Starting phenix.real_space_refine on Fri Sep 11 18:18:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6bhu_7099/09_2026/6bhu_7099.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bhu_7099/09_2026/6bhu_7099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6bhu_7099/09_2026/6bhu_7099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bhu_7099/09_2026/6bhu_7099.map" model { file = "/net/cci-nas-00/data/ceres_data/6bhu_7099/09_2026/6bhu_7099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bhu_7099/09_2026/6bhu_7099.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6bhu_7099/09_2026/6bhu_7099.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6bhu_7099/09_2026/6bhu_7099.cif" } resolution = 3.14 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= 0.008 sd= 0.236 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 47 5.16 5 C 6616 2.51 5 N 1727 2.21 5 O 1875 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10273 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1328, 10125 Classifications: {'peptide': 1328} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'PTRANS': 44, 'TRANS': 1283} Chain breaks: 8 Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 360 Unresolved non-hydrogen dihedrals: 120 Planarities with less than four sites: {'UNK:plan-1': 120} Unresolved non-hydrogen planarities: 120 Chain: "A" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 148 Unusual residues: {' MG': 2, 'ATP': 2, 'CLR': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 2.50, per 1000 atoms: 0.24 Number of scatterers: 10273 At special positions: 0 Unit cell: (144.609, 98.857, 97.223, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 6 15.00 Mg 2 11.99 O 1875 8.00 N 1727 7.00 C 6616 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 303.0 milliseconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2518 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 5 sheets defined 77.6% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 30 through 40 Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 76 through 99 Processing helix chain 'A' and resid 106 through 130 removed outlier: 3.520A pdb=" N UNK A 130 " --> pdb=" O UNK A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 152 removed outlier: 3.519A pdb=" N UNK A 148 " --> pdb=" O UNK A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 158 removed outlier: 4.215A pdb=" N UNK A 157 " --> pdb=" O UNK A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 194 removed outlier: 3.625A pdb=" N UNK A 194 " --> pdb=" O UNK A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 Processing helix chain 'A' and resid 224 through 234 removed outlier: 3.563A pdb=" N MET A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG A 233 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN A 234 " --> pdb=" O GLN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.569A pdb=" N ASP A 240 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 241 " --> pdb=" O SER A 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 237 through 241' Processing helix chain 'A' and resid 249 through 268 Proline residue: A 255 - end of helix removed outlier: 3.954A pdb=" N SER A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 327 through 355 Proline residue: A 343 - end of helix removed outlier: 3.629A pdb=" N ASN A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 408 removed outlier: 4.228A pdb=" N TYR A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 408 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 removed outlier: 3.762A pdb=" N SER A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 441 removed outlier: 3.550A pdb=" N ILE A 423 " --> pdb=" O THR A 419 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA A 431 " --> pdb=" O MET A 427 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR A 439 " --> pdb=" O MET A 435 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 462 removed outlier: 3.733A pdb=" N SER A 446 " --> pdb=" O ASN A 442 " (cutoff:3.500A) Proline residue: A 448 - end of helix removed outlier: 3.534A pdb=" N LEU A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 510 removed outlier: 3.692A pdb=" N MET A 473 " --> pdb=" O GLY A 469 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 474 " --> pdb=" O VAL A 470 " (cutoff:3.500A) Proline residue: A 478 - end of helix removed outlier: 3.781A pdb=" N THR A 489 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 507 " --> pdb=" O LYS A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.726A pdb=" N LEU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 555 Processing helix chain 'A' and resid 555 through 571 removed outlier: 3.874A pdb=" N LEU A 559 " --> pdb=" O CYS A 555 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR A 568 " --> pdb=" O THR A 564 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 569 " --> pdb=" O PHE A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 590 removed outlier: 3.655A pdb=" N PHE A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 598 removed outlier: 4.071A pdb=" N LEU A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A 598 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 621 removed outlier: 3.591A pdb=" N VAL A 602 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 612 " --> pdb=" O GLN A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 630 removed outlier: 3.847A pdb=" N SER A 629 " --> pdb=" O ASP A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 691 Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 733 through 744 Processing helix chain 'A' and resid 746 through 753 removed outlier: 3.738A pdb=" N LEU A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 785 removed outlier: 3.700A pdb=" N ALA A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 810 Processing helix chain 'A' and resid 831 through 835 Processing helix chain 'A' and resid 851 through 859 removed outlier: 3.816A pdb=" N ASP A 859 " --> pdb=" O LEU A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 866 Processing helix chain 'A' and resid 958 through 970 removed outlier: 3.956A pdb=" N TYR A 962 " --> pdb=" O LYS A 958 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 969 " --> pdb=" O TYR A 965 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY A 970 " --> pdb=" O MET A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 1000 removed outlier: 3.559A pdb=" N SER A 974 " --> pdb=" O GLY A 970 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 992 " --> pdb=" O SER A 988 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASP A1000 " --> pdb=" O SER A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1058 removed outlier: 3.577A pdb=" N THR A1011 " --> pdb=" O THR A1007 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN A1012 " --> pdb=" O GLN A1008 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER A1016 " --> pdb=" O GLN A1012 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL A1017 " --> pdb=" O VAL A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1066 removed outlier: 3.924A pdb=" N PHE A1063 " --> pdb=" O PRO A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1110 removed outlier: 3.846A pdb=" N LEU A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG A1074 " --> pdb=" O ASN A1070 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU A1078 " --> pdb=" O ARG A1074 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU A1079 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ILE A1086 " --> pdb=" O VAL A1082 " (cutoff:3.500A) Proline residue: A1087 - end of helix Processing helix chain 'A' and resid 1117 through 1147 removed outlier: 3.611A pdb=" N LEU A1121 " --> pdb=" O ILE A1117 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR A1125 " --> pdb=" O LEU A1121 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A1127 " --> pdb=" O LEU A1123 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A1134 " --> pdb=" O ARG A1130 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER A1135 " --> pdb=" O PHE A1131 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN A1138 " --> pdb=" O ALA A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1160 removed outlier: 3.652A pdb=" N PHE A1154 " --> pdb=" O VAL A1150 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A1159 " --> pdb=" O ASN A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1168 Processing helix chain 'A' and resid 1169 through 1220 removed outlier: 3.685A pdb=" N PHE A1173 " --> pdb=" O GLU A1169 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A1183 " --> pdb=" O LEU A1179 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN A1184 " --> pdb=" O LYS A1180 " (cutoff:3.500A) Proline residue: A1190 - end of helix Processing helix chain 'A' and resid 1225 through 1257 removed outlier: 3.575A pdb=" N VAL A1229 " --> pdb=" O SER A1225 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A1230 " --> pdb=" O ALA A1226 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU A1231 " --> pdb=" O GLY A1227 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A1233 " --> pdb=" O VAL A1229 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER A1234 " --> pdb=" O GLY A1230 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A1235 " --> pdb=" O LEU A1231 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A1236 " --> pdb=" O SER A1232 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A1237 " --> pdb=" O VAL A1233 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLN A1238 " --> pdb=" O SER A1234 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A1240 " --> pdb=" O SER A1236 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A1247 " --> pdb=" O LEU A1243 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A1248 " --> pdb=" O ASN A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1264 Processing helix chain 'A' and resid 1265 through 1267 No H-bonds generated for 'chain 'A' and resid 1265 through 1267' Processing helix chain 'A' and resid 1332 through 1340 removed outlier: 3.643A pdb=" N THR A1336 " --> pdb=" O LYS A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1367 removed outlier: 3.649A pdb=" N PHE A1367 " --> pdb=" O HIS A1363 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1388 removed outlier: 3.552A pdb=" N LEU A1387 " --> pdb=" O LEU A1383 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.891A pdb=" N VAL A1398 " --> pdb=" O SER A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1414 Processing helix chain 'A' and resid 1430 through 1446 removed outlier: 3.635A pdb=" N LEU A1436 " --> pdb=" O GLY A1432 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG A1445 " --> pdb=" O ARG A1441 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS A1446 " --> pdb=" O ALA A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1460 through 1475 removed outlier: 3.855A pdb=" N ASP A1465 " --> pdb=" O LEU A1461 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1491 Processing helix chain 'A' and resid 1509 through 1517 removed outlier: 3.934A pdb=" N ARG A1517 " --> pdb=" O LEU A1513 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1528 Processing sheet with id=AA1, first strand: chain 'A' and resid 664 through 669 removed outlier: 5.740A pdb=" N ILE A 664 " --> pdb=" O ASN A 648 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE A 644 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL A 704 " --> pdb=" O ILE A 644 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL A 646 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL A 702 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ASN A 648 " --> pdb=" O GLY A 700 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR A 650 " --> pdb=" O VAL A 698 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 708 through 711 removed outlier: 6.591A pdb=" N ALA A 709 " --> pdb=" O LEU A 790 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N TYR A 789 " --> pdb=" O LEU A 823 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N VAL A 825 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU A 791 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 837 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL A 840 " --> pdb=" O SER A 847 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1315 through 1316 removed outlier: 4.182A pdb=" N TYR A1297 " --> pdb=" O GLU A1347 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU A1347 " --> pdb=" O TYR A1297 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1370 through 1372 removed outlier: 6.271A pdb=" N GLY A1323 " --> pdb=" O ILE A1497 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LEU A1499 " --> pdb=" O GLY A1323 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL A1325 " --> pdb=" O LEU A1499 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1381 through 1382 645 hydrogen bonds defined for protein. 1887 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: 1.91 Time building geometry restraints manager: 1.08 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: 1738 1.33 - 1.45: 2600 1.45 - 1.57: 6048 1.57 - 1.69: 10 1.69 - 1.81: 79 Bond restraints: 10475 Sorted by residual: bond pdb=" C4 ATP A1602 " pdb=" C5 ATP A1602 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.20e+01 bond pdb=" C4 ATP A1601 " pdb=" C5 ATP A1601 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.17e+01 bond pdb=" C5 ATP A1601 " pdb=" C6 ATP A1601 " ideal model delta sigma weight residual 1.409 1.485 -0.076 1.00e-02 1.00e+04 5.72e+01 bond pdb=" C5 ATP A1602 " pdb=" C6 ATP A1602 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.25e+01 bond pdb=" C8 ATP A1601 " pdb=" N7 ATP A1601 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.34e+01 ... (remaining 10470 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 14113 3.69 - 7.38: 131 7.38 - 11.07: 10 11.07 - 14.77: 0 14.77 - 18.46: 4 Bond angle restraints: 14258 Sorted by residual: angle pdb=" PB ATP A1602 " pdb=" O3B ATP A1602 " pdb=" PG ATP A1602 " ideal model delta sigma weight residual 139.87 121.41 18.46 1.00e+00 1.00e+00 3.41e+02 angle pdb=" PB ATP A1601 " pdb=" O3B ATP A1601 " pdb=" PG ATP A1601 " ideal model delta sigma weight residual 139.87 121.57 18.30 1.00e+00 1.00e+00 3.35e+02 angle pdb=" PA ATP A1602 " pdb=" O3A ATP A1602 " pdb=" PB ATP A1602 " ideal model delta sigma weight residual 136.83 121.48 15.35 1.00e+00 1.00e+00 2.36e+02 angle pdb=" PA ATP A1601 " pdb=" O3A ATP A1601 " pdb=" PB ATP A1601 " ideal model delta sigma weight residual 136.83 121.79 15.04 1.00e+00 1.00e+00 2.26e+02 angle pdb=" C5 ATP A1602 " pdb=" C4 ATP A1602 " pdb=" N3 ATP A1602 " ideal model delta sigma weight residual 126.80 118.41 8.39 1.00e+00 1.00e+00 7.03e+01 ... (remaining 14253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 5767 16.96 - 33.91: 361 33.91 - 50.87: 75 50.87 - 67.82: 10 67.82 - 84.77: 6 Dihedral angle restraints: 6219 sinusoidal: 2344 harmonic: 3875 Sorted by residual: dihedral pdb=" CA TYR A 318 " pdb=" C TYR A 318 " pdb=" N LYS A 319 " pdb=" CA LYS A 319 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA ALA A1110 " pdb=" C ALA A1110 " pdb=" N THR A1111 " pdb=" CA THR A1111 " ideal model delta harmonic sigma weight residual 180.00 -159.78 -20.22 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" C ARG A1486 " pdb=" N ARG A1486 " pdb=" CA ARG A1486 " pdb=" CB ARG A1486 " ideal model delta harmonic sigma weight residual -122.60 -112.59 -10.01 0 2.50e+00 1.60e-01 1.60e+01 ... (remaining 6216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1438 0.083 - 0.167: 217 0.167 - 0.250: 31 0.250 - 0.334: 4 0.334 - 0.417: 1 Chirality restraints: 1691 Sorted by residual: chirality pdb=" CA CYS A 682 " pdb=" N CYS A 682 " pdb=" C CYS A 682 " pdb=" CB CYS A 682 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" CA ILE A1483 " pdb=" N ILE A1483 " pdb=" C ILE A1483 " pdb=" CB ILE A1483 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA LEU A1487 " pdb=" N LEU A1487 " pdb=" C LEU A1487 " pdb=" CB LEU A1487 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 1688 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 825 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C VAL A 825 " -0.045 2.00e-02 2.50e+03 pdb=" O VAL A 825 " 0.017 2.00e-02 2.50e+03 pdb=" N THR A 826 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A1486 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.27e+00 pdb=" C ARG A1486 " -0.031 2.00e-02 2.50e+03 pdb=" O ARG A1486 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU A1487 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 824 " -0.008 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C LEU A 824 " 0.031 2.00e-02 2.50e+03 pdb=" O LEU A 824 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL A 825 " -0.010 2.00e-02 2.50e+03 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 15 2.51 - 3.11: 6631 3.11 - 3.71: 15455 3.71 - 4.30: 20868 4.30 - 4.90: 35631 Nonbonded interactions: 78600 Sorted by model distance: nonbonded pdb=" OG SER A1333 " pdb="MG MG A1604 " model vdw 1.915 2.170 nonbonded pdb=" O1G ATP A1601 " pdb="MG MG A1603 " model vdw 1.988 2.170 nonbonded pdb=" O1B ATP A1601 " pdb="MG MG A1603 " model vdw 2.000 2.170 nonbonded pdb=" OE1 GLN A 713 " pdb="MG MG A1603 " model vdw 2.003 2.170 nonbonded pdb=" OG SER A 685 " pdb="MG MG A1603 " model vdw 2.017 2.170 ... (remaining 78595 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.260 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.930 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 10475 Z= 0.602 Angle : 1.220 18.457 14258 Z= 0.862 Chirality : 0.062 0.417 1691 Planarity : 0.004 0.042 1766 Dihedral : 12.263 84.775 3701 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.21), residues: 1200 helix: -0.39 (0.16), residues: 715 sheet: -1.21 (0.52), residues: 74 loop : -2.45 (0.25), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1137 TYR 0.020 0.002 TYR A1032 PHE 0.012 0.002 PHE A1063 TRP 0.012 0.001 TRP A 520 HIS 0.006 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00822 / 0.60 (10475) covalent geometry : angle 1.21978 / 0.86 (14258) hydrogen bonds : bond 0.21543 / 11.98 ( 645) hydrogen bonds : angle 7.52659 / 4.83 ( 1887) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8251 (tt) cc_final: 0.8039 (tt) REVERT: A 237 GLU cc_start: 0.7673 (tp30) cc_final: 0.7052 (tt0) REVERT: A 239 THR cc_start: 0.7639 (m) cc_final: 0.7390 (p) REVERT: A 246 LYS cc_start: 0.7523 (mtmt) cc_final: 0.7023 (mmtt) REVERT: A 251 GLU cc_start: 0.8340 (tt0) cc_final: 0.7951 (tp30) REVERT: A 473 MET cc_start: 0.7092 (mtm) cc_final: 0.6837 (mtm) REVERT: A 576 ILE cc_start: 0.8121 (mm) cc_final: 0.7830 (mm) REVERT: A 641 THR cc_start: 0.8021 (p) cc_final: 0.7776 (t) REVERT: A 694 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7172 (mm-30) REVERT: A 696 ASP cc_start: 0.8116 (t70) cc_final: 0.7662 (t0) REVERT: A 864 GLU cc_start: 0.8627 (tt0) cc_final: 0.8211 (mm-30) REVERT: A 946 LEU cc_start: 0.6795 (tp) cc_final: 0.6588 (tp) REVERT: A 993 TYR cc_start: 0.7574 (t80) cc_final: 0.6683 (t80) REVERT: A 1027 ILE cc_start: 0.8173 (mm) cc_final: 0.7918 (mp) REVERT: A 1245 TRP cc_start: 0.7185 (m100) cc_final: 0.6674 (m-10) REVERT: A 1248 ARG cc_start: 0.6464 (mtp-110) cc_final: 0.6137 (mtp85) REVERT: A 1252 GLU cc_start: 0.6828 (mm-30) cc_final: 0.6521 (mm-30) REVERT: A 1280 MET cc_start: 0.9096 (mtm) cc_final: 0.8771 (mtp) REVERT: A 1284 LYS cc_start: 0.8973 (mttt) cc_final: 0.8736 (ptmm) REVERT: A 1303 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8262 (tp30) REVERT: A 1355 ILE cc_start: 0.8037 (mm) cc_final: 0.7811 (tt) REVERT: A 1513 LEU cc_start: 0.8025 (mt) cc_final: 0.7793 (mp) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.0997 time to fit residues: 34.2875 Evaluate side-chains 145 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 ASN A 432 GLN A 956 GLN A1392 GLN A1454 GLN A1485 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.132655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.105665 restraints weight = 17462.834| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.63 r_work: 0.3277 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10475 Z= 0.163 Angle : 0.569 9.685 14258 Z= 0.297 Chirality : 0.039 0.166 1691 Planarity : 0.005 0.064 1766 Dihedral : 6.333 89.532 1446 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.18 % Allowed : 9.02 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.24), residues: 1200 helix: 1.68 (0.19), residues: 723 sheet: -1.40 (0.49), residues: 86 loop : -1.92 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 615 TYR 0.023 0.002 TYR A1032 PHE 0.020 0.001 PHE A 551 TRP 0.011 0.001 TRP A 223 HIS 0.008 0.001 HIS A 985 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (10475) covalent geometry : angle 0.56856 / 0.30 (14258) hydrogen bonds : bond 0.06131 / 3.40 ( 645) hydrogen bonds : angle 4.47939 / 2.99 ( 1887) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8832 (tt) cc_final: 0.8564 (tt) REVERT: A 237 GLU cc_start: 0.8293 (tp30) cc_final: 0.7763 (tt0) REVERT: A 246 LYS cc_start: 0.8300 (mtmt) cc_final: 0.7761 (mmtt) REVERT: A 696 ASP cc_start: 0.8526 (t70) cc_final: 0.8181 (t0) REVERT: A 849 MET cc_start: 0.9233 (mtp) cc_final: 0.8959 (mtm) REVERT: A 1027 ILE cc_start: 0.8872 (mm) cc_final: 0.8655 (mm) REVERT: A 1245 TRP cc_start: 0.8047 (m100) cc_final: 0.7692 (m-10) REVERT: A 1353 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.8017 (m-30) REVERT: A 1447 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7625 (t) outliers start: 23 outliers final: 13 residues processed: 185 average time/residue: 0.0877 time to fit residues: 24.0410 Evaluate side-chains 147 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1353 ASP Chi-restraints excluded: chain A residue 1447 THR Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1490 ILE Chi-restraints excluded: chain A residue 1503 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 89 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN A 533 GLN A 725 ASN A 956 GLN A1048 HIS A1184 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.132888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.106269 restraints weight = 17680.957| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.66 r_work: 0.3279 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10475 Z= 0.130 Angle : 0.506 7.048 14258 Z= 0.261 Chirality : 0.037 0.161 1691 Planarity : 0.004 0.058 1766 Dihedral : 5.994 87.599 1446 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.94 % Allowed : 11.40 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.24), residues: 1200 helix: 2.24 (0.19), residues: 725 sheet: -1.10 (0.49), residues: 87 loop : -1.81 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1248 TYR 0.022 0.001 TYR A1032 PHE 0.014 0.001 PHE A 329 TRP 0.014 0.001 TRP A 459 HIS 0.008 0.001 HIS A 985 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (10475) covalent geometry : angle 0.50571 / 0.26 (14258) hydrogen bonds : bond 0.05305 / 2.94 ( 645) hydrogen bonds : angle 4.01697 / 2.70 ( 1887) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.374 Fit side-chains REVERT: A 219 ILE cc_start: 0.8826 (tt) cc_final: 0.8536 (tt) REVERT: A 237 GLU cc_start: 0.8253 (tp30) cc_final: 0.7796 (tt0) REVERT: A 246 LYS cc_start: 0.8336 (mtmt) cc_final: 0.7794 (mmtt) REVERT: A 338 MET cc_start: 0.8901 (mmp) cc_final: 0.8584 (mmt) REVERT: A 369 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8447 (mp) REVERT: A 466 VAL cc_start: 0.6905 (OUTLIER) cc_final: 0.6645 (t) REVERT: A 591 ILE cc_start: 0.8219 (tt) cc_final: 0.7751 (mm) REVERT: A 656 ASN cc_start: 0.8765 (m-40) cc_final: 0.8188 (t0) REVERT: A 696 ASP cc_start: 0.8373 (t70) cc_final: 0.8048 (t0) REVERT: A 849 MET cc_start: 0.9150 (mtp) cc_final: 0.8912 (mtm) REVERT: A 964 ASP cc_start: 0.7755 (m-30) cc_final: 0.7361 (m-30) REVERT: A 1013 VAL cc_start: 0.8341 (t) cc_final: 0.8131 (p) REVERT: A 1245 TRP cc_start: 0.7900 (m100) cc_final: 0.7490 (m-10) REVERT: A 1278 GLN cc_start: 0.8554 (tp40) cc_final: 0.8263 (tp40) REVERT: A 1447 THR cc_start: 0.8042 (OUTLIER) cc_final: 0.7771 (t) outliers start: 31 outliers final: 17 residues processed: 162 average time/residue: 0.0832 time to fit residues: 20.3826 Evaluate side-chains 146 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 820 LYS Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1447 THR Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1503 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 58 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 95 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 54 optimal weight: 0.0370 chunk 86 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN A 956 GLN A1256 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.133591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.106726 restraints weight = 17789.383| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.69 r_work: 0.3287 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10475 Z= 0.113 Angle : 0.483 6.172 14258 Z= 0.247 Chirality : 0.036 0.151 1691 Planarity : 0.004 0.052 1766 Dihedral : 5.806 84.883 1446 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.85 % Allowed : 12.25 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.24), residues: 1200 helix: 2.43 (0.19), residues: 727 sheet: -1.05 (0.49), residues: 81 loop : -1.68 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 633 TYR 0.021 0.001 TYR A1032 PHE 0.018 0.001 PHE A1030 TRP 0.016 0.001 TRP A 459 HIS 0.006 0.001 HIS A 985 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (10475) covalent geometry : angle 0.48251 / 0.25 (14258) hydrogen bonds : bond 0.04845 / 2.70 ( 645) hydrogen bonds : angle 3.87177 / 2.61 ( 1887) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.388 Fit side-chains REVERT: A 219 ILE cc_start: 0.8831 (tt) cc_final: 0.8528 (tt) REVERT: A 237 GLU cc_start: 0.8241 (tp30) cc_final: 0.7719 (tt0) REVERT: A 246 LYS cc_start: 0.8337 (mtmt) cc_final: 0.7779 (mmtt) REVERT: A 338 MET cc_start: 0.8888 (mmp) cc_final: 0.8609 (mmt) REVERT: A 369 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8433 (mp) REVERT: A 425 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.8270 (m-40) REVERT: A 515 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8360 (mp) REVERT: A 591 ILE cc_start: 0.8161 (tt) cc_final: 0.7649 (mm) REVERT: A 696 ASP cc_start: 0.8312 (t70) cc_final: 0.8004 (t0) REVERT: A 849 MET cc_start: 0.9167 (mtp) cc_final: 0.8942 (mtm) REVERT: A 960 SER cc_start: 0.7620 (p) cc_final: 0.6973 (t) REVERT: A 964 ASP cc_start: 0.7692 (m-30) cc_final: 0.7206 (m-30) REVERT: A 1013 VAL cc_start: 0.8295 (t) cc_final: 0.8078 (p) REVERT: A 1085 MET cc_start: 0.8249 (tpp) cc_final: 0.7732 (mtt) REVERT: A 1245 TRP cc_start: 0.7861 (m100) cc_final: 0.7538 (m-10) REVERT: A 1278 GLN cc_start: 0.8567 (tp40) cc_final: 0.8298 (tp40) REVERT: A 1393 TYR cc_start: 0.7768 (OUTLIER) cc_final: 0.6818 (p90) REVERT: A 1447 THR cc_start: 0.8094 (OUTLIER) cc_final: 0.7870 (t) outliers start: 30 outliers final: 18 residues processed: 162 average time/residue: 0.0841 time to fit residues: 20.8227 Evaluate side-chains 153 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 820 LYS Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1447 THR Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1490 ILE Chi-restraints excluded: chain A residue 1496 VAL Chi-restraints excluded: chain A residue 1503 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 80 optimal weight: 0.0870 chunk 3 optimal weight: 20.0000 chunk 55 optimal weight: 0.0050 chunk 90 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 11 optimal weight: 9.9990 overall best weight: 0.5974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 382 HIS A 597 ASN A 956 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.133644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.106539 restraints weight = 17714.263| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.68 r_work: 0.3285 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10475 Z= 0.111 Angle : 0.480 7.500 14258 Z= 0.242 Chirality : 0.036 0.152 1691 Planarity : 0.003 0.049 1766 Dihedral : 5.546 81.438 1446 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.32 % Allowed : 13.01 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.24), residues: 1200 helix: 2.60 (0.19), residues: 727 sheet: -0.85 (0.50), residues: 80 loop : -1.64 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1221 TYR 0.020 0.001 TYR A1032 PHE 0.017 0.001 PHE A 340 TRP 0.016 0.001 TRP A 459 HIS 0.006 0.001 HIS A 985 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (10475) covalent geometry : angle 0.48007 / 0.24 (14258) hydrogen bonds : bond 0.04635 / 2.57 ( 645) hydrogen bonds : angle 3.77415 / 2.55 ( 1887) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8821 (tt) cc_final: 0.8510 (tt) REVERT: A 237 GLU cc_start: 0.8220 (tp30) cc_final: 0.7731 (mt-10) REVERT: A 246 LYS cc_start: 0.8356 (mtmt) cc_final: 0.7795 (mmtt) REVERT: A 338 MET cc_start: 0.8806 (mmp) cc_final: 0.8542 (mmt) REVERT: A 515 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8385 (mp) REVERT: A 578 ASP cc_start: 0.6848 (OUTLIER) cc_final: 0.6481 (t0) REVERT: A 591 ILE cc_start: 0.8139 (tt) cc_final: 0.7709 (mm) REVERT: A 695 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8400 (ttp) REVERT: A 696 ASP cc_start: 0.8329 (t70) cc_final: 0.8039 (t0) REVERT: A 824 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8367 (pp) REVERT: A 960 SER cc_start: 0.7637 (p) cc_final: 0.6925 (t) REVERT: A 964 ASP cc_start: 0.7680 (m-30) cc_final: 0.7180 (m-30) REVERT: A 1013 VAL cc_start: 0.8320 (t) cc_final: 0.8105 (p) REVERT: A 1085 MET cc_start: 0.8230 (tpp) cc_final: 0.7751 (mtt) REVERT: A 1245 TRP cc_start: 0.7843 (m100) cc_final: 0.7537 (m-10) REVERT: A 1278 GLN cc_start: 0.8598 (tp40) cc_final: 0.8297 (tp40) REVERT: A 1393 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.6960 (p90) outliers start: 35 outliers final: 22 residues processed: 158 average time/residue: 0.0856 time to fit residues: 20.2660 Evaluate side-chains 153 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 820 LYS Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1375 ASP Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1459 VAL Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1496 VAL Chi-restraints excluded: chain A residue 1503 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 54 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.131447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.104342 restraints weight = 17809.776| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.67 r_work: 0.3255 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10475 Z= 0.132 Angle : 0.506 8.261 14258 Z= 0.255 Chirality : 0.037 0.154 1691 Planarity : 0.003 0.048 1766 Dihedral : 5.387 76.726 1446 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.23 % Allowed : 13.77 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.24), residues: 1200 helix: 2.53 (0.19), residues: 729 sheet: -0.72 (0.50), residues: 80 loop : -1.61 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 593 TYR 0.019 0.001 TYR A1032 PHE 0.013 0.001 PHE A1030 TRP 0.016 0.001 TRP A 459 HIS 0.005 0.001 HIS A 985 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (10475) covalent geometry : angle 0.50577 / 0.25 (14258) hydrogen bonds : bond 0.04973 / 2.77 ( 645) hydrogen bonds : angle 3.81965 / 2.58 ( 1887) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8805 (tt) cc_final: 0.8492 (tt) REVERT: A 237 GLU cc_start: 0.8216 (tp30) cc_final: 0.7644 (mt-10) REVERT: A 246 LYS cc_start: 0.8379 (mtmt) cc_final: 0.7818 (mmtt) REVERT: A 338 MET cc_start: 0.8826 (mmp) cc_final: 0.8525 (mmt) REVERT: A 369 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8253 (mp) REVERT: A 515 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8418 (mp) REVERT: A 591 ILE cc_start: 0.8139 (tt) cc_final: 0.7665 (mm) REVERT: A 656 ASN cc_start: 0.8846 (m-40) cc_final: 0.8225 (t0) REVERT: A 695 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8393 (ttp) REVERT: A 696 ASP cc_start: 0.8284 (t70) cc_final: 0.7969 (t0) REVERT: A 824 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8379 (pp) REVERT: A 964 ASP cc_start: 0.7764 (m-30) cc_final: 0.7342 (m-30) REVERT: A 1013 VAL cc_start: 0.8329 (t) cc_final: 0.8113 (p) REVERT: A 1085 MET cc_start: 0.8266 (tpp) cc_final: 0.7654 (mtt) REVERT: A 1245 TRP cc_start: 0.7849 (m100) cc_final: 0.7570 (m-10) REVERT: A 1278 GLN cc_start: 0.8590 (tp40) cc_final: 0.8327 (tp40) REVERT: A 1383 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8707 (tt) REVERT: A 1393 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.7087 (p90) outliers start: 34 outliers final: 24 residues processed: 158 average time/residue: 0.0819 time to fit residues: 19.7267 Evaluate side-chains 160 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1375 ASP Chi-restraints excluded: chain A residue 1383 LEU Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1496 VAL Chi-restraints excluded: chain A residue 1503 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 131 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 827 HIS A 956 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.130340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.103238 restraints weight = 17561.643| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.63 r_work: 0.3225 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10475 Z= 0.145 Angle : 0.517 9.407 14258 Z= 0.260 Chirality : 0.037 0.148 1691 Planarity : 0.003 0.048 1766 Dihedral : 5.287 73.399 1446 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.42 % Allowed : 13.96 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.24), residues: 1200 helix: 2.49 (0.19), residues: 729 sheet: -0.58 (0.50), residues: 81 loop : -1.53 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 593 TYR 0.020 0.001 TYR A1032 PHE 0.013 0.001 PHE A1030 TRP 0.019 0.001 TRP A 459 HIS 0.005 0.001 HIS A 985 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (10475) covalent geometry : angle 0.51698 / 0.26 (14258) hydrogen bonds : bond 0.05135 / 2.86 ( 645) hydrogen bonds : angle 3.83682 / 2.59 ( 1887) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8821 (tt) cc_final: 0.8495 (tt) REVERT: A 237 GLU cc_start: 0.8230 (tp30) cc_final: 0.7653 (mt-10) REVERT: A 246 LYS cc_start: 0.8283 (mtmt) cc_final: 0.7735 (mmtt) REVERT: A 338 MET cc_start: 0.8764 (mmp) cc_final: 0.8519 (mmt) REVERT: A 515 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8422 (mp) REVERT: A 591 ILE cc_start: 0.8173 (tt) cc_final: 0.7772 (mm) REVERT: A 656 ASN cc_start: 0.8880 (m-40) cc_final: 0.8111 (p0) REVERT: A 695 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8557 (ttp) REVERT: A 696 ASP cc_start: 0.8281 (t70) cc_final: 0.7946 (t0) REVERT: A 824 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8399 (pp) REVERT: A 964 ASP cc_start: 0.7783 (m-30) cc_final: 0.7393 (m-30) REVERT: A 1013 VAL cc_start: 0.8343 (t) cc_final: 0.8108 (p) REVERT: A 1085 MET cc_start: 0.8187 (tpp) cc_final: 0.7637 (mtt) REVERT: A 1245 TRP cc_start: 0.7836 (m100) cc_final: 0.7575 (m-10) REVERT: A 1278 GLN cc_start: 0.8609 (tp40) cc_final: 0.8365 (tp40) REVERT: A 1393 TYR cc_start: 0.8065 (OUTLIER) cc_final: 0.7254 (p90) outliers start: 36 outliers final: 27 residues processed: 154 average time/residue: 0.0834 time to fit residues: 19.8658 Evaluate side-chains 161 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1375 ASP Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1459 VAL Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1496 VAL Chi-restraints excluded: chain A residue 1503 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 956 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.131509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.104832 restraints weight = 17672.793| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.64 r_work: 0.3242 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10475 Z= 0.121 Angle : 0.505 10.633 14258 Z= 0.251 Chirality : 0.036 0.150 1691 Planarity : 0.003 0.048 1766 Dihedral : 5.100 70.429 1446 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.51 % Allowed : 14.06 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.25), residues: 1200 helix: 2.62 (0.19), residues: 729 sheet: -0.43 (0.51), residues: 81 loop : -1.47 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 593 TYR 0.020 0.001 TYR A1032 PHE 0.015 0.001 PHE A1030 TRP 0.018 0.001 TRP A 459 HIS 0.005 0.001 HIS A 985 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (10475) covalent geometry : angle 0.50514 / 0.25 (14258) hydrogen bonds : bond 0.04734 / 2.63 ( 645) hydrogen bonds : angle 3.73032 / 2.53 ( 1887) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8665 (tt) cc_final: 0.8346 (tt) REVERT: A 237 GLU cc_start: 0.8138 (tp30) cc_final: 0.7513 (mt-10) REVERT: A 246 LYS cc_start: 0.8169 (mtmt) cc_final: 0.7616 (mmtt) REVERT: A 338 MET cc_start: 0.8693 (mmp) cc_final: 0.8475 (mmt) REVERT: A 515 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8228 (mp) REVERT: A 568 TYR cc_start: 0.8221 (t80) cc_final: 0.8000 (t80) REVERT: A 656 ASN cc_start: 0.8941 (m-40) cc_final: 0.8066 (p0) REVERT: A 695 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8463 (ttp) REVERT: A 824 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8116 (pp) REVERT: A 964 ASP cc_start: 0.7666 (m-30) cc_final: 0.7262 (m-30) REVERT: A 1013 VAL cc_start: 0.8290 (t) cc_final: 0.8060 (p) REVERT: A 1085 MET cc_start: 0.8039 (tpp) cc_final: 0.7487 (mtt) REVERT: A 1245 TRP cc_start: 0.7724 (m100) cc_final: 0.7438 (m-10) REVERT: A 1278 GLN cc_start: 0.8649 (tp40) cc_final: 0.8419 (tp40) REVERT: A 1393 TYR cc_start: 0.8088 (OUTLIER) cc_final: 0.7375 (p90) outliers start: 37 outliers final: 25 residues processed: 156 average time/residue: 0.0849 time to fit residues: 19.8698 Evaluate side-chains 161 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 820 LYS Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1375 ASP Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1496 VAL Chi-restraints excluded: chain A residue 1503 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 107 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 131 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.131427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.104398 restraints weight = 17561.645| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.70 r_work: 0.3238 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 10475 Z= 0.122 Angle : 0.513 11.342 14258 Z= 0.255 Chirality : 0.036 0.150 1691 Planarity : 0.004 0.049 1766 Dihedral : 4.976 68.449 1446 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.94 % Allowed : 15.10 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.24), residues: 1200 helix: 2.65 (0.19), residues: 728 sheet: -0.37 (0.51), residues: 81 loop : -1.41 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 593 TYR 0.020 0.001 TYR A1032 PHE 0.015 0.001 PHE A1030 TRP 0.019 0.001 TRP A 459 HIS 0.005 0.001 HIS A 985 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (10475) covalent geometry : angle 0.51315 / 0.25 (14258) hydrogen bonds : bond 0.04672 / 2.60 ( 645) hydrogen bonds : angle 3.69668 / 2.51 ( 1887) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8648 (tt) cc_final: 0.8327 (tt) REVERT: A 237 GLU cc_start: 0.8145 (tp30) cc_final: 0.7488 (mt-10) REVERT: A 246 LYS cc_start: 0.8047 (mtmt) cc_final: 0.7639 (mmtt) REVERT: A 338 MET cc_start: 0.8694 (mmp) cc_final: 0.8423 (mmt) REVERT: A 515 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8167 (mp) REVERT: A 591 ILE cc_start: 0.8076 (tt) cc_final: 0.7695 (mm) REVERT: A 656 ASN cc_start: 0.8948 (m-40) cc_final: 0.8450 (m-40) REVERT: A 695 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8448 (ttp) REVERT: A 824 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8076 (pp) REVERT: A 964 ASP cc_start: 0.7661 (m-30) cc_final: 0.7247 (m-30) REVERT: A 1013 VAL cc_start: 0.8240 (t) cc_final: 0.8007 (p) REVERT: A 1085 MET cc_start: 0.8074 (tpp) cc_final: 0.7517 (mtt) REVERT: A 1245 TRP cc_start: 0.7697 (m100) cc_final: 0.7412 (m-10) REVERT: A 1278 GLN cc_start: 0.8671 (tp40) cc_final: 0.8434 (tp40) REVERT: A 1393 TYR cc_start: 0.8080 (OUTLIER) cc_final: 0.7349 (p90) REVERT: A 1422 CYS cc_start: 0.8365 (t) cc_final: 0.8047 (p) outliers start: 31 outliers final: 26 residues processed: 154 average time/residue: 0.0820 time to fit residues: 19.5637 Evaluate side-chains 162 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 820 LYS Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1375 ASP Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1496 VAL Chi-restraints excluded: chain A residue 1503 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 28 optimal weight: 0.9990 chunk 57 optimal weight: 0.0570 chunk 109 optimal weight: 4.9990 chunk 68 optimal weight: 0.0670 chunk 34 optimal weight: 0.0970 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.4234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.133819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.106576 restraints weight = 17427.190| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.71 r_work: 0.3275 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 10475 Z= 0.107 Angle : 0.500 11.935 14258 Z= 0.248 Chirality : 0.036 0.149 1691 Planarity : 0.004 0.053 1766 Dihedral : 4.789 65.290 1446 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.37 % Allowed : 15.95 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.25), residues: 1200 helix: 2.67 (0.19), residues: 741 sheet: -0.18 (0.53), residues: 79 loop : -1.39 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 593 TYR 0.020 0.001 TYR A1032 PHE 0.018 0.001 PHE A 365 TRP 0.020 0.001 TRP A 459 HIS 0.005 0.001 HIS A 985 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (10475) covalent geometry : angle 0.49964 / 0.25 (14258) hydrogen bonds : bond 0.04235 / 2.37 ( 645) hydrogen bonds : angle 3.59212 / 2.44 ( 1887) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.340 Fit side-chains REVERT: A 219 ILE cc_start: 0.8609 (tt) cc_final: 0.8293 (tt) REVERT: A 246 LYS cc_start: 0.8246 (mtmt) cc_final: 0.7658 (mmtt) REVERT: A 338 MET cc_start: 0.8655 (mmp) cc_final: 0.8409 (mmt) REVERT: A 515 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8170 (mp) REVERT: A 591 ILE cc_start: 0.8040 (tt) cc_final: 0.7618 (mm) REVERT: A 656 ASN cc_start: 0.8991 (m-40) cc_final: 0.8507 (m-40) REVERT: A 695 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8382 (ttp) REVERT: A 824 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8017 (pp) REVERT: A 994 TRP cc_start: 0.7753 (t-100) cc_final: 0.7015 (t60) REVERT: A 1013 VAL cc_start: 0.8217 (t) cc_final: 0.7946 (p) REVERT: A 1176 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.8022 (mt0) REVERT: A 1203 GLU cc_start: 0.8367 (tt0) cc_final: 0.8003 (tt0) REVERT: A 1245 TRP cc_start: 0.7656 (m100) cc_final: 0.7339 (m-10) REVERT: A 1278 GLN cc_start: 0.8670 (tp40) cc_final: 0.8464 (tp40) REVERT: A 1422 CYS cc_start: 0.8268 (t) cc_final: 0.8018 (p) outliers start: 25 outliers final: 19 residues processed: 152 average time/residue: 0.0802 time to fit residues: 18.8836 Evaluate side-chains 158 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 820 LYS Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1176 GLN Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1375 ASP Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1496 VAL Chi-restraints excluded: chain A residue 1503 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 33 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 34 optimal weight: 0.0040 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.132300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.105302 restraints weight = 17682.344| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.70 r_work: 0.3252 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10475 Z= 0.120 Angle : 0.518 11.784 14258 Z= 0.255 Chirality : 0.036 0.150 1691 Planarity : 0.004 0.050 1766 Dihedral : 4.772 64.566 1446 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.66 % Allowed : 16.05 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.25), residues: 1200 helix: 2.65 (0.19), residues: 736 sheet: -0.16 (0.53), residues: 79 loop : -1.34 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 593 TYR 0.019 0.001 TYR A1032 PHE 0.024 0.001 PHE A 365 TRP 0.021 0.001 TRP A 459 HIS 0.011 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (10475) covalent geometry : angle 0.51768 / 0.26 (14258) hydrogen bonds : bond 0.04488 / 2.51 ( 645) hydrogen bonds : angle 3.63459 / 2.47 ( 1887) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2460.95 seconds wall clock time: 42 minutes 59.71 seconds (2579.71 seconds total)