Starting phenix.real_space_refine on Thu Mar 13 15:30:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y1k_33564/03_2025/7y1k_33564.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y1k_33564/03_2025/7y1k_33564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y1k_33564/03_2025/7y1k_33564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y1k_33564/03_2025/7y1k_33564.map" model { file = "/net/cci-nas-00/data/ceres_data/7y1k_33564/03_2025/7y1k_33564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y1k_33564/03_2025/7y1k_33564.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.068 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 5 5.49 5 Mg 2 5.21 5 S 38 5.16 5 C 5528 2.51 5 N 1413 2.21 5 O 1524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8510 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 8417 Classifications: {'peptide': 1164} Incomplete info: {'truncation_to_alanine': 193} Link IDs: {'PTRANS': 34, 'TRANS': 1129} Chain breaks: 6 Unresolved non-hydrogen bonds: 762 Unresolved non-hydrogen angles: 934 Unresolved non-hydrogen dihedrals: 634 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 26, 'PHE:plan': 8, 'GLU:plan': 33, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 489 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 93 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'BJX': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 5.99, per 1000 atoms: 0.70 Number of scatterers: 8510 At special positions: 0 Unit cell: (71.724, 100.08, 133.44, 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 38 16.00 P 5 15.00 Mg 2 11.99 O 1524 8.00 N 1413 7.00 C 5528 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: 2.74 Conformation dependent library (CDL) restraints added in 1.1 seconds 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2192 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 6 sheets defined 73.5% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.753A pdb=" N ASN A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 241 removed outlier: 3.819A pdb=" N ASN A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR A 233 " --> pdb=" O TRP A 229 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU A 234 " --> pdb=" O TRP A 230 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 240 " --> pdb=" O ILE A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 274 Processing helix chain 'A' and resid 284 through 312 removed outlier: 6.399A pdb=" N ARG A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Proline residue: A 296 - end of helix Processing helix chain 'A' and resid 312 through 325 removed outlier: 3.669A pdb=" N LEU A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 394 removed outlier: 3.700A pdb=" N THR A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 416 removed outlier: 3.547A pdb=" N GLY A 408 " --> pdb=" O GLU A 404 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A 409 " --> pdb=" O MET A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 427 Processing helix chain 'A' and resid 429 through 449 Proline residue: A 435 - end of helix Processing helix chain 'A' and resid 451 through 462 removed outlier: 4.300A pdb=" N VAL A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 497 removed outlier: 3.516A pdb=" N GLU A 487 " --> pdb=" O ASP A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 505 removed outlier: 3.691A pdb=" N LEU A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 559 removed outlier: 3.535A pdb=" N SER A 514 " --> pdb=" O ILE A 510 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 543 " --> pdb=" O MET A 539 " (cutoff:3.500A) Proline residue: A 544 - end of helix removed outlier: 3.566A pdb=" N VAL A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR A 557 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 607 removed outlier: 3.682A pdb=" N HIS A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR A 580 " --> pdb=" O HIS A 576 " (cutoff:3.500A) Proline residue: A 581 - end of helix removed outlier: 4.454A pdb=" N SER A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N THR A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 607 " --> pdb=" O ASN A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 715 removed outlier: 4.413A pdb=" N LEU A 711 " --> pdb=" O LYS A 707 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 714 " --> pdb=" O LEU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 768 Processing helix chain 'A' and resid 773 through 784 Processing helix chain 'A' and resid 786 through 793 removed outlier: 3.521A pdb=" N ASP A 791 " --> pdb=" O GLN A 787 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 792 " --> pdb=" O PRO A 788 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 793 " --> pdb=" O ASP A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 809 through 824 removed outlier: 3.570A pdb=" N ARG A 815 " --> pdb=" O GLY A 811 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 816 " --> pdb=" O GLN A 812 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N CYS A 817 " --> pdb=" O ARG A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 838 removed outlier: 4.450A pdb=" N ALA A 837 " --> pdb=" O PRO A 834 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 838 " --> pdb=" O PHE A 835 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 834 through 838' Processing helix chain 'A' and resid 839 through 849 Processing helix chain 'A' and resid 852 through 859 removed outlier: 3.502A pdb=" N ASP A 857 " --> pdb=" O LYS A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 removed outlier: 3.684A pdb=" N TYR A 871 " --> pdb=" O LYS A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 899 Processing helix chain 'A' and resid 899 through 912 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 986 through 1016 removed outlier: 3.679A pdb=" N ALA A1012 " --> pdb=" O ASP A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1075 removed outlier: 3.940A pdb=" N VAL A1053 " --> pdb=" O THR A1049 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A1059 " --> pdb=" O TRP A1055 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN A1070 " --> pdb=" O HIS A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1083 removed outlier: 3.731A pdb=" N PHE A1080 " --> pdb=" O PRO A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1094 removed outlier: 3.514A pdb=" N ILE A1088 " --> pdb=" O PRO A1084 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A1091 " --> pdb=" O LEU A1087 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE A1092 " --> pdb=" O ILE A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1102 Processing helix chain 'A' and resid 1102 through 1128 Processing helix chain 'A' and resid 1130 through 1176 removed outlier: 3.934A pdb=" N ALA A1134 " --> pdb=" O VAL A1130 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA A1136 " --> pdb=" O LEU A1132 " (cutoff:3.500A) Proline residue: A1137 - end of helix removed outlier: 3.560A pdb=" N VAL A1140 " --> pdb=" O ALA A1136 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A1150 " --> pdb=" O GLN A1146 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL A1151 " --> pdb=" O LYS A1147 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A1165 " --> pdb=" O ASP A1161 " (cutoff:3.500A) Proline residue: A1166 - end of helix Processing helix chain 'A' and resid 1177 through 1185 removed outlier: 3.627A pdb=" N ILE A1181 " --> pdb=" O GLY A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1237 removed outlier: 3.694A pdb=" N ALA A1204 " --> pdb=" O THR A1200 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A1222 " --> pdb=" O ARG A1218 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N CYS A1225 " --> pdb=" O TYR A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1258 removed outlier: 3.630A pdb=" N LEU A1248 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A1255 " --> pdb=" O ALA A1251 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN A1256 " --> pdb=" O LEU A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1285 removed outlier: 3.621A pdb=" N LEU A1265 " --> pdb=" O VAL A1261 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A1273 " --> pdb=" O GLU A1269 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A1275 " --> pdb=" O GLN A1271 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLU A1285 " --> pdb=" O PHE A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1298 Processing helix chain 'A' and resid 1301 through 1305 removed outlier: 4.073A pdb=" N GLU A1305 " --> pdb=" O TRP A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1349 through 1357 removed outlier: 3.723A pdb=" N PHE A1356 " --> pdb=" O SER A1352 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1384 Processing helix chain 'A' and resid 1399 through 1404 Processing helix chain 'A' and resid 1410 through 1421 removed outlier: 3.753A pdb=" N LEU A1414 " --> pdb=" O THR A1410 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TRP A1415 " --> pdb=" O ASP A1411 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A1418 " --> pdb=" O LEU A1414 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1430 removed outlier: 3.977A pdb=" N SER A1429 " --> pdb=" O ASN A1425 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A1430 " --> pdb=" O MET A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1443 removed outlier: 3.821A pdb=" N GLU A1443 " --> pdb=" O GLU A1440 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1461 removed outlier: 3.587A pdb=" N LEU A1452 " --> pdb=" O GLY A1448 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS A1454 " --> pdb=" O ARG A1450 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A1455 " --> pdb=" O GLN A1451 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A1460 " --> pdb=" O ALA A1456 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG A1461 " --> pdb=" O ARG A1457 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1491 removed outlier: 3.826A pdb=" N ILE A1482 " --> pdb=" O ALA A1478 " (cutoff:3.500A) Processing helix chain 'A' and resid 1502 through 1507 Processing helix chain 'A' and resid 1525 through 1533 removed outlier: 3.526A pdb=" N LEU A1530 " --> pdb=" O GLY A1526 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A1533 " --> pdb=" O LEU A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1542 Processing sheet with id=AA1, first strand: chain 'A' and resid 684 through 691 removed outlier: 5.353A pdb=" N SER A 685 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N PHE A 675 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE A 689 " --> pdb=" O THR A 671 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N THR A 671 " --> pdb=" O ILE A 689 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ILE A 691 " --> pdb=" O LYS A 669 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N LYS A 669 " --> pdb=" O ILE A 691 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A 671 " --> pdb=" O LYS A 724 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 724 " --> pdb=" O THR A 671 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLY A 673 " --> pdb=" O GLU A 722 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLU A 722 " --> pdb=" O GLY A 673 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE A 675 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR A 720 " --> pdb=" O PHE A 675 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 830 through 832 removed outlier: 7.272A pdb=" N LEU A 831 " --> pdb=" O VAL A 865 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR A 697 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR A 866 " --> pdb=" O THR A 697 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ILE A 699 " --> pdb=" O THR A 866 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE A 878 " --> pdb=" O GLU A 889 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLU A 889 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA A 880 " --> pdb=" O LEU A 887 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1325 through 1328 removed outlier: 5.168A pdb=" N LEU A1313 " --> pdb=" O HIS A1327 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU A1313 " --> pdb=" O ASP A1363 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASP A1363 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1339 through 1342 removed outlier: 6.460A pdb=" N GLY A1339 " --> pdb=" O LEU A1513 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N PHE A1515 " --> pdb=" O GLY A1339 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N CYS A1341 " --> pdb=" O PHE A1515 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER A1516 " --> pdb=" O LEU A1520 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LEU A1520 " --> pdb=" O SER A1516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1386 through 1388 removed outlier: 6.755A pdb=" N LEU A1466 " --> pdb=" O VAL A1497 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE A1499 " --> pdb=" O LEU A1466 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET A1468 " --> pdb=" O ILE A1499 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1397 through 1398 586 hydrogen bonds defined for protein. 1710 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: 3.27 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1317 1.31 - 1.43: 2306 1.43 - 1.56: 4988 1.56 - 1.69: 8 1.69 - 1.81: 59 Bond restraints: 8678 Sorted by residual: bond pdb=" C16 BJX A1604 " pdb=" N1 BJX A1604 " ideal model delta sigma weight residual 1.344 1.452 -0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C21 BJX A1604 " pdb=" O1 BJX A1604 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.16e+00 bond pdb=" N SER A1349 " pdb=" CA SER A1349 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.28e-02 6.10e+03 4.29e+00 bond pdb=" N ALA A 558 " pdb=" CA ALA A 558 " ideal model delta sigma weight residual 1.459 1.434 0.025 1.28e-02 6.10e+03 3.73e+00 bond pdb=" CA ALA A 558 " pdb=" C ALA A 558 " ideal model delta sigma weight residual 1.523 1.497 0.025 1.35e-02 5.49e+03 3.56e+00 ... (remaining 8673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 11701 1.95 - 3.89: 136 3.89 - 5.84: 37 5.84 - 7.79: 8 7.79 - 9.73: 2 Bond angle restraints: 11884 Sorted by residual: angle pdb=" N MET A1284 " pdb=" CA MET A1284 " pdb=" C MET A1284 " ideal model delta sigma weight residual 111.07 120.80 -9.73 1.07e+00 8.73e-01 8.28e+01 angle pdb=" N LYS A1348 " pdb=" CA LYS A1348 " pdb=" C LYS A1348 " ideal model delta sigma weight residual 111.14 119.97 -8.83 1.08e+00 8.57e-01 6.69e+01 angle pdb=" N GLU A1285 " pdb=" CA GLU A1285 " pdb=" C GLU A1285 " ideal model delta sigma weight residual 108.42 116.14 -7.72 1.54e+00 4.22e-01 2.51e+01 angle pdb=" N SER A1346 " pdb=" CA SER A1346 " pdb=" C SER A1346 " ideal model delta sigma weight residual 110.80 118.15 -7.35 2.13e+00 2.20e-01 1.19e+01 angle pdb=" N SER A 559 " pdb=" CA SER A 559 " pdb=" C SER A 559 " ideal model delta sigma weight residual 109.07 114.53 -5.46 1.61e+00 3.86e-01 1.15e+01 ... (remaining 11879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.47: 4981 31.47 - 62.94: 95 62.94 - 94.41: 5 94.41 - 125.88: 2 125.88 - 157.35: 2 Dihedral angle restraints: 5085 sinusoidal: 1703 harmonic: 3382 Sorted by residual: dihedral pdb=" O1B ADP A1605 " pdb=" O3A ADP A1605 " pdb=" PB ADP A1605 " pdb=" PA ADP A1605 " ideal model delta sinusoidal sigma weight residual -60.00 -169.59 109.59 1 2.00e+01 2.50e-03 3.20e+01 dihedral pdb=" O2A ADP A1605 " pdb=" O3A ADP A1605 " pdb=" PA ADP A1605 " pdb=" PB ADP A1605 " ideal model delta sinusoidal sigma weight residual -60.00 43.72 -103.72 1 2.00e+01 2.50e-03 2.97e+01 dihedral pdb=" O BJX A1604 " pdb=" C16 BJX A1604 " pdb=" C17 BJX A1604 " pdb=" C18 BJX A1604 " ideal model delta sinusoidal sigma weight residual 10.31 167.66 -157.35 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 5082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1222 0.050 - 0.099: 214 0.099 - 0.149: 46 0.149 - 0.198: 0 0.198 - 0.248: 3 Chirality restraints: 1485 Sorted by residual: chirality pdb=" CA LYS A1348 " pdb=" N LYS A1348 " pdb=" C LYS A1348 " pdb=" CB LYS A1348 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA MET A1284 " pdb=" N MET A1284 " pdb=" C MET A1284 " pdb=" CB MET A1284 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA SER A1346 " pdb=" N SER A1346 " pdb=" C SER A1346 " pdb=" CB SER A1346 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1482 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A1104 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO A1105 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A1105 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1105 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A1345 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C GLY A1345 " -0.031 2.00e-02 2.50e+03 pdb=" O GLY A1345 " 0.012 2.00e-02 2.50e+03 pdb=" N SER A1346 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A1103 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO A1104 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A1104 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1104 " -0.024 5.00e-02 4.00e+02 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 63 2.59 - 3.17: 7921 3.17 - 3.74: 13526 3.74 - 4.32: 17781 4.32 - 4.90: 29180 Nonbonded interactions: 68471 Sorted by model distance: nonbonded pdb="MG MG A1603 " pdb=" O2B ADP A1605 " model vdw 2.011 2.170 nonbonded pdb=" O2B ATP A1601 " pdb="MG MG A1602 " model vdw 2.021 2.170 nonbonded pdb=" O1G ATP A1601 " pdb="MG MG A1602 " model vdw 2.077 2.170 nonbonded pdb=" O3B ATP A1601 " pdb="MG MG A1602 " model vdw 2.121 2.170 nonbonded pdb="MG MG A1603 " pdb=" O1B ADP A1605 " model vdw 2.159 2.170 ... (remaining 68466 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.190 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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: 0.020 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 : 0.005 0.108 8678 Z= 0.282 Angle : 0.606 9.734 11884 Z= 0.318 Chirality : 0.041 0.248 1485 Planarity : 0.004 0.046 1452 Dihedral : 12.888 157.353 2893 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.96 % Allowed : 7.39 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.25), residues: 1150 helix: 0.93 (0.19), residues: 745 sheet: -1.05 (0.84), residues: 37 loop : 0.49 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 507 HIS 0.004 0.001 HIS A 555 PHE 0.008 0.001 PHE A 569 TYR 0.011 0.001 TYR A 290 ARG 0.002 0.000 ARG A1461 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.926 Fit side-chains REVERT: A 239 HIS cc_start: 0.8650 (OUTLIER) cc_final: 0.8248 (m90) REVERT: A 356 PHE cc_start: 0.8518 (t80) cc_final: 0.8278 (t80) REVERT: A 479 LYS cc_start: 0.9225 (tttt) cc_final: 0.8695 (ttmm) REVERT: A 571 SER cc_start: 0.8710 (m) cc_final: 0.8499 (t) REVERT: A 698 MET cc_start: 0.3873 (mtp) cc_final: 0.3274 (ttm) REVERT: A 823 TYR cc_start: 0.6147 (t80) cc_final: 0.5500 (t80) REVERT: A 1050 SER cc_start: 0.9380 (m) cc_final: 0.9167 (p) REVERT: A 1089 LEU cc_start: 0.9183 (tp) cc_final: 0.8953 (tt) REVERT: A 1228 LEU cc_start: 0.9136 (tp) cc_final: 0.8879 (tt) REVERT: A 1271 GLN cc_start: 0.8715 (mt0) cc_final: 0.8465 (mt0) REVERT: A 1317 TYR cc_start: 0.4463 (OUTLIER) cc_final: 0.3633 (p90) REVERT: A 1373 ILE cc_start: 0.8880 (pt) cc_final: 0.8472 (pt) outliers start: 24 outliers final: 5 residues processed: 195 average time/residue: 0.1672 time to fit residues: 47.5234 Evaluate side-chains 123 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 1186 HIS Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1317 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.130158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.104484 restraints weight = 17536.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.107243 restraints weight = 8186.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.108981 restraints weight = 4813.977| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8678 Z= 0.216 Angle : 0.597 7.502 11884 Z= 0.308 Chirality : 0.041 0.185 1485 Planarity : 0.004 0.054 1452 Dihedral : 10.561 149.955 1300 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.45 % Allowed : 12.32 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.25), residues: 1150 helix: 1.66 (0.18), residues: 775 sheet: -1.20 (0.87), residues: 39 loop : 0.13 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 507 HIS 0.005 0.001 HIS A 555 PHE 0.017 0.001 PHE A1184 TYR 0.014 0.001 TYR A1009 ARG 0.007 0.001 ARG A1218 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.849 Fit side-chains REVERT: A 239 HIS cc_start: 0.8704 (OUTLIER) cc_final: 0.8401 (m90) REVERT: A 255 MET cc_start: 0.8234 (mtp) cc_final: 0.7731 (ttm) REVERT: A 823 TYR cc_start: 0.6169 (t80) cc_final: 0.5622 (t80) REVERT: A 993 MET cc_start: 0.8838 (tmm) cc_final: 0.8273 (tmm) REVERT: A 997 LYS cc_start: 0.9207 (ttmt) cc_final: 0.8628 (ttmt) REVERT: A 1050 SER cc_start: 0.9444 (m) cc_final: 0.9208 (p) REVERT: A 1071 LYS cc_start: 0.8421 (tptt) cc_final: 0.8192 (tptt) REVERT: A 1259 ASN cc_start: 0.8876 (OUTLIER) cc_final: 0.8346 (t0) REVERT: A 1271 GLN cc_start: 0.8463 (mt0) cc_final: 0.7898 (mp10) REVERT: A 1373 ILE cc_start: 0.8505 (pt) cc_final: 0.8199 (pt) outliers start: 28 outliers final: 18 residues processed: 163 average time/residue: 0.1578 time to fit residues: 38.3727 Evaluate side-chains 123 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1146 GLN Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1460 VAL Chi-restraints excluded: chain A residue 1529 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 38 optimal weight: 4.9990 chunk 102 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.132224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.106540 restraints weight = 17932.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.109357 restraints weight = 8307.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.110966 restraints weight = 4821.543| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8678 Z= 0.172 Angle : 0.550 8.548 11884 Z= 0.272 Chirality : 0.040 0.208 1485 Planarity : 0.004 0.056 1452 Dihedral : 9.381 152.940 1296 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.20 % Allowed : 14.41 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.25), residues: 1150 helix: 2.00 (0.18), residues: 780 sheet: -1.05 (0.91), residues: 39 loop : 0.22 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 507 HIS 0.003 0.001 HIS A1001 PHE 0.015 0.001 PHE A1149 TYR 0.010 0.001 TYR A 290 ARG 0.004 0.000 ARG A1218 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: A 231 MET cc_start: 0.8553 (mmm) cc_final: 0.7993 (tpt) REVERT: A 239 HIS cc_start: 0.8686 (OUTLIER) cc_final: 0.8409 (m90) REVERT: A 255 MET cc_start: 0.8073 (mtp) cc_final: 0.7863 (ttm) REVERT: A 504 LEU cc_start: 0.8147 (mt) cc_final: 0.7928 (mt) REVERT: A 718 MET cc_start: 0.7480 (ptm) cc_final: 0.7095 (ptm) REVERT: A 823 TYR cc_start: 0.6077 (t80) cc_final: 0.5600 (t80) REVERT: A 993 MET cc_start: 0.8859 (tmm) cc_final: 0.8128 (tmm) REVERT: A 997 LYS cc_start: 0.9164 (ttmt) cc_final: 0.8490 (ttmt) REVERT: A 1050 SER cc_start: 0.9455 (m) cc_final: 0.9170 (p) REVERT: A 1259 ASN cc_start: 0.8808 (OUTLIER) cc_final: 0.8262 (t0) REVERT: A 1271 GLN cc_start: 0.8312 (mt0) cc_final: 0.7759 (mp10) REVERT: A 1317 TYR cc_start: 0.4454 (OUTLIER) cc_final: 0.3332 (p90) REVERT: A 1373 ILE cc_start: 0.8269 (pt) cc_final: 0.7988 (pt) outliers start: 26 outliers final: 16 residues processed: 161 average time/residue: 0.1473 time to fit residues: 36.4907 Evaluate side-chains 142 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1317 TYR Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1529 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 59 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 3 optimal weight: 0.5980 chunk 55 optimal weight: 0.1980 chunk 76 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.128095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.101488 restraints weight = 18020.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.104231 restraints weight = 8642.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.105940 restraints weight = 5109.384| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8678 Z= 0.168 Angle : 0.566 8.044 11884 Z= 0.272 Chirality : 0.041 0.245 1485 Planarity : 0.004 0.057 1452 Dihedral : 8.882 147.443 1293 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.33 % Allowed : 16.63 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.25), residues: 1150 helix: 2.11 (0.18), residues: 786 sheet: -1.03 (0.93), residues: 39 loop : 0.09 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1260 HIS 0.003 0.001 HIS A1001 PHE 0.012 0.001 PHE A 569 TYR 0.012 0.001 TYR A1257 ARG 0.003 0.000 ARG A1218 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 1.025 Fit side-chains REVERT: A 219 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7763 (t80) REVERT: A 239 HIS cc_start: 0.8749 (OUTLIER) cc_final: 0.8440 (m90) REVERT: A 487 GLU cc_start: 0.7746 (tp30) cc_final: 0.7336 (tp30) REVERT: A 698 MET cc_start: 0.3567 (mtp) cc_final: 0.3009 (ttm) REVERT: A 718 MET cc_start: 0.7613 (ptm) cc_final: 0.7328 (ptm) REVERT: A 823 TYR cc_start: 0.6135 (t80) cc_final: 0.5811 (t80) REVERT: A 993 MET cc_start: 0.8857 (tmm) cc_final: 0.8384 (tmm) REVERT: A 1071 LYS cc_start: 0.8365 (tptt) cc_final: 0.8155 (tptt) REVERT: A 1195 LEU cc_start: 0.8639 (mt) cc_final: 0.8438 (mp) REVERT: A 1259 ASN cc_start: 0.8806 (OUTLIER) cc_final: 0.8264 (t0) REVERT: A 1271 GLN cc_start: 0.8310 (mt0) cc_final: 0.7780 (mp10) REVERT: A 1317 TYR cc_start: 0.4336 (OUTLIER) cc_final: 0.4024 (p90) REVERT: A 1373 ILE cc_start: 0.8179 (pt) cc_final: 0.7955 (pt) REVERT: A 1418 LEU cc_start: 0.6441 (tp) cc_final: 0.6224 (tp) outliers start: 27 outliers final: 19 residues processed: 152 average time/residue: 0.1413 time to fit residues: 33.8257 Evaluate side-chains 142 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1317 TYR Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1460 VAL Chi-restraints excluded: chain A residue 1529 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 20.0000 chunk 23 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 115 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.128039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.101469 restraints weight = 17901.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.104133 restraints weight = 8597.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.105868 restraints weight = 5095.542| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8678 Z= 0.166 Angle : 0.550 8.346 11884 Z= 0.264 Chirality : 0.040 0.250 1485 Planarity : 0.003 0.057 1452 Dihedral : 8.559 145.225 1291 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 4.19 % Allowed : 17.86 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.25), residues: 1150 helix: 2.25 (0.18), residues: 785 sheet: -0.46 (0.81), residues: 50 loop : 0.17 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 507 HIS 0.003 0.001 HIS A1001 PHE 0.014 0.001 PHE A 569 TYR 0.014 0.001 TYR A 228 ARG 0.003 0.000 ARG A1218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.894 Fit side-chains REVERT: A 219 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7779 (t80) REVERT: A 239 HIS cc_start: 0.8750 (OUTLIER) cc_final: 0.8452 (m90) REVERT: A 390 ASN cc_start: 0.8582 (OUTLIER) cc_final: 0.8091 (t0) REVERT: A 487 GLU cc_start: 0.7945 (tp30) cc_final: 0.7567 (tp30) REVERT: A 823 TYR cc_start: 0.6001 (t80) cc_final: 0.5570 (t80) REVERT: A 993 MET cc_start: 0.8894 (tmm) cc_final: 0.8335 (tmm) REVERT: A 1056 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7725 (tmm) REVERT: A 1071 LYS cc_start: 0.8478 (tptt) cc_final: 0.8251 (tptt) REVERT: A 1259 ASN cc_start: 0.8817 (OUTLIER) cc_final: 0.8297 (t0) REVERT: A 1271 GLN cc_start: 0.8297 (mt0) cc_final: 0.8051 (mt0) REVERT: A 1418 LEU cc_start: 0.6367 (tp) cc_final: 0.6167 (tp) REVERT: A 1422 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.6185 (tm-30) outliers start: 34 outliers final: 21 residues processed: 150 average time/residue: 0.1363 time to fit residues: 32.2847 Evaluate side-chains 143 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1002 SER Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1146 GLN Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1422 GLN Chi-restraints excluded: chain A residue 1460 VAL Chi-restraints excluded: chain A residue 1529 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 chunk 32 optimal weight: 0.0670 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.128284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.101630 restraints weight = 17745.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.104271 restraints weight = 8609.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.106022 restraints weight = 5150.656| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8678 Z= 0.172 Angle : 0.557 10.498 11884 Z= 0.264 Chirality : 0.040 0.249 1485 Planarity : 0.003 0.057 1452 Dihedral : 8.370 143.744 1291 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.06 % Allowed : 18.47 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.25), residues: 1150 helix: 2.32 (0.18), residues: 778 sheet: -0.39 (0.82), residues: 50 loop : 0.24 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 507 HIS 0.003 0.001 HIS A1001 PHE 0.015 0.001 PHE A 552 TYR 0.024 0.001 TYR A1143 ARG 0.002 0.000 ARG A1382 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.932 Fit side-chains REVERT: A 219 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7745 (t80) REVERT: A 239 HIS cc_start: 0.8778 (OUTLIER) cc_final: 0.8436 (m90) REVERT: A 487 GLU cc_start: 0.8135 (tp30) cc_final: 0.7745 (tp30) REVERT: A 823 TYR cc_start: 0.6053 (t80) cc_final: 0.5751 (t80) REVERT: A 892 LEU cc_start: -0.0205 (OUTLIER) cc_final: -0.0635 (tm) REVERT: A 993 MET cc_start: 0.8887 (tmm) cc_final: 0.8156 (tmm) REVERT: A 1056 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7740 (tmm) REVERT: A 1071 LYS cc_start: 0.8513 (tptt) cc_final: 0.8269 (tptt) REVERT: A 1259 ASN cc_start: 0.8845 (OUTLIER) cc_final: 0.8335 (t0) REVERT: A 1271 GLN cc_start: 0.8285 (mt0) cc_final: 0.8036 (mt0) REVERT: A 1422 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6210 (tm-30) outliers start: 33 outliers final: 22 residues processed: 145 average time/residue: 0.1715 time to fit residues: 39.5403 Evaluate side-chains 141 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1002 SER Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1146 GLN Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1317 TYR Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1422 GLN Chi-restraints excluded: chain A residue 1460 VAL Chi-restraints excluded: chain A residue 1529 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 53 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 chunk 112 optimal weight: 8.9990 chunk 3 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.127947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.101195 restraints weight = 17971.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.103856 restraints weight = 8710.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.105560 restraints weight = 5195.732| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8678 Z= 0.178 Angle : 0.555 9.461 11884 Z= 0.264 Chirality : 0.040 0.279 1485 Planarity : 0.003 0.057 1452 Dihedral : 8.126 141.564 1289 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.94 % Allowed : 19.33 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.25), residues: 1150 helix: 2.29 (0.18), residues: 787 sheet: -0.29 (0.83), residues: 50 loop : 0.14 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 507 HIS 0.003 0.001 HIS A1001 PHE 0.015 0.001 PHE A 569 TYR 0.024 0.001 TYR A1143 ARG 0.002 0.000 ARG A1218 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: A 219 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7793 (t80) REVERT: A 239 HIS cc_start: 0.8785 (OUTLIER) cc_final: 0.8427 (m90) REVERT: A 487 GLU cc_start: 0.8360 (tp30) cc_final: 0.8151 (tp30) REVERT: A 675 PHE cc_start: 0.7858 (m-80) cc_final: 0.7637 (m-80) REVERT: A 823 TYR cc_start: 0.6085 (t80) cc_final: 0.5754 (t80) REVERT: A 892 LEU cc_start: -0.0164 (OUTLIER) cc_final: -0.0575 (tm) REVERT: A 993 MET cc_start: 0.8933 (tmm) cc_final: 0.8346 (tmm) REVERT: A 1056 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7742 (tmm) REVERT: A 1071 LYS cc_start: 0.8545 (tptt) cc_final: 0.8302 (tptt) REVERT: A 1259 ASN cc_start: 0.8871 (OUTLIER) cc_final: 0.8363 (t0) REVERT: A 1271 GLN cc_start: 0.8281 (mt0) cc_final: 0.8016 (mt0) REVERT: A 1352 SER cc_start: 0.9509 (t) cc_final: 0.9259 (p) outliers start: 32 outliers final: 22 residues processed: 142 average time/residue: 0.1472 time to fit residues: 33.1033 Evaluate side-chains 142 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1002 SER Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1146 GLN Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1317 TYR Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1460 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 87 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 80 optimal weight: 0.0470 chunk 75 optimal weight: 0.0050 chunk 113 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 overall best weight: 0.4292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.130108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.103117 restraints weight = 17854.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.105843 restraints weight = 8661.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.107583 restraints weight = 5150.863| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8678 Z= 0.143 Angle : 0.567 9.130 11884 Z= 0.266 Chirality : 0.040 0.333 1485 Planarity : 0.003 0.057 1452 Dihedral : 7.917 139.062 1289 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.08 % Allowed : 20.94 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.25), residues: 1150 helix: 2.38 (0.19), residues: 783 sheet: -0.25 (0.84), residues: 50 loop : 0.19 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 677 HIS 0.003 0.001 HIS A1001 PHE 0.012 0.001 PHE A 569 TYR 0.025 0.001 TYR A1143 ARG 0.002 0.000 ARG A1218 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 219 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7732 (t80) REVERT: A 239 HIS cc_start: 0.8764 (OUTLIER) cc_final: 0.8417 (m90) REVERT: A 487 GLU cc_start: 0.8425 (tp30) cc_final: 0.8216 (tp30) REVERT: A 823 TYR cc_start: 0.6065 (t80) cc_final: 0.5728 (t80) REVERT: A 892 LEU cc_start: -0.0177 (OUTLIER) cc_final: -0.0593 (tm) REVERT: A 993 MET cc_start: 0.8843 (tmm) cc_final: 0.8374 (tmm) REVERT: A 1056 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7660 (tmm) REVERT: A 1071 LYS cc_start: 0.8518 (tptt) cc_final: 0.8278 (tptt) REVERT: A 1259 ASN cc_start: 0.8869 (OUTLIER) cc_final: 0.8351 (t0) REVERT: A 1271 GLN cc_start: 0.8209 (mt0) cc_final: 0.7944 (mt0) REVERT: A 1352 SER cc_start: 0.9497 (t) cc_final: 0.9255 (p) outliers start: 25 outliers final: 16 residues processed: 148 average time/residue: 0.1927 time to fit residues: 44.0465 Evaluate side-chains 141 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1002 SER Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1146 GLN Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1317 TYR Chi-restraints excluded: chain A residue 1460 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 40 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.129371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.102290 restraints weight = 18090.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.105042 restraints weight = 8827.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.106838 restraints weight = 5218.685| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8678 Z= 0.161 Angle : 0.566 9.733 11884 Z= 0.266 Chirality : 0.040 0.324 1485 Planarity : 0.003 0.056 1452 Dihedral : 7.744 137.010 1289 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.20 % Allowed : 21.18 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.25), residues: 1150 helix: 2.44 (0.18), residues: 777 sheet: -0.21 (0.83), residues: 50 loop : 0.22 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 507 HIS 0.002 0.000 HIS A1001 PHE 0.013 0.001 PHE A 569 TYR 0.024 0.001 TYR A1143 ARG 0.002 0.000 ARG A1218 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 219 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7752 (t80) REVERT: A 239 HIS cc_start: 0.8784 (OUTLIER) cc_final: 0.8414 (m90) REVERT: A 823 TYR cc_start: 0.6032 (t80) cc_final: 0.5685 (t80) REVERT: A 892 LEU cc_start: -0.0185 (OUTLIER) cc_final: -0.0592 (tm) REVERT: A 993 MET cc_start: 0.8865 (tmm) cc_final: 0.8354 (tmm) REVERT: A 1056 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7664 (tmm) REVERT: A 1071 LYS cc_start: 0.8535 (tptt) cc_final: 0.8310 (tptt) REVERT: A 1259 ASN cc_start: 0.8861 (OUTLIER) cc_final: 0.8355 (t0) REVERT: A 1271 GLN cc_start: 0.8235 (mt0) cc_final: 0.7967 (mt0) REVERT: A 1323 PRO cc_start: 0.8223 (Cg_exo) cc_final: 0.8023 (Cg_endo) REVERT: A 1352 SER cc_start: 0.9493 (t) cc_final: 0.9257 (p) REVERT: A 1422 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.6860 (tm-30) outliers start: 26 outliers final: 17 residues processed: 140 average time/residue: 0.1486 time to fit residues: 33.0508 Evaluate side-chains 138 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1317 TYR Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1422 GLN Chi-restraints excluded: chain A residue 1460 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 2 optimal weight: 0.0050 chunk 91 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 54 optimal weight: 0.0570 chunk 74 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.4712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.130739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.103723 restraints weight = 17906.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.106451 restraints weight = 8694.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.108228 restraints weight = 5170.596| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8678 Z= 0.141 Angle : 0.564 10.651 11884 Z= 0.262 Chirality : 0.039 0.346 1485 Planarity : 0.003 0.057 1452 Dihedral : 7.575 134.472 1289 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.71 % Allowed : 21.92 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.25), residues: 1150 helix: 2.53 (0.19), residues: 776 sheet: -0.18 (0.82), residues: 50 loop : 0.25 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 677 HIS 0.003 0.000 HIS A1001 PHE 0.022 0.001 PHE A 675 TYR 0.023 0.001 TYR A1143 ARG 0.002 0.000 ARG A1218 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: A 219 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7734 (t80) REVERT: A 239 HIS cc_start: 0.8774 (OUTLIER) cc_final: 0.8372 (m90) REVERT: A 747 SER cc_start: 0.8684 (OUTLIER) cc_final: 0.8113 (p) REVERT: A 823 TYR cc_start: 0.6070 (t80) cc_final: 0.5595 (t80) REVERT: A 892 LEU cc_start: -0.0132 (OUTLIER) cc_final: -0.0540 (tm) REVERT: A 993 MET cc_start: 0.8882 (tmm) cc_final: 0.8364 (tmm) REVERT: A 1050 SER cc_start: 0.9454 (m) cc_final: 0.9227 (p) REVERT: A 1056 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7630 (tmm) REVERT: A 1071 LYS cc_start: 0.8499 (tptt) cc_final: 0.8284 (tptt) REVERT: A 1220 ASP cc_start: 0.7184 (m-30) cc_final: 0.6963 (t0) REVERT: A 1259 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8351 (t0) REVERT: A 1271 GLN cc_start: 0.8216 (mt0) cc_final: 0.7957 (mt0) REVERT: A 1323 PRO cc_start: 0.8175 (Cg_exo) cc_final: 0.7973 (Cg_endo) REVERT: A 1352 SER cc_start: 0.9484 (t) cc_final: 0.9245 (p) outliers start: 22 outliers final: 13 residues processed: 138 average time/residue: 0.1382 time to fit residues: 30.0998 Evaluate side-chains 135 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1317 TYR Chi-restraints excluded: chain A residue 1460 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 54 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 0.0870 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.128388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.101250 restraints weight = 18231.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.103941 restraints weight = 8953.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.105644 restraints weight = 5366.548| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8678 Z= 0.202 Angle : 0.595 11.908 11884 Z= 0.279 Chirality : 0.040 0.298 1485 Planarity : 0.003 0.056 1452 Dihedral : 7.576 134.389 1289 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.59 % Allowed : 21.92 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.25), residues: 1150 helix: 2.38 (0.18), residues: 779 sheet: -0.16 (0.83), residues: 50 loop : 0.21 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 507 HIS 0.003 0.001 HIS A 555 PHE 0.014 0.001 PHE A 569 TYR 0.025 0.001 TYR A1143 ARG 0.003 0.000 ARG A1218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2569.52 seconds wall clock time: 46 minutes 53.03 seconds (2813.03 seconds total)