.96 1.51e+00 4.39e-01 3.52e+01 angle pdb=" N GLY A 202 " pdb=" CA GLY A 202 " pdb=" C GLY A 202 " ideal model delta sigma weight residual 112.73 106.25 6.48 1.20e+00 6.94e-01 2.92e+01 angle pdb=" O GLY D 495 " pdb=" C GLY D 495 " pdb=" N GLY D 496 " ideal model delta sigma weight residual 121.85 124.71 -2.86 5.60e-01 3.19e+00 2.61e+01 ... (remaining 18226 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 7197 17.79 - 35.58: 638 35.58 - 53.38: 103 53.38 - 71.17: 13 71.17 - 88.96: 8 Dihedral angle restraints: 7959 sinusoidal: 2969 harmonic: 4990 Sorted by residual: dihedral pdb=" CA PRO A 402 " pdb=" C PRO A 402 " pdb=" N LYS A 403 " pdb=" CA LYS A 403 " ideal model delta harmonic sigma weight residual -180.00 -130.01 -49.99 0 5.00e+00 4.00e-02 1.00e+02 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 -136.34 -43.66 0 5.00e+00 4.00e-02 7.63e+01 dihedral pdb=" CA PRO B 402 " pdb=" C PRO B 402 " pdb=" N LYS B 403 " pdb=" CA LYS B 403 " ideal model delta harmonic sigma weight residual -180.00 -139.76 -40.24 0 5.00e+00 4.00e-02 6.48e+01 ... (remaining 7956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2022 0.093 - 0.185: 165 0.185 - 0.278: 11 0.278 - 0.370: 2 0.370 - 0.463: 2 Chirality restraints: 2202 Sorted by residual: chirality pdb=" CB VAL C 499 " pdb=" CA VAL C 499 " pdb=" CG1 VAL C 499 " pdb=" CG2 VAL C 499 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CG LEU A 146 " pdb=" CB LEU A 146 " pdb=" CD1 LEU A 146 " pdb=" CD2 LEU A 146 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" CA PRO A 402 " pdb=" N PRO A 402 " pdb=" C PRO A 402 " pdb=" CB PRO A 402 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 2199 not shown) Planarity restraints: 2303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP F1368 " 0.064 5.00e-02 4.00e+02 9.82e-02 1.54e+01 pdb=" N PRO F1369 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO F1369 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO F1369 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 154 " -0.019 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C PRO B 154 " 0.065 2.00e-02 2.50e+03 pdb=" O PRO B 154 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU B 155 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 206 " -0.019 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C VAL A 206 " 0.064 2.00e-02 2.50e+03 pdb=" O VAL A 206 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA A 207 " -0.021 2.00e-02 2.50e+03 ... (remaining 2300 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 294 2.64 - 3.21: 13974 3.21 - 3.77: 22257 3.77 - 4.34: 29980 4.34 - 4.90: 46141 Nonbonded interactions: 112646 Sorted by model distance: nonbonded pdb=" OD1 ASP F1047 " pdb=" NZ LYS F1048 " model vdw 2.078 3.120 nonbonded pdb=" O LYS B 153 " pdb=" N ASP B 401 " model vdw 2.081 3.120 nonbonded pdb=" O LYS E1071 " pdb=" OH TYR E1327 " model vdw 2.105 3.040 nonbonded pdb=" OG1 THR E1154 " pdb=" O LEU E1187 " model vdw 2.121 3.040 nonbonded pdb=" O ILE B 89 " pdb=" OG SER B 92 " model vdw 2.123 3.040 ... (remaining 112641 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' and (resid 1 through 312 or resid 324 through 342 or resid 380 throug \ h 462)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 411 through 506) } 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 group one per residue 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: 4.490 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.530 Find NCS groups from input model: 0.360 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: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1338 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 : 0.004 0.085 13418 Z= 0.212 Angle : 0.990 14.643 18231 Z= 0.570 Chirality : 0.054 0.463 2202 Planarity : 0.007 0.098 2303 Dihedral : 13.688 88.959 4747 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 28.60 Ramachandran Plot: Outliers : 1.15 % Allowed : 12.19 % Favored : 86.66 % Rotamer: Outliers : 0.07 % Allowed : 0.07 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.36 % 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: -1.99 (0.20), residues: 1739 helix: -0.38 (0.17), residues: 895 sheet: -1.75 (0.46), residues: 118 loop : -2.44 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 502 TYR 0.034 0.002 TYR B 224 PHE 0.051 0.003 PHE B 17 TRP 0.021 0.002 TRP C 415 HIS 0.021 0.002 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.21 (13418) covalent geometry : angle 0.98953 / 0.57 (18231) hydrogen bonds : bond 0.14492 / 9.74 ( 723) hydrogen bonds : angle 6.45737 / 4.75 ( 2097) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3478 Ramachandran restraints generated. 1739 Oldfield, 0 Emsley, 1739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3478 Ramachandran restraints generated. 1739 Oldfield, 0 Emsley, 1739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 239 ASP cc_start: 0.1423 (m-30) cc_final: 0.1073 (m-30) REVERT: B 263 MET cc_start: 0.3201 (ptt) cc_final: 0.2281 (ptt) REVERT: B 264 ASN cc_start: 0.5246 (t0) cc_final: 0.4311 (p0) REVERT: B 415 TRP cc_start: 0.1399 (t60) cc_final: 0.0823 (t60) REVERT: A 106 TYR cc_start: 0.2234 (t80) cc_final: 0.2033 (t80) REVERT: A 195 THR cc_start: 0.1736 (p) cc_final: 0.0721 (m) REVERT: A 199 LEU cc_start: 0.2419 (mt) cc_final: 0.2206 (mt) REVERT: F 1113 MET cc_start: -0.2469 (ppp) cc_final: -0.3187 (pmm) REVERT: F 1133 MET cc_start: 0.2190 (mmp) cc_final: 0.1163 (mmt) REVERT: F 1275 MET cc_start: -0.1351 (ppp) cc_final: -0.1802 (ptm) REVERT: F 1331 LEU cc_start: 0.5323 (mt) cc_final: 0.4542 (mt) outliers start: 1 outliers final: 0 residues processed: 168 average time/residue: 0.0995 time to fit residues: 25.1525 Evaluate side-chains 125 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 0.1980 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.2980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 HIS B 187 GLN B 222 ASN B 435 GLN A 34 ASN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 427 HIS D 458 ASN ** D 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1205 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5576 r_free = 0.5576 target = 0.246979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5011 r_free = 0.5011 target = 0.164859 restraints weight = 24146.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5045 r_free = 0.5045 target = 0.167798 restraints weight = 16381.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.5067 r_free = 0.5067 target = 0.170235 restraints weight = 11837.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.5089 r_free = 0.5089 target = 0.171816 restraints weight = 9417.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.5100 r_free = 0.5100 target = 0.173206 restraints weight = 6945.170| |-----------------------------------------------------------------------------| r_work (final): 0.4664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2418 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13418 Z= 0.187 Angle : 0.838 11.553 18231 Z= 0.432 Chirality : 0.050 0.296 2202 Planarity : 0.006 0.092 2303 Dihedral : 6.310 44.079 1833 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 1.04 % Allowed : 10.41 % Favored : 88.56 % Rotamer: Outliers : 1.29 % Allowed : 8.97 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.36 % 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: -1.99 (0.20), residues: 1739 helix: -0.32 (0.16), residues: 943 sheet: -1.87 (0.45), residues: 110 loop : -2.63 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 350 TYR 0.031 0.002 TYR B 10 PHE 0.038 0.002 PHE D 497 TRP 0.012 0.001 TRP A 203 HIS 0.015 0.002 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 (13418) covalent geometry : angle 0.83832 / 0.43 (18231) hydrogen bonds : bond 0.05383 / 3.62 ( 723) hydrogen bonds : angle 5.58207 / 4.08 ( 2097) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3478 Ramachandran restraints generated. 1739 Oldfield, 0 Emsley, 1739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3478 Ramachandran restraints generated. 1739 Oldfield, 0 Emsley, 1739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: -0.1209 (OUTLIER) cc_final: -0.1615 (ptm) REVERT: B 41 MET cc_start: 0.0784 (ptp) cc_final: 0.0466 (mtp) REVERT: B 263 MET cc_start: 0.1895 (ptt) cc_final: 0.1501 (ptt) REVERT: B 264 ASN cc_start: 0.5206 (t0) cc_final: 0.4371 (p0) REVERT: B 415 TRP cc_start: 0.0170 (t60) cc_final: -0.0354 (t60) REVERT: A 83 MET cc_start: 0.4742 (mtt) cc_final: 0.4036 (mtm) REVERT: A 195 THR cc_start: 0.2559 (p) cc_final: 0.0586 (m) REVERT: D 423 GLU cc_start: 0.6659 (mp0) cc_final: 0.6193 (tt0) REVERT: E 1102 MET cc_start: -0.2701 (mpp) cc_final: -0.3103 (mtt) REVERT: F 1102 MET cc_start: 0.1481 (tmm) cc_final: 0.1130 (ttt) REVERT: F 1115 MET cc_start: 0.0302 (mmm) cc_final: -0.0746 (mmm) REVERT: F 1133 MET cc_start: 0.3027 (mmp) cc_final: 0.2519 (mmt) REVERT: F 1327 TYR cc_start: 0.2281 (t80) cc_final: 0.2008 (t80) outliers start: 18 outliers final: 6 residues processed: 141 average time/residue: 0.0889 time to fit residues: 19.8390 Evaluate side-chains 124 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 491 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 122 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 36 optimal weight: 0.0670 chunk 95 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 162 optimal weight: 20.0000 overall best weight: 1.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 ASN ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1322 GLN E1330 ASN F1330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5613 r_free = 0.5613 target = 0.245838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5045 r_free = 0.5045 target = 0.163828 restraints weight = 24728.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.5086 r_free = 0.5086 target = 0.166569 restraints weight = 17212.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5104 r_free = 0.5104 target = 0.168690 restraints weight = 13310.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.5122 r_free = 0.5122 target = 0.170010 restraints weight = 10577.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.5144 r_free = 0.5144 target = 0.172131 restraints weight = 8414.640| |-----------------------------------------------------------------------------| r_work (final): 0.4711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2889 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13418 Z= 0.196 Angle : 0.803 11.581 18231 Z= 0.414 Chirality : 0.049 0.312 2202 Planarity : 0.006 0.084 2303 Dihedral : 6.144 43.556 1833 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.98 % Allowed : 9.43 % Favored : 89.59 % Rotamer: Outliers : 3.23 % Allowed : 11.13 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.30 % 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: -1.92 (0.19), residues: 1739 helix: -0.32 (0.16), residues: 939 sheet: -1.42 (0.48), residues: 107 loop : -2.60 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 31 TYR 0.031 0.002 TYR B 106 PHE 0.023 0.002 PHE B 103 TRP 0.015 0.001 TRP C 477 HIS 0.014 0.002 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.20 (13418) covalent geometry : angle 0.80278 / 0.41 (18231) hydrogen bonds : bond 0.04971 / 3.39 ( 723) hydrogen bonds : angle 5.34169 / 3.89 ( 2097) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3478 Ramachandran restraints generated. 1739 Oldfield, 0 Emsley, 1739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3478 Ramachandran restraints generated. 1739 Oldfield, 0 Emsley, 1739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 117 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: -0.0646 (OUTLIER) cc_final: -0.2052 (ppp) REVERT: B 41 MET cc_start: 0.1265 (ptp) cc_final: 0.0739 (mtp) REVERT: B 113 MET cc_start: 0.3912 (OUTLIER) cc_final: 0.3347 (ptt) REVERT: B 263 MET cc_start: 0.2155 (ptt) cc_final: 0.1596 (ptt) REVERT: B 264 ASN cc_start: 0.5689 (t0) cc_final: 0.4887 (p0) REVERT: B 403 LYS cc_start: -0.2517 (OUTLIER) cc_final: -0.3656 (mtmm) REVERT: A 1 MET cc_start: 0.3987 (pmm) cc_final: 0.2841 (mmm) REVERT: A 83 MET cc_start: 0.4279 (mtt) cc_final: 0.3948 (mtp) REVERT: A 113 MET cc_start: 0.6676 (pmm) cc_final: 0.6248 (pmm) REVERT: A 446 MET cc_start: -0.0341 (mmm) cc_final: -0.0672 (mmt) REVERT: E 1102 MET cc_start: -0.2519 (mpp) cc_final: -0.2919 (mtt) REVERT: E 1330 ASN cc_start: -0.0267 (OUTLIER) cc_final: -0.0546 (t0) REVERT: F 1113 MET cc_start: -0.4234 (pmm) cc_final: -0.4552 (pmm) REVERT: F 1133 MET cc_start: 0.3455 (mmp) cc_final: 0.3148 (mmt) outliers start: 45 outliers final: 21 residues processed: 154 average time/residue: 0.0809 time to fit residues: 20.0635 Evaluate side-chains 132 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 403 LYS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain E residue 1088 THR Chi-restraints excluded: chain E residue 1154 THR Chi-restraints excluded: chain E residue 1170 VAL Chi-restraints excluded: chain E residue 1330 ASN Chi-restraints excluded: chain E residue 1334 LEU Chi-restraints excluded: chain F residue 1072 VAL Chi-restraints excluded: chain F residue 1321 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 99 optimal weight: 0.7980 chunk 121 optimal weight: 20.0000 chunk 4 optimal weight: 0.7980 chunk 98 optimal weight: 0.0010 chunk 113 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 134 optimal weight: 20.0000 chunk 54 optimal weight: 0.0040 chunk 5 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 HIS ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1084 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5601 r_free = 0.5601 target = 0.248415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5043 r_free = 0.5043 target = 0.167994 restraints weight = 24218.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5089 r_free = 0.5089 target = 0.170679 restraints weight = 17467.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.5114 r_free = 0.5114 target = 0.172642 restraints weight = 12732.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.5136 r_free = 0.5136 target = 0.174092 restraints weight = 10110.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.5150 r_free = 0.5150 target = 0.175649 restraints weight = 7688.928| |-----------------------------------------------------------------------------| r_work (final): 0.4732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2779 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 13418 Z= 0.152 Angle : 0.742 12.661 18231 Z= 0.380 Chirality : 0.046 0.266 2202 Planarity : 0.006 0.081 2303 Dihedral : 5.936 45.567 1833 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.81 % Allowed : 9.83 % Favored : 89.36 % Rotamer: Outliers : 2.23 % Allowed : 13.71 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.36 % 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: -1.46 (0.20), residues: 1739 helix: 0.20 (0.17), residues: 929 sheet: -1.45 (0.47), residues: 111 loop : -2.52 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 265 TYR 0.030 0.002 TYR E1327 PHE 0.021 0.002 PHE C 497 TRP 0.016 0.001 TRP F1368 HIS 0.007 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (13418) covalent geometry : angle 0.74180 / 0.38 (18231) hydrogen bonds : bond 0.04504 / 3.07 ( 723) hydrogen bonds : angle 5.04062 / 3.69 ( 2097) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3478 Ramachandran restraints generated. 1739 Oldfield, 0 Emsley, 1739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3478 Ramachandran restraints generated. 1739 Oldfield, 0 Emsley, 1739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: -0.0657 (OUTLIER) cc_final: -0.1980 (ppp) REVERT: B 41 MET cc_start: 0.1158 (ptp) cc_final: 0.0468 (mtp) REVERT: B 263 MET cc_start: 0.2131 (ptt) cc_final: 0.1395 (ptt) REVERT: B 264 ASN cc_start: 0.5741 (t0) cc_final: 0.4953 (p0) REVERT: B 403 LYS cc_start: -0.2836 (OUTLIER) cc_final: -0.3833 (mtmm) REVERT: B 427 MET cc_start: -0.2978 (mtt) cc_final: -0.3297 (mtm) REVERT: A 1 MET cc_start: 0.4026 (pmm) cc_final: 0.2965 (mmm) REVERT: A 10 TYR cc_start: 0.4609 (m-10) cc_final: 0.4343 (m-80) REVERT: A 83 MET cc_start: 0.4423 (mtt) cc_final: 0.4104 (mtp) REVERT: A 113 MET cc_start: 0.6812 (pmm) cc_final: 0.6506 (pmm) REVERT: A 446 MET cc_start: -0.0720 (mmm) cc_final: -0.1100 (mmt) REVERT: E 1102 MET cc_start: -0.2836 (mpp) cc_final: -0.3377 (mtt) REVERT: E 1115 MET cc_start: -0.0722 (mtt) cc_final: -0.1954 (ttm) REVERT: E 1133 MET cc_start: 0.4523 (mmm) cc_final: 0.4024 (ppp) REVERT: F 1133 MET cc_start: 0.3321 (mmp) cc_final: 0.2880 (mmt) outliers start: 31 outliers final: 17 residues processed: 135 average time/residue: 0.0730 time to fit residues: 16.1565 Evaluate side-chains 125 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 403 LYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 443 TRP Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain E residue 1005 ILE Chi-restraints excluded: chain E residue 1023 VAL Chi-restraints excluded: chain E residue 1154 THR Chi-restraints excluded: chain E residue 1170 VAL Chi-restraints excluded: chain E residue 1229 VAL Chi-restraints excluded: chain F residue 1072 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 163 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 135 optimal weight: 30.0000 chunk 70 optimal weight: 20.0000 chunk 119 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 153 optimal weight: 6.9990 chunk 171 optimal weight: 20.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 222 ASN ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN A 391 ASN A 436 ASN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1330 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5594 r_free = 0.5594 target = 0.241175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.5040 r_free = 0.5040 target = 0.164467 restraints weight = 23519.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.5075 r_free = 0.5075 target = 0.167837 restraints weight = 16732.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.5096 r_free = 0.5096 target = 0.169789 restraints weight = 12711.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.5118 r_free = 0.5118 target = 0.172852 restraints weight = 10057.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.5142 r_free = 0.5142 target = 0.174826 restraints weight = 8618.842| |-----------------------------------------------------------------------------| r_work (final): 0.4925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3538 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.176 13418 Z= 0.264 Angle : 0.931 12.057 18231 Z= 0.479 Chirality : 0.054 0.457 2202 Planarity : 0.007 0.072 2303 Dihedral : 6.363 44.763 1833 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 25.76 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.24 % Favored : 88.96 % Rotamer: Outliers : 3.95 % Allowed : 15.65 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.36 % 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: -2.29 (0.19), residues: 1739 helix: -0.86 (0.16), residues: 942 sheet: -1.24 (0.48), residues: 111 loop : -2.43 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E1151 TYR 0.027 0.003 TYR A 224 PHE 0.029 0.003 PHE C 494 TRP 0.029 0.002 TRP A 203 HIS 0.014 0.003 HIS D 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.26 (13418) covalent geometry : angle 0.93089 / 0.48 (18231) hydrogen bonds : bond 0.05766 / 3.98 ( 723) hydrogen bonds : angle 5.78856 / 4.17 ( 2097) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3478 Ramachandran restraints generated. 1739 Oldfield, 0 Emsley, 1739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3478 Ramachandran restraints generated. 1739 Oldfield, 0 Emsley, 1739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 118 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 LYS cc_start: -0.2679 (OUTLIER) cc_final: -0.3640 (mtmm) REVERT: A 7 THR cc_start: 0.6630 (m) cc_final: 0.6325 (p) REVERT: A 64 MET cc_start: 0.5544 (tpt) cc_final: 0.5277 (tpt) REVERT: A 83 MET cc_start: 0.4908 (mtt) cc_final: 0.4671 (mtp) REVERT: A 181 THR cc_start: 0.3068 (OUTLIER) cc_final: 0.1583 (m) REVERT: A 191 LEU cc_start: 0.6016 (OUTLIER) cc_final: 0.5563 (tp) REVERT: A 194 MET cc_start: 0.2387 (tmm) cc_final: 0.1990 (tmm) REVERT: A 446 MET cc_start: -0.0087 (mmm) cc_final: -0.1007 (mmt) REVERT: E 1115 MET cc_start: -0.0424 (mtt) cc_final: -0.0903 (ttm) REVERT: E 1133 MET cc_start: 0.4565 (mmm) cc_final: 0.4093 (ppp) REVERT: F 1113 MET cc_start: -0.4445 (pmm) cc_final: -0.4831 (pmm) REVERT: F 1115 MET cc_start: -0.1069 (mmm) cc_final: -0.1370 (mmm) REVERT: F 1133 MET cc_start: 0.2784 (mmp) cc_final: 0.1472 (mmt) outliers start: 55 outliers final: 35 residues processed: 159 average time/residue: 0.0824 time to fit residues: 21.0208 Evaluate side-chains 148 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 403 LYS Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 402 PRO Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 450 HIS Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 422 LYS Chi-restraints excluded: chain D residue 439 TYR Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain E residue 1023 VAL Chi-restraints excluded: chain E residue 1154 THR Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1170 VAL Chi-restraints excluded: chain E residue 1229 VAL Chi-restraints excluded: chain E residue 1239 MET Chi-restraints excluded: chain E residue 1334 LEU Chi-restraints excluded: chain F residue 1072 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 46 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 148 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 166 optimal weight: 40.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 222 ASN ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN A 419 ASN A 435 GLN C 474 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1325 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5614 r_free = 0.5614 target = 0.250248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5095 r_free = 0.5095 target = 0.169144 restraints weight = 24158.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.5126 r_free = 0.5126 target = 0.172565 restraints weight = 16969.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.5159 r_free = 0.5159 target = 0.175641 restraints weight = 12381.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.5168 r_free = 0.5168 target = 0.176637 restraints weight = 10183.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.5188 r_free = 0.5188 target = 0.178154 restraints weight = 8655.794| |-----------------------------------------------------------------------------| r_work (final): 0.4926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3450 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 13418 Z= 0.155 Angle : 0.755 13.020 18231 Z= 0.384 Chirality : 0.046 0.264 2202 Planarity : 0.006 0.069 2303 Dihedral : 5.987 45.052 1833 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.75 % Allowed : 9.20 % Favored : 90.05 % Rotamer: Outliers : 3.95 % Allowed : 17.09 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.12 % 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: -1.55 (0.20), residues: 1739 helix: -0.06 (0.16), residues: 937 sheet: -1.12 (0.48), residues: 111 loop : -2.37 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 265 TYR 0.038 0.002 TYR B 224 PHE 0.026 0.002 PHE C 497 TRP 0.016 0.001 TRP D 415 HIS 0.008 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (13418) covalent geometry : angle 0.75478 / 0.38 (18231) hydrogen bonds : bond 0.04544 / 3.13 ( 723) hydrogen bonds : angle 5.15311 / 3.75 ( 2097) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3478 Ramachandran restraints generated. 1739 Oldfield, 0 Emsley, 1739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3478 Ramachandran restraints generated. 1739 Oldfield, 0 Emsley, 1739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 116 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.5489 (m-10) cc_final: 0.5225 (m-80) REVERT: A 64 MET cc_start: 0.5840 (tpt) cc_final: 0.5451 (tpt) REVERT: A 83 MET cc_start: 0.5204 (mtt) cc_final: 0.4932 (mtp) REVERT: A 181 THR cc_start: 0.2444 (OUTLIER) cc_final: 0.1029 (m) REVERT: A 345 HIS cc_start: 0.3190 (OUTLIER) cc_final: 0.2967 (t-90) REVERT: A 446 MET cc_start: -0.0911 (mmm) cc_final: -0.1295 (mmt) REVERT: C 488 ILE cc_start: 0.4334 (OUTLIER) cc_final: 0.3906 (tp) REVERT: C 506 MET cc_start: 0.5735 (tpp) cc_final: 0.5201 (tmm) REVERT: E 1115 MET cc_start: 0.0238 (mtt) cc_final: -0.0952 (ttm) REVERT: E 1133 MET cc_start: 0.4482 (mmm) cc_final: 0.4149 (ppp) REVERT: F 1133 MET cc_start: 0.3641 (mmp) cc_final: 0.2478 (mmt) outliers start: 55 outliers final: 33 residues processed: 155 average time/residue: 0.0835 time to fit residues: 20.7095 Evaluate side-chains 143 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 403 LYS Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 402 PRO Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 450 HIS Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 439 TYR Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain E residue 1005 ILE Chi-restraints excluded: chain E residue 1023 VAL Chi-restraints excluded: chain E residue 1088 THR Chi-restraints excluded: chain E residue 1154 THR Chi-restraints excluded: chain E residue 1170 VAL Chi-restraints excluded: chain E residue 1229 VAL Chi-restraints excluded: chain E residue 1334 LEU Chi-restraints excluded: chain F residue 1072 VAL Chi-restraints excluded: chain F residue 1367 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 55 optimal weight: 0.2980 chunk 108 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 129 optimal weight: 0.0000 chunk 29 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 34 ASN ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 HIS ** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1205 GLN ** E1330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1322 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5613 r_free = 0.5613 target = 0.242703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5056 r_free = 0.5056 target = 0.166366 restraints weight = 23515.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.5076 r_free = 0.5076 target = 0.168069 restraints weight = 17547.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5116 r_free = 0.5116 target = 0.171888 restraints weight = 14210.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.5137 r_free = 0.5137 target = 0.173857 restraints weight = 11496.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.5152 r_free = 0.5152 target = 0.176102 restraints weight = 9022.118| |-----------------------------------------------------------------------------| r_work (final): 0.4956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3921 moved from start: 0.7189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 13418 Z= 0.217 Angle : 0.872 16.388 18231 Z= 0.443 Chirality : 0.051 0.284 2202 Planarity : 0.006 0.070 2303 Dihedral : 6.077 43.215 1833 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 22.77 Ramachandran Plot: Outliers : 0.63 % Allowed : 9.89 % Favored : 89.48 % Rotamer: Outliers : 4.31 % Allowed : 17.44 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.18 % 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: -1.89 (0.19), residues: 1739 helix: -0.53 (0.16), residues: 935 sheet: -0.83 (0.49), residues: 109 loop : -2.29 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 160 TYR 0.038 0.003 TYR B 224 PHE 0.048 0.003 PHE C 497 TRP 0.049 0.003 TRP D 415 HIS 0.012 0.002 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.22 (13418) covalent geometry : angle 0.87158 / 0.44 (18231) hydrogen bonds : bond 0.05097 / 3.49 ( 723) hydrogen bonds : angle 5.53562 / 4.01 ( 2097) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3478 Ramachandran restraints generated. 1739 Oldfield, 0 Emsley, 1739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3478 Ramachandran restraints generated. 1739 Oldfield, 0 Emsley, 1739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 118 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.0553 (OUTLIER) cc_final: -0.0815 (ppp) REVERT: B 93 PHE cc_start: 0.5765 (m-80) cc_final: 0.5496 (m-80) REVERT: B 403 LYS cc_start: -0.3022 (OUTLIER) cc_final: -0.4024 (mtmm) REVERT: A 1 MET cc_start: 0.4763 (mmm) cc_final: 0.4275 (mpp) REVERT: A 64 MET cc_start: 0.6241 (tpt) cc_final: 0.5983 (tpt) REVERT: A 80 MET cc_start: 0.7410 (pmm) cc_final: 0.6768 (pmm) REVERT: A 83 MET cc_start: 0.5877 (mtt) cc_final: 0.5296 (mtm) REVERT: A 194 MET cc_start: 0.4070 (ttp) cc_final: 0.3539 (tmm) REVERT: A 345 HIS cc_start: 0.3030 (OUTLIER) cc_final: 0.2614 (t-90) REVERT: A 355 MET cc_start: -0.4318 (mpp) cc_final: -0.4539 (ptt) REVERT: A 403 LYS cc_start: 0.2568 (OUTLIER) cc_final: 0.1423 (tmmt) REVERT: A 446 MET cc_start: -0.0630 (mmm) cc_final: -0.0986 (mmt) REVERT: C 506 MET cc_start: 0.5941 (tpp) cc_final: 0.5358 (tmm) REVERT: E 1102 MET cc_start: -0.3049 (mpp) cc_final: -0.3410 (mtm) REVERT: E 1115 MET cc_start: -0.0690 (mtt) cc_final: -0.1855 (ttm) REVERT: E 1133 MET cc_start: 0.4466 (mmm) cc_final: 0.4051 (ppp) REVERT: F 1115 MET cc_start: -0.1317 (mmm) cc_final: -0.2804 (mtt) REVERT: F 1133 MET cc_start: 0.2678 (mmp) cc_final: 0.1487 (mmt) outliers start: 60 outliers final: 41 residues processed: 159 average time/residue: 0.0787 time to fit residues: 19.9404 Evaluate side-chains 158 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 113 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 403 LYS Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 402 PRO Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 450 HIS Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 439 TYR Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 494 PHE Chi-restraints excluded: chain E residue 1005 ILE Chi-restraints excluded: chain E residue 1023 VAL Chi-restraints excluded: chain E residue 1088 THR Chi-restraints excluded: chain E residue 1154 THR Chi-restraints excluded: chain E residue 1170 VAL Chi-restraints excluded: chain E residue 1229 VAL Chi-restraints excluded: chain E residue 1334 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 143 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 167 optimal weight: 50.0000 chunk 81 optimal weight: 0.0670 chunk 60 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 34 ASN B 35 ASN ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1330 ASN F1322 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5616 r_free = 0.5616 target = 0.244516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5082 r_free = 0.5082 target = 0.168626 restraints weight = 23092.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5112 r_free = 0.5112 target = 0.171831 restraints weight = 16984.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.5132 r_free = 0.5132 target = 0.173758 restraints weight = 13207.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.5155 r_free = 0.5155 target = 0.176829 restraints weight = 10588.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.5178 r_free = 0.5178 target = 0.178911 restraints weight = 9008.226| |-----------------------------------------------------------------------------| r_work (final): 0.4977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3967 moved from start: 0.7685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 13418 Z= 0.175 Angle : 0.803 14.124 18231 Z= 0.405 Chirality : 0.047 0.248 2202 Planarity : 0.006 0.072 2303 Dihedral : 5.917 42.960 1833 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.63 % Allowed : 9.37 % Favored : 89.99 % Rotamer: Outliers : 3.45 % Allowed : 18.95 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.12 % 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: -1.56 (0.20), residues: 1739 helix: -0.17 (0.16), residues: 935 sheet: -0.60 (0.50), residues: 109 loop : -2.29 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 160 TYR 0.046 0.002 TYR B 224 PHE 0.039 0.002 PHE C 497 TRP 0.025 0.001 TRP D 415 HIS 0.008 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (13418) covalent geometry : angle 0.80328 / 0.41 (18231) hydrogen bonds : bond 0.04683 / 3.24 ( 723) hydrogen bonds : angle 5.21602 / 3.82 ( 2097) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3478 Ramachandran restraints generated. 1739 Oldfield, 0 Emsley, 1739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3478 Ramachandran restraints generated. 1739 Oldfield, 0 Emsley, 1739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 119 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.0756 (OUTLIER) cc_final: -0.0611 (ppp) REVERT: B 93 PHE cc_start: 0.6005 (m-80) cc_final: 0.5733 (m-80) REVERT: B 403 LYS cc_start: -0.2323 (OUTLIER) cc_final: -0.3390 (pttm) REVERT: A 1 MET cc_start: 0.4544 (mmm) cc_final: 0.4048 (mpp) REVERT: A 80 MET cc_start: 0.7427 (pmm) cc_final: 0.6724 (pmm) REVERT: A 83 MET cc_start: 0.6224 (mtt) cc_final: 0.5759 (mtp) REVERT: A 194 MET cc_start: 0.4666 (ttp) cc_final: 0.3873 (tmm) REVERT: A 345 HIS cc_start: 0.3004 (OUTLIER) cc_final: 0.2622 (t-90) REVERT: A 445 HIS cc_start: 0.2302 (m90) cc_final: 0.1348 (m-70) REVERT: A 446 MET cc_start: -0.0673 (mmm) cc_final: -0.1159 (mmt) REVERT: C 506 MET cc_start: 0.6048 (tpp) cc_final: 0.5494 (tmm) REVERT: E 1115 MET cc_start: -0.0926 (mtt) cc_final: -0.1907 (ttm) REVERT: F 1115 MET cc_start: -0.1467 (mmm) cc_final: -0.2614 (mtp) REVERT: F 1133 MET cc_start: 0.2613 (mmp) cc_final: 0.1445 (mmt) REVERT: F 1334 LEU cc_start: -0.0735 (OUTLIER) cc_final: -0.1094 (tt) outliers start: 48 outliers final: 31 residues processed: 154 average time/residue: 0.0795 time to fit residues: 19.6145 Evaluate side-chains 151 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 403 LYS Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 402 PRO Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 450 HIS Chi-restraints excluded: chain D residue 439 TYR Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain E residue 1023 VAL Chi-restraints excluded: chain E residue 1088 THR Chi-restraints excluded: chain E residue 1154 THR Chi-restraints excluded: chain E residue 1170 VAL Chi-restraints excluded: chain E residue 1229 VAL Chi-restraints excluded: chain E residue 1334 LEU Chi-restraints excluded: chain F residue 1072 VAL Chi-restraints excluded: chain F residue 1334 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 105 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 74 optimal weight: 30.0000 chunk 145 optimal weight: 7.9990 chunk 164 optimal weight: 40.0000 chunk 59 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 8 optimal weight: 0.4980 chunk 108 optimal weight: 6.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 ASN ** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1012 ASN F1012 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5588 r_free = 0.5588 target = 0.235359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5031 r_free = 0.5031 target = 0.161354 restraints weight = 25427.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.5064 r_free = 0.5064 target = 0.164792 restraints weight = 18374.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.5084 r_free = 0.5084 target = 0.166711 restraints weight = 14314.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.5106 r_free = 0.5106 target = 0.169388 restraints weight = 11497.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5115 r_free = 0.5115 target = 0.170226 restraints weight = 9901.453| |-----------------------------------------------------------------------------| r_work (final): 0.4977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5109 moved from start: 1.0181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.123 13418 Z= 0.334 Angle : 1.114 14.926 18231 Z= 0.574 Chirality : 0.060 0.389 2202 Planarity : 0.007 0.070 2303 Dihedral : 6.871 38.801 1833 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 31.81 Ramachandran Plot: Outliers : 0.81 % Allowed : 11.44 % Favored : 87.75 % Rotamer: Outliers : 3.66 % Allowed : 20.03 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -2.61 (0.19), residues: 1739 helix: -1.32 (0.16), residues: 928 sheet: -0.75 (0.47), residues: 124 loop : -2.38 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 502 TYR 0.037 0.004 TYR B 224 PHE 0.074 0.006 PHE D 494 TRP 0.055 0.003 TRP A 203 HIS 0.017 0.003 HIS C 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00717 / 0.33 (13418) covalent geometry : angle 1.11360 / 0.57 (18231) hydrogen bonds : bond 0.07093 / 4.94 ( 723) hydrogen bonds : angle 6.71219 / 4.85 ( 2097) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3478 Ramachandran restraints generated. 1739 Oldfield, 0 Emsley, 1739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3478 Ramachandran restraints generated. 1739 Oldfield, 0 Emsley, 1739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 147 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.1371 (OUTLIER) cc_final: 0.0396 (ppp) REVERT: B 93 PHE cc_start: 0.6571 (m-80) cc_final: 0.6230 (m-80) REVERT: B 113 MET cc_start: 0.4476 (ptt) cc_final: 0.4011 (ptt) REVERT: B 403 LYS cc_start: -0.1530 (OUTLIER) cc_final: -0.2618 (pttm) REVERT: A 61 LEU cc_start: 0.9021 (mm) cc_final: 0.8813 (mm) REVERT: A 83 MET cc_start: 0.7223 (mtt) cc_final: 0.6860 (mtp) REVERT: A 194 MET cc_start: 0.7738 (ttp) cc_final: 0.6967 (ttt) REVERT: C 506 MET cc_start: 0.6667 (tpp) cc_final: 0.6045 (tmm) REVERT: E 1133 MET cc_start: 0.4612 (mmm) cc_final: 0.3813 (ppp) REVERT: F 1115 MET cc_start: -0.1242 (mmm) cc_final: -0.2253 (mtp) REVERT: F 1133 MET cc_start: 0.3059 (mmp) cc_final: 0.2034 (mmt) REVERT: F 1334 LEU cc_start: -0.0854 (OUTLIER) cc_final: -0.1093 (tt) outliers start: 51 outliers final: 32 residues processed: 178 average time/residue: 0.0848 time to fit residues: 24.2559 Evaluate side-chains 167 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 403 LYS Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 402 PRO Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain D residue 422 LYS Chi-restraints excluded: chain D residue 439 TYR Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain E residue 1023 VAL Chi-restraints excluded: chain E residue 1154 THR Chi-restraints excluded: chain E residue 1170 VAL Chi-restraints excluded: chain E residue 1229 VAL Chi-restraints excluded: chain E residue 1334 LEU Chi-restraints excluded: chain F residue 1033 VAL Chi-restraints excluded: chain F residue 1072 VAL Chi-restraints excluded: chain F residue 1169 MET Chi-restraints excluded: chain F residue 1334 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 16 optimal weight: 0.9980 chunk 168 optimal weight: 20.0000 chunk 75 optimal weight: 0.0570 chunk 57 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 144 optimal weight: 0.3980 chunk 78 optimal weight: 0.1980 chunk 166 optimal weight: 20.0000 chunk 157 optimal weight: 20.0000 chunk 169 optimal weight: 8.9990 chunk 118 optimal weight: 20.0000 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 121 HIS ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1147 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5629 r_free = 0.5629 target = 0.244122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5110 r_free = 0.5110 target = 0.170713 restraints weight = 23473.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.5145 r_free = 0.5145 target = 0.174370 restraints weight = 17130.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5169 r_free = 0.5169 target = 0.176654 restraints weight = 13182.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.5188 r_free = 0.5188 target = 0.178384 restraints weight = 10726.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.5204 r_free = 0.5204 target = 0.180545 restraints weight = 8660.158| |-----------------------------------------------------------------------------| r_work (final): 0.5069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4796 moved from start: 1.0280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 13418 Z= 0.180 Angle : 0.873 13.175 18231 Z= 0.436 Chirality : 0.051 0.358 2202 Planarity : 0.006 0.072 2303 Dihedral : 6.206 39.335 1833 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.69 % Allowed : 9.14 % Favored : 90.17 % Rotamer: Outliers : 2.01 % Allowed : 22.25 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.88 (0.19), residues: 1739 helix: -0.53 (0.16), residues: 927 sheet: -0.35 (0.52), residues: 102 loop : -2.33 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 31 TYR 0.045 0.002 TYR B 224 PHE 0.033 0.002 PHE D 428 TRP 0.021 0.002 TRP A 203 HIS 0.007 0.001 HIS B 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (13418) covalent geometry : angle 0.87329 / 0.44 (18231) hydrogen bonds : bond 0.05298 / 3.65 ( 723) hydrogen bonds : angle 5.66396 / 4.15 ( 2097) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3478 Ramachandran restraints generated. 1739 Oldfield, 0 Emsley, 1739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3478 Ramachandran restraints generated. 1739 Oldfield, 0 Emsley, 1739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.1863 (OUTLIER) cc_final: 0.0912 (ppp) REVERT: B 93 PHE cc_start: 0.6474 (m-80) cc_final: 0.6177 (m-80) REVERT: B 163 MET cc_start: 0.3784 (mmt) cc_final: 0.3450 (mmp) REVERT: B 403 LYS cc_start: -0.1294 (OUTLIER) cc_final: -0.2298 (pttm) REVERT: A 83 MET cc_start: 0.7424 (mtt) cc_final: 0.7133 (mtm) REVERT: C 454 MET cc_start: 0.7398 (mpp) cc_final: 0.6904 (ptp) REVERT: C 506 MET cc_start: 0.6607 (tpp) cc_final: 0.5856 (tmm) REVERT: E 1133 MET cc_start: 0.4359 (mmm) cc_final: 0.3463 (ppp) REVERT: F 1115 MET cc_start: -0.1247 (mmm) cc_final: -0.2435 (mtp) REVERT: F 1169 MET cc_start: 0.0937 (OUTLIER) cc_final: 0.0345 (mmm) REVERT: F 1334 LEU cc_start: -0.0740 (OUTLIER) cc_final: -0.1237 (tt) outliers start: 28 outliers final: 19 residues processed: 165 average time/residue: 0.0896 time to fit residues: 23.6083 Evaluate side-chains 162 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 403 LYS Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 402 PRO Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain D residue 439 TYR Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain E residue 1023 VAL Chi-restraints excluded: chain E residue 1154 THR Chi-restraints excluded: chain E residue 1229 VAL Chi-restraints excluded: chain E residue 1334 LEU Chi-restraints excluded: chain F residue 1072 VAL Chi-restraints excluded: chain F residue 1169 MET Chi-restraints excluded: chain F residue 1334 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 48 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 154 optimal weight: 0.9990 chunk 122 optimal weight: 0.0470 chunk 86 optimal weight: 0.8980 chunk 150 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5637 r_free = 0.5637 target = 0.246618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.5109 r_free = 0.5109 target = 0.172846 restraints weight = 23247.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.5145 r_free = 0.5145 target = 0.175816 restraints weight = 17324.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.5167 r_free = 0.5167 target = 0.177779 restraints weight = 13653.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5191 r_free = 0.5191 target = 0.180174 restraints weight = 10863.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.5204 r_free = 0.5204 target = 0.182034 restraints weight = 9476.559| |-----------------------------------------------------------------------------| r_work (final): 0.5001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4778 moved from start: 1.0513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 13418 Z= 0.163 Angle : 0.840 12.130 18231 Z= 0.420 Chirality : 0.051 0.389 2202 Planarity : 0.006 0.078 2303 Dihedral : 5.880 36.634 1833 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.69 % Allowed : 9.32 % Favored : 89.99 % Rotamer: Outliers : 1.94 % Allowed : 22.61 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.46 (0.20), residues: 1739 helix: -0.12 (0.17), residues: 916 sheet: -0.23 (0.52), residues: 102 loop : -2.20 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F1140 TYR 0.046 0.002 TYR B 224 PHE 0.035 0.002 PHE C 424 TRP 0.020 0.002 TRP A 227 HIS 0.005 0.001 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (13418) covalent geometry : angle 0.83950 / 0.42 (18231) hydrogen bonds : bond 0.05010 / 3.44 ( 723) hydrogen bonds : angle 5.40541 / 3.94 ( 2097) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3310.41 seconds wall clock time: 57 minutes 29.52 seconds (3449.52 seconds total)